Command line: [exonerate --exhaustive yes -m p2g --showtargetgff -q ../SelM-human.fa -t SelM-NIVO01044519.1.subseq] Hostname: [sitdoc] C4 Alignment: ------------ Query: SPP00000017_1.0 # Protein # Selenoprotein M (SelM) # Homo sapiens # Complete Target: NIVO01044519.1:subseq(733635,745166) Ammotragus lervia isolate NAZ scaffold2533_len1482783_cov71, whole genome shotgun sequence Model: protein2genome:local Raw score: 142 Query range: 1 -> 135 Target range: 130436 -> 661577 2 : SerLeuLeuLeuProProLeuAlaLeuLeuLeuLeuLeuAla{A} >>>> Target : 16 ||||||||||||! !|||||| !! !|||||||||! !|||{|} 74 SerLeuLeuLeuGlnProLeuAsnProLeuLeuLeuCysAla{A}++ 130437 : TCCCTGCTTCTTCAGCCTCTGAACCCCTTGCTTCTGTGTGCA{G}gt........... : 130482 17 : Intron 1 >>>> {la}Leu{V} >>>> Target Intron 2 >>>> {al : 18 987 bp {||} !{!} 10607 bp {.! ++{la}Thr{A}++ ++{la 130483 : ..............ag{CC}ACA{G}gt.........................ag{cc : 216080 19 : }AlaProAlaThrAlaAlaThr >>>> Target Intron 3 >>>> AlaTyr{ : 28 }:::|||||||||||||||!.! 60334 bp |||:!!{ }SerProAlaThrAlaAlaAsn+- ++AlaHis{ 216081 : }tctcccgCCACAGCAGCCAATga.........................agGCACAC{ : 276443 29 : Ar} >>>> Target Intron 4 >>>> {g}ProAspTrp >>>> Target : 32 ||} 58482 bp {|} !!|||||| 457 Ar}++ ++{g}ThrAspTrp++ 276444 : AG}gt.........................ag{A}ACGGACTGGgt............ : 334939 33 : Intron 5 >>>> AsnArg >>>> Target Intron 6 >>>> LeuSerGl : 36 69 bp !:! 59222 bp :!!! !|| ++AlaLys++ ++ValTyrGl 334940 : .............agGCGAAGgt.........................agGTCTATGG : 439940 37 : yLeuThrArgAlaArgValGluThrCysGly{G} >>>> Target Intron 7 > : 47 |||| !||| !!!.!! !:!! !||||||{|} 26967 bp yLeuLeuArgProAsnGlyGlnLeuCysGly{G}++ 439941 : GCTTCTGAGGCCCAACGGCCAGCTTTGCGGA{G}gt...................... : 439976 48 : >>> {ly}UnkGlnLeuAsnArg >>>> Target Intron 8 >>>> LeuLy : 54 {||} :!!||| ||| 5570 bp :!!|| ++{ly}GlyGluLeuValArg++ ++ValLy 439977 : ...ag{GA}GGGGAGCTGGTACGGgt.........................agGTCAA : 472531 55 : sGluValLysAlaPheValThrGln{A} >>>> Target Intron 9 >>>> { : 63 |..!:!!|||! ! !:!! !:!!{!} 24245 bp { sSerLeuLysGluAspLeuGlnLys{V}++ ++{ 472532 : GTCACTTAAGGAGGATTTGCAGAAA{G}gt.........................ag{ : 496804 64 : sp}IleProPheTyrHisAsnLeuValMetLysHisLeu{Pr} >>>> Target I : 76 !}|||||| ! !|||...|||! !:!! !||| !{! } 2243 al}IleProAlaSerHisGlyLeuAspValGlyHisLys{Gl}+- 496805 : TC}ATCCCAGCATCCCATGGGCTGGATGTGGGACACAAG{CA}gg............. : 496846 77 : ntron 10 >>>> {o}GlyAlaAspProGluLeuValLeu{Le} >>>> Targe : 85 8 bp {!}..!:!!!!:||||||:!!||||||{:!} 5 ++{n}AsnSerGluProGluIleValLeu{Me}++ 496847 : .............ag{A}AATTCAGAACCTGAGATCGTTCTC{AT}gt.......... : 519311 86 : t Intron 11 >>>> {u}GlyArgArgTyr >>>> Target Intron 12 > : 90 5516 bp {!}||||||!:! ! 940 bp ++{t}GlyArgLysGlu++ 519312 : ................ag{G}GGGAGGAAAGAGgt....................... : 574840 91 : >>> GluGluLeuGluArgIleProLeuSerGluMet >>>> Target Intron : 101 :::::: ... :::|||||| !! ..! 78084 bp ++LysAspProHisProLeuProLeuProProGln++ 574841 : ...agAaggacccccacccccttccGCTGCCTCCCCAGgt.................. : 575813 102 : 13 >>>> ThrArgGluGlu >>>> Target Intron 14 >>>> IleAsn : 106 |||! ! !||| 7578 bp |||!.! ++ThrThrLeuGlu++ -+IleThr 575814 : ........agacaACTCTAGAGgt..........................tgATCACC : 661488 107 : AlaLeuValGlnGluLeuGlyPheTyrArgLysAlaAlaProAspAlaGlnValProP : 126 ! !|||...!!:! ! !! ! !|||! !!.!!.! !|||||| !|||||| ***AlaValSerAspCysProSerValArgIleGlyGlyAspAspAlaGlyValProA 661489 : TAGGCTGTCAGTGATTGCCCTTCTGTCCGGATAGGTGGTGACGATGCCGGAGTACCTG : 661548 127 : roGluTyrValTrpAlaProAlaLysPro : 135 !!||| :!!||| !|||||| ! ||| laGluAlaIleTrpArgProAlaAspPro 661549 : CGGAAGCGATTTGGAGGCCAGCGGATCCA : 661577 vulgar: SPP00000017_1.0 1 135 . NIVO01044519.1:subseq(733635,745166) 130436 661577 + 142 M 14 42 S 0 1 5 0 2 I 0 74983 3 0 2 S 1 2 M 1 3 S 0 1 5 0 2 I 0 10603 3 0 2 S 1 2 M 7 21 5 0 2 I 0 60330 3 0 2 M 2 6 S 0 2 5 0 2 I 0 58478 3 0 2 S 1 1 M 3 9 5 0 2 I 0 45765 3 0 2 M 2 6 5 0 2 I 0 59218 3 0 2 M 13 39 S 0 1 5 0 2 I 0 26963 3 0 2 S 1 2 M 5 15 5 0 2 I 0 5566 3 0 2 M 10 30 S 0 1 5 0 2 I 0 24241 3 0 2 S 1 2 M 12 36 S 0 2 5 0 2 I 0 22434 3 0 2 S 1 1 M 8 24 S 0 2 5 0 2 I 0 55512 3 0 2 S 1 1 M 4 12 5 0 2 I 0 936 3 0 2 M 11 33 5 0 2 I 0 78080 3 0 2 M 4 12 5 0 2 I 0 7574 3 0 2 M 31 93 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-17 ##type DNA # # # seqname source feature start end score strand frame attributes # NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local gene 130437 661577 142 + . gene_id 1 ; sequence SPP00000017_1.0 ; gene_orientation + NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 130437 130479 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 130437 130479 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 130480 130481 . + . intron_id 1 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 130480 205466 . + . intron_id 1 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 205465 205466 . + . intron_id 0 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 205467 205472 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 205467 205472 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 205473 205474 . + . intron_id 2 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 205473 216079 . + . intron_id 2 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 216078 216079 . + . intron_id 1 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 216080 216102 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 216080 216102 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 216103 216104 . + . intron_id 3 ; splice_site "GA" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 216103 276436 . + . intron_id 3 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 276435 276436 . + . intron_id 2 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 276437 276444 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 276437 276444 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 276445 276446 . + . intron_id 4 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 276445 334926 . + . intron_id 4 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 334925 334926 . + . intron_id 3 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 334927 334936 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 334927 334936 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 334937 334938 . + . intron_id 5 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 334937 380705 . + . intron_id 5 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 380704 380705 . + . intron_id 4 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 380706 380711 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 380706 380711 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 380712 380713 . + . intron_id 6 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 380712 439933 . + . intron_id 6 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 439932 439933 . + . intron_id 5 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 439934 439973 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 439934 439973 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 439974 439975 . + . intron_id 7 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 439974 466940 . + . intron_id 7 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 466939 466940 . + . intron_id 6 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 466941 466957 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 466941 466957 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 466958 466959 . + . intron_id 8 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 466958 472527 . + . intron_id 8 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 472526 472527 . + . intron_id 7 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 472528 472558 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 472528 472558 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 472559 472560 . + . intron_id 9 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 472559 496803 . + . intron_id 9 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 496802 496803 . + . intron_id 8 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 496804 496843 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 496804 496843 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 496844 496845 . + . intron_id 10 ; splice_site "GG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 496844 519281 . + . intron_id 10 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 519280 519281 . + . intron_id 9 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 519282 519308 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 519282 519308 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 519309 519310 . + . intron_id 11 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 519309 574824 . + . intron_id 11 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 574823 574824 . + . intron_id 10 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 574825 574837 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 574825 574837 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 574838 574839 . + . intron_id 12 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 574838 575777 . + . intron_id 12 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 575776 575777 . + . intron_id 11 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 575778 575810 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 575778 575810 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 575811 575812 . + . intron_id 13 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 575811 653894 . + . intron_id 13 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 653893 653894 . + . intron_id 12 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 653895 653906 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 653895 653906 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 653907 653908 . + . intron_id 14 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 653907 661484 . + . intron_id 14 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 661483 661484 . + . intron_id 13 ; splice_site "TG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 661485 661577 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 661485 661577 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local similarity 130437 661577 142 + . alignment_id 1 ; Query SPP00000017_1.0 ; Align 130437 2 42 ; Align 205469 17 3 ; Align 216082 19 21 ; Align 276437 26 6 ; Align 334928 29 9 ; Align 380706 32 6 ; Align 439934 34 39 ; Align 466943 48 15 ; Align 472528 53 30 ; Align 496806 64 36 ; Align 519283 77 24 ; Align 574826 86 12 ; Align 575778 90 33 ; Align 653895 101 12 ; Align 661485 105 93 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000017_1.0 # Protein # Selenoprotein M (SelM) # Homo sapiens # Complete Target: NIVO01044519.1:subseq(733635,745166) Ammotragus lervia isolate NAZ scaffold2533_len1482783_cov71, whole genome shotgun sequence Model: protein2genome:local Raw score: 130 Query range: 0 -> 144 Target range: 797 -> 734269 1 : MetSerLeuLeuLeuPro{Pr} >>>> Target Intron 1 >>>> {o}LeuA : 9 |||...||| :::|||{! } 37701 bp {!}|||| MetGlyLeuAlaValPro{Ar}++ ++{g}LeuA 798 : atgggcttagctgtccca{cG}gt.........................ag{G}TTGG : 38523 10 : laLeuLeuLeuLeuLeuAlaAlaLeu >>>> Target Intron 2 >>>> {V} : 18 ||||| !! !|||! !||| ! ! 16294 bp {!} laLeuLysProLeuSerAlaLysGlu++ ++{A} 38524 : CACTTAAACCGCTCTCTGCCAAGGAGgt.........................ag{g} : 54844 19 : >>>> Target Intron 3 >>>> {al}AlaProAlaThrAlaAlaThrAla : 27 19834 bp { !} !|||||||||.!!.!!! ! ! ++ ++{sp}HisProAlaThrThrThrLysGln+ 54845 : gt.........................ag{AC}CACCCAGCCACCACTACCAAACAGg : 74705 28 : >>>> Target Intron 4 >>>> TyrArgProAspTrpAsn{Ar} >>>> T : 33 60521 bp ! !|||...|||!..{||} + ++GlyThrProSerTrpThr{Ar}++ 74706 : t.........................agGGGACTCCATCGTGGACA{AG}gt...... : 135248 34 : arget Intron 5 >>>> {g}LeuSerGlyLeuThrArgAlaArgValGluThrC : 45 34478 bp {|} ! !!!.!! !:!!|||!.!||||||:!! !! ++{g}ThrProAlaCysSerArgGlyArgValGlnProT 135249 : ...................ag{A}ACACCCGCCTGCTCCAGGGGACGTGTGCAGCCCA : 169758 46 : ysGlyGlyUnkGlnLeuAsnArgLeu >>>> Target Intron 6 >>>> > : 54 !||||||...||| !::: !!! ! 11430 bp hrGlyGlySerGlnAlaSerGlyGln++ ++++ 169759 : CCGGAGGCAGCCAGGCCTCAGGGCAGgt.........................aggt. : 181217 55 : >>> Target Intron 7 >>>> LysGluValLysAlaPheValThrGln >>> : 63 73224 bp ..!|||...! !|||! !:!!||| ++PheArgValSerAspPheGluSerGln++ 181218 : ........................agTTTCGAGTCTCTGATTTTGAGTCCCAGgt... : 254468 64 : > Target Intron 8 >>>> AspIleProPheTyr >>>> Target Intro : 68 72796 bp |||::: ...::: 30276 bp ++AspValTrpLeuTrp++ 254469 : ......................aggatgtctggctctgggt................. : 327279 69 : n 9 >>>> HisAsnLeuVal >>>> Target Intron 10 >>>> MetLys : 73 |||:!!:!!:!! 23141 bp !||| ++HisAspValMet++ ++AlaLys 327280 : ........agCATGATGTCATGgt..........................agGCGAAG : 380709 74 : >>>> Target Intron 11 >>>> HisLeuPro >>>> Target Intro : 77 20750 bp .!.! !||| 83557 bp ++ ++GluTrpPro++ 380710 : gt..........................agGAATGGCCGgt................. : 401473 78 : n 12 >>>> GlyAlaAspProGluLeuValLeuLeuGly{Ar} >>>> Target : 87 |||::::::|||...||| |||||||||{||} 17 ++GlySerAsnProHisLeu---LeuLeuGly{Ar}++ 401474 : .........agggatcgaacccccatctc---ctgcttggc{ag}gt........... : 485059 88 : Intron 13 >>>> {g}ArgTyrGlu >>>> Target Intron 14 >>>> : 91 884 bp {|}||| !!||| 66072 bp ++{g}ArgAspGlu+- + 485060 : ...............ag{G}AGGGACGAGga..........................a : 569021 92 : GluLeuGluArgIlePro{L} >>>> Target Intron 15 >>>> {eu}Se : 98 !!:|||:!!! !:!!|||{ } 61230 bp { !}.. +AspLeuGlnLeuLeuPro{A}++ ++{la}Gl 569022 : gGACCTGCAGCTTCTCCCT{G}gt..........................ag{CT}CA : 630274 99 : rGluMetThrArgGluGluIle >>>> Target Intron 16 >>>> AsnAla : 107 !:!!:!!||||||:!!! :!: 23597 bp ....!! nGlnLeuThrArgGlnValVal++ ++ThrThr 630275 : GCAACTGACTCGTCAGGTTGTGgt..........................agacaACT : 653898 108 : LeuVal >>>> Target Intron 17 >>>> GlnGluLeuGlyPhe >>>> : 115 |||! ! 22451 bp !|||||||||.!. LeuGlu++ ++AlaGluLeuGlyMet++ 653899 : CTAGAGgt..........................agGCAGAGCTTGGGATGgt..... : 676375 116 : Target Intron 18 >>>> TyrArgLysAlaAlaProAspAlaGlnVal >>> : 125 395 bp !:! ! !!||||||..! !!||| ! ++ArgLysLeuProAlaProSerProGlnSer++ 676376 : .....................agAGAAAGTTGCCTGCACCGTCCCCTCAGAGTgt... : 676800 126 : > Target Intron 19 >>>> ProPro{G} >>>> Target Intron 20 : 127 19174 bp ||||||{!} 16790 bp -+ProPro{A}++ 676801 : .......................cgccccca{g}gt...................... : 695981 128 : >>>> {lu}TyrVal{Tr} >>>> Target Intron 21 >>>> {p}AlaPr : 132 {!:}||||||{||} 21448 bp {|} ++{sp}TyrVal{Tr}++ ++{p}ProAr 695982 : ....ag{AC}TATGTG{TG}gt..........................ag{G}Cccag : 734231 133 : oAlaLysProProGluGluThrSerAspHisAlaAsp : 144 ...||| |||||| |||! :!! !||| gGlyLysGluLysGluGluGluSerGlyAsnGlnAsp 734232 : ggggaaggagaaggaggaggagtctGGAAACCAGGAT : 734269 vulgar: SPP00000017_1.0 0 144 . NIVO01044519.1:subseq(733635,745166) 797 734269 + 130 M 6 18 S 0 2 5 0 2 I 0 37697 3 0 2 S 1 1 M 10 30 5 0 2 I 0 16290 3 0 2 S 0 1 5 0 2 I 0 19830 3 0 2 S 1 2 M 8 24 5 0 2 I 0 60517 3 0 2 M 6 18 S 0 2 5 0 2 I 0 34474 3 0 2 S 1 1 M 20 60 5 0 2 I 0 11426 3 0 2 5 0 2 I 0 73220 3 0 2 M 9 27 5 0 2 I 0 72792 3 0 2 M 5 15 5 0 2 I 0 30272 3 0 2 M 4 12 5 0 2 I 0 23137 3 0 2 M 2 6 5 0 2 I 0 20746 3 0 2 M 3 9 5 0 2 I 0 83553 3 0 2 M 6 18 G 1 0 M 3 9 S 0 2 5 0 2 I 0 17880 3 0 2 S 1 1 M 3 9 5 0 2 I 0 66068 3 0 2 M 6 18 S 0 1 5 0 2 I 0 61226 3 0 2 S 1 2 M 8 24 5 0 2 I 0 23593 3 0 2 M 4 12 5 0 2 I 0 22447 3 0 2 M 5 15 5 0 2 I 0 391 3 0 2 M 10 30 5 0 2 I 0 19170 3 0 2 M 2 6 S 0 1 5 0 2 I 0 16786 3 0 2 S 1 2 M 2 6 S 0 2 5 0 2 I 0 21444 3 0 2 S 1 1 M 14 42 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-17 ##type DNA # # # seqname source feature start end score strand frame attributes # NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local gene 798 734269 130 + . gene_id 2 ; sequence SPP00000017_1.0 ; gene_orientation + NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 798 817 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 798 817 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 818 819 . + . intron_id 1 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 818 38518 . + . intron_id 1 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 38517 38518 . + . intron_id 0 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 38519 38549 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 38519 38549 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 38550 38551 . + . intron_id 2 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 38550 54843 . + . intron_id 2 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 54842 54843 . + . intron_id 1 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 54844 54844 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 54844 54844 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 54845 54846 . + . intron_id 3 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 54845 74678 . + . intron_id 3 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 74677 74678 . + . intron_id 2 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 74679 74704 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 74679 74704 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 74705 74706 . + . intron_id 4 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 74705 135225 . + . intron_id 4 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 135224 135225 . + . intron_id 3 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 135226 135245 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 135226 135245 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 135246 135247 . + . intron_id 5 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 135246 169723 . + . intron_id 5 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 169722 169723 . + . intron_id 4 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 169724 169784 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 169724 169784 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 169785 169786 . + . intron_id 6 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 169785 181214 . + . intron_id 6 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 181213 181214 . + . intron_id 5 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 181215 181216 . + . intron_id 7 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 181215 254438 . + . intron_id 7 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 254437 254438 . + . intron_id 6 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 254439 254465 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 254439 254465 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 254466 254467 . + . intron_id 8 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 254466 327261 . + . intron_id 8 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 327260 327261 . + . intron_id 7 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 327262 327276 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 327262 327276 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 327277 327278 . + . intron_id 9 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 327277 357552 . + . intron_id 9 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 357551 357552 . + . intron_id 8 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 357553 357564 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 357553 357564 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 357565 357566 . + . intron_id 10 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 357565 380705 . + . intron_id 10 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 380704 380705 . + . intron_id 9 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 380706 380711 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 380706 380711 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 380712 380713 . + . intron_id 11 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 380712 401461 . + . intron_id 11 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 401460 401461 . + . intron_id 10 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 401462 401470 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 401462 401470 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 401471 401472 . + . intron_id 12 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 401471 485027 . + . intron_id 12 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 485026 485027 . + . intron_id 11 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 485028 485056 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 485028 485056 . + . insertions 0 ; deletions 1 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 485057 485058 . + . intron_id 13 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 485057 502940 . + . intron_id 13 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 502939 502940 . + . intron_id 12 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 502941 502950 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 502941 502950 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 502951 502952 . + . intron_id 14 ; splice_site "GA" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 502951 569022 . + . intron_id 14 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 569021 569022 . + . intron_id 13 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 569023 569041 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 569023 569041 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 569042 569043 . + . intron_id 15 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 569042 630271 . + . intron_id 15 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 630270 630271 . + . intron_id 14 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 630272 630297 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 630272 630297 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 630298 630299 . + . intron_id 16 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 630298 653894 . + . intron_id 16 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 653893 653894 . + . intron_id 15 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 653895 653906 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 653895 653906 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 653907 653908 . + . intron_id 17 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 653907 676357 . + . intron_id 17 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 676356 676357 . + . intron_id 16 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 676358 676372 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 676358 676372 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 676373 676374 . + . intron_id 18 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 676373 676767 . + . intron_id 18 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 676766 676767 . + . intron_id 17 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 676768 676797 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 676768 676797 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 676798 676799 . + . intron_id 19 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 676798 695971 . + . intron_id 19 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 695970 695971 . + . intron_id 18 ; splice_site "cg" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 695972 695978 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 695972 695978 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 695979 695980 . + . intron_id 20 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 695979 712768 . + . intron_id 20 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 712767 712768 . + . intron_id 19 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 712769 712778 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 712769 712778 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 712779 712780 . + . intron_id 21 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 712779 734226 . + . intron_id 21 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 734225 734226 . + . intron_id 20 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 734227 734269 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 734227 734269 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local similarity 798 734269 130 + . alignment_id 2 ; Query SPP00000017_1.0 ; Align 798 1 18 ; Align 38520 8 30 ; Align 74681 19 24 ; Align 135226 27 18 ; Align 169725 34 60 ; Align 254439 54 27 ; Align 327262 63 15 ; Align 357553 68 12 ; Align 380706 72 6 ; Align 401462 74 9 ; Align 485028 77 18 ; Align 485046 84 9 ; Align 502942 88 9 ; Align 569023 91 18 ; Align 630274 98 24 ; Align 653895 106 12 ; Align 676358 110 15 ; Align 676768 115 30 ; Align 695972 125 6 ; Align 712771 128 6 ; Align 734228 131 42 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000017_1.0 # Protein # Selenoprotein M (SelM) # Homo sapiens # Complete Target: NIVO01044519.1:subseq(733635,745166) Ammotragus lervia isolate NAZ scaffold2533_len1482783_cov71, whole genome shotgun sequence Model: protein2genome:local Raw score: 116 Query range: 7 -> 144 Target range: 677 -> 700576 8 : LeuAlaLeuLeuLeuLeuLeuAlaAlaLeuValAla >>>> Target Intron 1 : 20 |||:::|||:::::: |||... ||||||... 28484 bp LeuSerLeuIleValThrLeuGlyLeuLeuValVal++ 678 : ctttctctaattgtgacgctagggcttctcgttgtggt.................... : 716 21 : >>>> ProAlaThrAlaAlaThrAlaTyrArgProAsp{Tr} >>>> Target : 31 ||| !!!:!|||.!!|||..!! !.! !:!!{||} 256 ++ProProSerAlaThrThrCysLeuAsnSerAsn{Tr}++ 717 : .....agCCCCCCAGTGCCACCACCTGTTTAAACAGTAAC{TG}gt............ : 29235 32 : Intron 2 >>>> {p} >>>> Target Intron 3 >>>> AsnArgLeu{S : 35 11 bp {|} 7706 bp |||||||||{! ++{p}++ ++AsnArgLeu{A 29236 : .............ag{g}gt.........................agAATCGATTG{A : 62560 36 : e} >>>> Target Intron 4 >>>> {r}GlyLeuThrArgAlaArg{V} > : 42 !} 72664 bp {!}|||||| !|||!.!!:!{|} r}++ ++{g}GlyLeuHisArgGlyGln{V}++ 62561 : G}gt.........................ag{G}GGACTCCATCGTGGACAA{G}gt. : 135248 43 : >>> Target Intron 5 >>>> {al} >>>> Target Intron 6 >>>> : 43 22498 bp {||} 23469 bp ++{al}+- + 135249 : ........................ag{TG}gg.........................a : 181213 44 : >>>> Target Intron 7 >>>> GluThrCysGlyGlyUnkGlnLeuAsnA : 52 91791 bp :!! !!! !||| ||||||! +++ ++LysGlyTrpLysGlyGluAlaLeuAsnP 181214 : ggt.........................agAAAGGCTGGAAAGGAGAGGCTTTAAATC : 273033 53 : rgLeuLysGluValLysAlaPheValThrGlnAspIleProPheTyrHisAsnLeuVa : 71 !||| ! ! !||||||:!! ! ! :!! !||| ! |||..!|||:! roLeuTrpLeuSerValAlaPheLeuGluTyrProLeu***PheGlnHisGlyLeuLe 273034 : CACTTTGGCTTTCTGTAGCATTTCTAGAATATCCACTTTAGTTTCAGCATGGTCTTCT : 273090 72 : lMet >>>> Target Intron 8 >>>> LysHis{Le} >>>> Target I : 75 !:!! 3341 bp !|||{ } 10426 uVal++ ++AlaHis{Ar}++ 273091 : AGTGgt.........................agGCACAC{AG}gt............. : 276447 76 : ntron 9 >>>> {u}Pro{Gl} >>>> Target Intron 10 >>>> {y}A : 78 1 bp {!}! !{ !} 63479 bp {!}! ++{g}Arg{Ar}++ ++{g}V 276448 : ............ag{G}CGA{AG}gt..........................ag{G}G : 444192 79 : laAspProGluLeuValLeuLeuGly{A} >>>> Target Intron 11 >>>> : 87 .!! !! !|||||||||:!!:!!! !{ } 39701 bp alGlyHisGluLeuValMetIleGlu{G}++ + 444193 : TCGGTCATGAGTTGGTAATGATTGAA{G}gt..........................a : 483919 88 : {rg}ArgTyrGluGluLeuGluArgIleProLeuSerGlu{M} >>>> Target : 100 {!!} ! ||| |||...|||:::||||||..!:!!{!} 58 +{ly}CysTyrMetThrLeuSerArgValProLeuGlnGln{I}++ 483920 : g{GT}TGctacatgacattgagcagagttcccttgcAACAA{A}gt............ : 483962 101 : Intron 12 >>>> {et}ThrArgGluGluIleAsnAlaLeu >>>> Target : 109 12 bp {!:}:!!!.!.!.|||:!!||| !! ! 97 ++{le}SerHisHisGluLeuAsnTrpGln+- 483963 : ..............ag{TT}TCACACCACGAATTAAACTGGCAGga............ : 489800 110 : Intron 13 >>>> ValGln >>>> Target Intron 14 >>>> GluLeu : 112 21 bp ..!||| 87835 bp ... ! ++ThrGln++ ++SerArg 489801 : ..............agACCCAAgt..........................agAGCAGG : 587363 113 : GlyPheTyrArgLysAlaAlaProAspAlaGln >>>> Target Intron 15 > : 124 ||| ! ! ! !|||!!:|||||| 66496 bp GlyGlnThrMetProLeuLeuProGluAlaGln++ 587364 : GGGCAGACGATGCCTCTATTGCCCGAGGCTCAGgt....................... : 587401 125 : >>> ValProProGlu >>>> Target Intron 16 >>>> TyrValTrp{A : 131 ... !!! !||| 200 bp :::||||||{| ++ThrThrLeuGlu++ ++TrpValTrp{A 587402 : ...agacaACTCTAGAGgt..........................agtgggtctgg{g : 654116 132 : } >>>> Target Intron 17 >>>> {la}ProAlaLysProPro{G} >>> : 137 } 14182 bp {||} !||| ||| !{!} }++ ++{la}LeuAlaAlaProGlu{A}+- 654117 : }gt..........................ag{cC}TTAGCTGCTCCAGAA{G}gc... : 668319 138 : > Target Intron 18 >>>> {lu}GluThrSerAspHisAlaAsp : 144 32237 bp {!:}:!! ! !!||||||.!!||| ++{sp}LysLeuArgAspHisThrAsp 668320 : .......................ag{AC}AAACTCCGCGATCATACGGAT : 700576 vulgar: SPP00000017_1.0 7 144 . NIVO01044519.1:subseq(733635,745166) 677 700576 + 116 M 12 36 5 0 2 I 0 28480 3 0 2 M 11 33 S 0 2 5 0 2 I 0 25607 3 0 2 S 1 1 5 0 2 I 0 7702 3 0 2 M 3 9 S 0 2 5 0 2 I 0 72660 3 0 2 S 1 1 M 6 18 S 0 1 5 0 2 I 0 22494 3 0 2 S 1 2 5 0 2 I 0 23465 3 0 2 5 0 2 I 0 91787 3 0 2 M 30 90 5 0 2 I 0 3337 3 0 2 M 2 6 S 0 2 5 0 2 I 0 104257 3 0 2 S 1 1 M 1 3 S 0 2 5 0 2 I 0 63475 3 0 2 S 1 1 M 9 27 S 0 1 5 0 2 I 0 39697 3 0 2 S 1 2 M 12 36 S 0 1 5 0 2 I 0 5808 3 0 2 S 1 2 M 8 24 5 0 2 I 0 9717 3 0 2 M 2 6 5 0 2 I 0 87831 3 0 2 M 13 39 5 0 2 I 0 66492 3 0 2 M 4 12 5 0 2 I 0 196 3 0 2 M 3 9 S 0 1 5 0 2 I 0 14178 3 0 2 S 1 2 M 5 15 S 0 1 5 0 2 I 0 32233 3 0 2 S 1 2 M 7 21 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-17 ##type DNA # # # seqname source feature start end score strand frame attributes # NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local gene 678 700576 116 + . gene_id 3 ; sequence SPP00000017_1.0 ; gene_orientation + NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 678 713 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 678 713 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 714 715 . + . intron_id 1 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 714 29197 . + . intron_id 1 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 29196 29197 . + . intron_id 0 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 29198 29232 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 29198 29232 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 29233 29234 . + . intron_id 2 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 29233 54843 . + . intron_id 2 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 54842 54843 . + . intron_id 1 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 54844 54844 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 54844 54844 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 54845 54846 . + . intron_id 3 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 54845 62550 . + . intron_id 3 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 62549 62550 . + . intron_id 2 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 62551 62561 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 62551 62561 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 62562 62563 . + . intron_id 4 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 62562 135225 . + . intron_id 4 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 135224 135225 . + . intron_id 3 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 135226 135245 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 135226 135245 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 135246 135247 . + . intron_id 5 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 135246 157743 . + . intron_id 5 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 157742 157743 . + . intron_id 4 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 157744 157745 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 157744 157745 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 157746 157747 . + . intron_id 6 ; splice_site "GG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 157746 181214 . + . intron_id 6 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 181213 181214 . + . intron_id 5 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 181215 181216 . + . intron_id 7 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 181215 273005 . + . intron_id 7 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 273004 273005 . + . intron_id 6 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 273006 273095 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 273006 273095 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 273096 273097 . + . intron_id 8 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 273096 276436 . + . intron_id 8 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 276435 276436 . + . intron_id 7 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 276437 276444 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 276437 276444 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 276445 276446 . + . intron_id 9 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 276445 380705 . + . intron_id 9 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 380704 380705 . + . intron_id 8 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 380706 380711 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 380706 380711 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 380712 380713 . + . intron_id 10 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 380712 444190 . + . intron_id 10 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 444189 444190 . + . intron_id 9 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 444191 444219 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 444191 444219 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 444220 444221 . + . intron_id 11 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 444220 483920 . + . intron_id 11 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 483919 483920 . + . intron_id 10 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 483921 483959 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 483921 483959 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 483960 483961 . + . intron_id 12 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 483960 489771 . + . intron_id 12 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 489770 489771 . + . intron_id 11 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 489772 489797 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 489772 489797 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 489798 489799 . + . intron_id 13 ; splice_site "GA" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 489798 499518 . + . intron_id 13 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 499517 499518 . + . intron_id 12 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 499519 499524 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 499519 499524 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 499525 499526 . + . intron_id 14 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 499525 587359 . + . intron_id 14 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 587358 587359 . + . intron_id 13 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 587360 587398 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 587360 587398 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 587399 587400 . + . intron_id 15 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 587399 653894 . + . intron_id 15 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 653893 653894 . + . intron_id 14 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 653895 653906 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 653895 653906 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 653907 653908 . + . intron_id 16 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 653907 654106 . + . intron_id 16 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 654105 654106 . + . intron_id 15 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 654107 654116 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 654107 654116 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 654117 654118 . + . intron_id 17 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 654117 668298 . + . intron_id 17 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 668297 668298 . + . intron_id 16 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 668299 668316 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 668299 668316 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 668317 668318 . + . intron_id 18 ; splice_site "GC" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 668317 700553 . + . intron_id 18 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 700552 700553 . + . intron_id 17 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 700554 700576 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 700554 700576 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local similarity 678 700576 116 + . alignment_id 3 ; Query SPP00000017_1.0 ; Align 678 8 36 ; Align 29198 20 33 ; Align 62551 32 9 ; Align 135227 36 18 ; Align 273006 43 90 ; Align 276437 73 6 ; Align 380707 76 3 ; Align 444192 78 27 ; Align 483923 88 36 ; Align 489774 101 24 ; Align 499519 109 6 ; Align 587360 111 39 ; Align 653895 124 12 ; Align 654107 128 9 ; Align 668301 132 15 ; Align 700556 138 21 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000017_1.0 # Protein # Selenoprotein M (SelM) # Homo sapiens # Complete Target: NIVO01044519.1:subseq(733635,745166) Ammotragus lervia isolate NAZ scaffold2533_len1482783_cov71, whole genome shotgun sequence Model: protein2genome:local Raw score: 111 Query range: 1 -> 145 Target range: 179427 -> 672538 2 : SerLeuLeuLeuProProLeuAlaLeu{L} >>>> Target Intron 1 >>>> : 11 ||| !||| !|||||| !|||!!!{ } 70819 bp SerAsnLeuAspProProThrAlaPhe{G}++ + 179428 : TCAAATCTGGACCCTCCCACTGCCTTT{G}gt.........................a : 250273 12 : {eu}LeuLeuLeuAlaAlaLeuValAlaProAlaThrAla{A} >>>> Target : 24 { !}::: ||||||:::|||::::::|||||| |||{!} 261 +{ly}IleGluLeuAlaSerLeuIleSerProAlaPheAla{G}++ 250274 : g{gg}atcgaacttgcgtctcttatatctcctgcatttgca{g}gt............ : 250316 25 : Intron 2 >>>> {la}ThrAla >>>> Target Intron 3 >>>> TyrA : 28 23 bp {.!}||| ! 16648 bp ! ++{ly}ThrGln++ ++MetI 250317 : .............ag{GC}ACACAGgt.........................agATGA : 293096 29 : rgProAspTrpAsn{Ar} >>>> Target Intron 4 >>>> {g}LeuSerGl : 36 !! !:!!||||||{||} 28090 bp {|}:::||||| leGlnAsnTrpAsn{Ar}++ ++{g}ValSerGl 293097 : TTCAGAATTGGAAC{AG}gt.........................ag{g}gtgtctgg : 321210 37 : yLeu{Th} >>>> Target Intron 5 >>>> {r}Arg{Al} >>>> Targ : 40 | {! } 59488 bp {!}|||{::} ySer{Ar}++ ++{g}Arg{Se}++ 321211 : ctca{ag}gt.........................ag{G}CGA{AG}gt......... : 380714 41 : et Intron 6 >>>> {a}Arg{V} >>>> Target Intron 7 >>>> {a : 42 7804 bp {!}!:!{|} 9361 bp {| ++{r}Lys{V}++ +-{a 380715 : ................ag{T}AAA{G}gt.........................at{T : 397882 43 : l}GluThrCysGlyGlyUnkGlnLeuAsnArgLeu{L} >>>> Target Intron : 54 |}!!:!:!|||..!!.! ||| !|||||| !{:} 23134 bp l}AspSerCysSerAlaPheGlnAlaAsnArgLys{G}++ 397883 : C}GACAGCTGTTCGGCATTTCAAGCAAATCGGAAA{G}gt.................. : 397920 55 : 8 >>>> {ys}GluValLys >>>> Target Intron 9 >>>> AlaPheV : 60 {!!}|||! !||| 42818 bp !.!.!.: +-{lu}GluGluLys++ ++ValLeuI 397921 : .......aa{AG}GAAGAAAAGgt.........................agGTTCTAA : 463887 61 : alThrGlnAspIleProPheTyrHisAsnLeuValMetLysHis >>>> Target : 75 !! !|||! :!:! ! !||| |||||| ... ::: 23 le***GlnAlaLeuHisHisTyrSerAsnLeuTyrPhe***Asn++ 463888 : TATGACAGGCACTGCACCATTattctaatctttatttttaaaatgt............ : 463934 76 : Intron 10 >>>> LeuProGlyAlaAspProGluLeuValLeuLeuGlyArgArg : 88 68 bp :!!|||||| !... !!|||!!!||||||||||||!:! ! ++IleProGlyArgSerThrGluPheValLeuLeuGlyLysSer 463935 : ..............agATCCCGGGACGCTCGACCGAGTTTGTCCTGTTGGGGAAATCA : 466339 89 : Tyr{G} >>>> Target Intron 11 >>>> {lu}Glu{Le} >>>> Targ : 92 {!} 16512 bp { }:!!{ } Leu{V}++ ++{al}Gln{Ar}++ 466340 : CTA{G}gt..........................ag{TC}CAA{AG}gt......... : 482867 93 : et Intron 12 >>>> {u}GluArgIleProLeuSerGluMetThr{A} >>>> : 102 2163 bp {!}:::||| |||:::||| :::...{ } ++{g}AspArgThrProIleSerCysLeuAla{G}++ 482868 : .................ag{g}gatcgaacccccatctcctgcttggca{g}gt.... : 485059 103 : Target Intron 13 >>>> {rg}GluGluIleAsnAlaLeuValGlnGlu > : 112 4540 bp {!!} ::: |||||| !||| ++{ly}AlaTrpVal***PheLeuValGlyGlu++ 485060 : ......................ag{gg}gcctgggtttgattcttggtagGGGAagt. : 489628 113 : >>> Target Intron 14 >>>> LeuGlyPheTyrArgLysAlaAlaProAsp{ : 122 5955 bp ||| ::: ...||||||||| { ++AlaGlyGlyPheLeuSerAlaAlaProPro{ 489629 : .........................aggcaggcggattcttatccgctgcaccacca{ : 495611 123 : A} >>>> Target Intron 15 >>>> {la}GlnValProProGluTyrValT : 130 !} 80166 bp { !} |||||| !.! G}+- ++{lu}GlyProProProProSerAlaA 495612 : g}gg..........................ag{Aa}ggacccccacccccttccGCTG : 575801 131 : rpAlaPro{A} >>>> Target Intron 16 >>>> {la}LysProProGluG : 138 :!!|||{|} 5663 bp {||}!:!||||||! ! laSerPro{A}++ ++{la}ArgProProGlyA 575802 : CCTCCCCA{G}gt..........................ag{CG}AGGCCCCCAGGTG : 581488 139 : luThrSerAspHis >>>> Target Intron 17 >>>> AlaAspLeu : 145 !: !!:!!|||!.! 91027 bp ||||||:!! spProAlaAspArg++ ++AlaAspIle 581489 : ACCCCGCCGACCGCgt..........................aggcAGACATC : 672538 vulgar: SPP00000017_1.0 1 145 . NIVO01044519.1:subseq(733635,745166) 179427 672538 + 111 M 9 27 S 0 1 5 0 2 I 0 70815 3 0 2 S 1 2 M 12 36 S 0 1 5 0 2 I 0 26119 3 0 2 S 1 2 M 2 6 5 0 2 I 0 16644 3 0 2 M 6 18 S 0 2 5 0 2 I 0 28086 3 0 2 S 1 1 M 4 12 S 0 2 5 0 2 I 0 59484 3 0 2 S 1 1 M 1 3 S 0 2 5 0 2 I 0 7800 3 0 2 S 1 1 M 1 3 S 0 1 5 0 2 I 0 9357 3 0 2 S 1 2 M 11 33 S 0 1 5 0 2 I 0 23130 3 0 2 S 1 2 M 3 9 5 0 2 I 0 42814 3 0 2 M 17 51 5 0 2 I 0 2364 3 0 2 M 15 45 S 0 1 5 0 2 I 0 16508 3 0 2 S 1 2 M 1 3 S 0 2 5 0 2 I 0 2159 3 0 2 S 1 1 M 9 27 S 0 1 5 0 2 I 0 4536 3 0 2 S 1 2 M 9 27 5 0 2 I 0 5951 3 0 2 M 10 30 S 0 1 5 0 2 I 0 80162 3 0 2 S 1 2 M 10 30 S 0 1 5 0 2 I 0 5659 3 0 2 S 1 2 M 9 27 5 0 2 I 0 91023 3 0 2 M 3 9 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-17 ##type DNA # # # seqname source feature start end score strand frame attributes # NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local gene 179428 672538 111 + . gene_id 4 ; sequence SPP00000017_1.0 ; gene_orientation + NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 179428 179455 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 179428 179455 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 179456 179457 . + . intron_id 1 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 179456 250274 . + . intron_id 1 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 250273 250274 . + . intron_id 0 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 250275 250313 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 250275 250313 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 250314 250315 . + . intron_id 2 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 250314 276436 . + . intron_id 2 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 276435 276436 . + . intron_id 1 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 276437 276444 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 276437 276444 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 276445 276446 . + . intron_id 3 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 276445 293092 . + . intron_id 3 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 293091 293092 . + . intron_id 2 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 293093 293112 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 293093 293112 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 293113 293114 . + . intron_id 4 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 293113 321202 . + . intron_id 4 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 321201 321202 . + . intron_id 3 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 321203 321217 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 321203 321217 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 321218 321219 . + . intron_id 5 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 321218 380705 . + . intron_id 5 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 380704 380705 . + . intron_id 4 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 380706 380711 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 380706 380711 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 380712 380713 . + . intron_id 6 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 380712 388515 . + . intron_id 6 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 388514 388515 . + . intron_id 5 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 388516 388520 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 388516 388520 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 388521 388522 . + . intron_id 7 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 388521 397881 . + . intron_id 7 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 397880 397881 . + . intron_id 6 ; splice_site "AT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 397882 397917 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 397882 397917 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 397918 397919 . + . intron_id 8 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 397918 421051 . + . intron_id 8 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 421050 421051 . + . intron_id 7 ; splice_site "AA" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 421052 421062 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 421052 421062 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 421063 421064 . + . intron_id 9 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 421063 463880 . + . intron_id 9 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 463879 463880 . + . intron_id 8 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 463881 463931 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 463881 463931 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 463932 463933 . + . intron_id 10 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 463932 466299 . + . intron_id 10 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 466298 466299 . + . intron_id 9 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 466300 466345 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 466300 466345 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 466346 466347 . + . intron_id 11 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 466346 482857 . + . intron_id 11 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 482856 482857 . + . intron_id 10 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 482858 482864 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 482858 482864 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 482865 482866 . + . intron_id 12 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 482865 485027 . + . intron_id 12 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 485026 485027 . + . intron_id 11 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 485028 485056 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 485028 485056 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 485057 485058 . + . intron_id 13 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 485057 489596 . + . intron_id 13 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 489595 489596 . + . intron_id 12 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 489597 489625 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 489597 489625 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 489626 489627 . + . intron_id 14 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 489626 495580 . + . intron_id 14 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 495579 495580 . + . intron_id 13 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 495581 495611 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 495581 495611 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 495612 495613 . + . intron_id 15 ; splice_site "gg" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 495612 575777 . + . intron_id 15 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 575776 575777 . + . intron_id 14 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 575778 575810 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 575778 575810 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 575811 575812 . + . intron_id 16 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 575811 581473 . + . intron_id 16 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 581472 581473 . + . intron_id 15 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 581474 581502 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 581474 581502 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 581503 581504 . + . intron_id 17 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 581503 672529 . + . intron_id 17 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 672528 672529 . + . intron_id 16 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 672530 672538 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 672530 672538 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local similarity 179428 672538 111 + . alignment_id 4 ; Query SPP00000017_1.0 ; Align 179428 2 27 ; Align 250277 12 36 ; Align 276439 25 6 ; Align 293093 27 18 ; Align 321204 34 12 ; Align 380707 39 3 ; Align 388517 41 3 ; Align 397884 43 33 ; Align 421054 55 9 ; Align 463881 58 51 ; Align 466300 75 45 ; Align 482860 91 3 ; Align 485029 93 27 ; Align 489599 103 27 ; Align 495581 112 30 ; Align 575780 123 30 ; Align 581476 134 27 ; Align 672530 143 9 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000017_1.0 # Protein # Selenoprotein M (SelM) # Homo sapiens # Complete Target: NIVO01044519.1:subseq(733635,745166) Ammotragus lervia isolate NAZ scaffold2533_len1482783_cov71, whole genome shotgun sequence Model: protein2genome:local Raw score: 111 Query range: 1 -> 142 Target range: 66867 -> 717087 2 : SerLeuLeuLeuProProLeuAlaLeuLeuLeuLeuLeuAlaAlaLeuValAla{P} : 20 ||| !|||! !||||||! !::!||| !! !:!!|||.!! !:!!:!! !!{ } SerThrLeuHisProProSerSerLeuThrTrpValLeuThrAsnMetIlePro{G}+ 66868 : TCAACTTTGCACCCACCTTCAAGTTTGACGTGGGTACTAACAAATATGATACCA{G}g : 66923 21 : >>>> Target Intron 1 >>>> {ro}AlaThrAlaAlaThr{Al} >>>> : 26 40399 bp { !}||| !||| ! !{ } + ++{ly}AlaGluAlaHisArg{Me}++ 66924 : t.........................ag{GA}GCAGAAGCCCACCGC{AT}gt..... : 107343 27 : Target Intron 2 >>>> {a}TyrArgProAspTrpAsnArgLeuSerGlyLeu : 37 55332 bp {!} !||| !! ! ! !:!||| !||||||||| ++{t}ThrArgSerProGlySerArgArgSerGlyLeu 107344 : ....................ag{G}ACCCGTTCCCCTGGCAGCAGAAGGTCAGGTTTG : 162704 38 : ThrArgAlaArgValGluThr{Cy} >>>> Target Intron 3 >>>> {s}G : 46 !!!:!||| ! ! ! !{||} 67694 bp {|}. ProLysAlaSerProLeuGlu{Cy}++ ++{s}S 162705 : CCAAAGGCATCGCCTCTGGAA{TG}gt.........................ag{C}A : 230425 47 : lyGlyUnkGlnLeuAsnArgLeuLysGluValLysAlaPheValThrGlnAsp{Il} : 64 !!|||... !.!.!.! ! ... |||::::::||||||{! } erGlySerThrAlaGlnAsnThrLeuAsnCysPheHisPheIleSerGlnAsp{Th}+ 230426 : GTGGAAGCACTGCACAAAACACACTCaactgttttcatttcatttctcaaGAC{AC}g : 230481 65 : >>>> Target Intron 4 >>>> {e}ProPheTyrHisAsnLeuValMetLys : 73 9851 bp {!}|||||| !!||| ! !:!! ||| - ++{r}ProPheAsnHisValGlnLeuTyrLys 230482 : c.........................ag{A}CCATTTAACCATGTACAACTATATaaa : 240357 74 : HisLeuPro >>>> Target Intron 5 >>>> GlyAlaAspProGluLeuVa : 83 |||::: 91973 bp |||::::::|||...|||:: HisMetAsp++ ++GlySerAsnProAsnLeuLe 240358 : catatggatgt.........................agggatcgaacccgaatctcct : 332360 84 : lLeuLeu{Gl} >>>> Target Intron 6 >>>> {y}Arg{Ar} >>>> T : 88 : { !} 48335 bp {!}|||{||} uHisCys{Ar}++ ++{g}Arg{Ar}++ 332361 : gcactgc{ag}gt.........................ag{G}CGA{AG}gt...... : 380714 89 : arget Intron 7 >>>> {g}TyrGluGluLeuGluArgIleProLeuSerGlu : 100 1318 bp {|}! !:!!! ||| !..! ! !||| !:!! ++{g}SerGlnAlaLeuTrpGluCysGlyLeuHisGln+ 380715 : ...................ag{G}TCCCAGGCCCTGTGGGAGTGCGGCCTACACCAGg : 382064 101 : >>>> Target Intron 8 >>>> MetThrArgGluGluIleAsn{A} >>>> : 107 7684 bp :!!|||..! !!.!.:!:!..{|} + ++ValThrGlu***HisLeuArg{A}++ 382065 : t.........................agGTGACAGAGTAGCATCTGAGG{G}gt.... : 389772 108 : Target Intron 9 >>>> {la}LeuValGlnGluLeu{G} >>>> Target : 113 53061 bp {||}||||||:!!||||||{|} 60 ++{la}LeuValLysGluLeu{G}++ 389773 : .....................ag{CT}TTAGTGAAAGAACTG{G}gt........... : 442851 114 : Intron 10 >>>> {ly}PheTyrArgLys >>>> Target Intron 11 > : 118 092 bp {||} |||!:! 77061 bp ++{ly}GlyThrArgArg++ 442852 : ...............ag{GA}GGGACGAGGAGGgt....................... : 502957 119 : >>> AlaAlaProAspAlaGlnVal{P} >>>> Target Intron 12 >>>> : 125 !.! ! !.!. !|||:!!{ } 62634 bp ++ValArgLysGlnLeuGlnIle{G}++ + 502958 : ...agGTAAGGAAACAGCTTCAGATA{G}gt..........................a : 642670 126 : {ro}ProGluTyrValTrpAlaPro >>>> Target Intron 13 >>>> Al : 133 { !}! !... |||||| !||| 74363 bp +{ly}ArgSerMetValTrpTrpPro++ ++Me 642671 : g{GT}CGAAGTATGGTGTGGTGGCCGgt..........................agAT : 717058 134 : aLysProProGluGluThrSerAspHis : 142 !..! !|||||||||!.!.!!|||||| tSerGluProGluGluAsnGlyAspHis 717059 : GTCAGAGCCAGAAGAGAACGGAGATCAC : 717087 vulgar: SPP00000017_1.0 1 142 . NIVO01044519.1:subseq(733635,745166) 66867 717087 + 111 M 18 54 S 0 1 5 0 2 I 0 40395 3 0 2 S 1 2 M 5 15 S 0 2 5 0 2 I 0 55328 3 0 2 S 1 1 M 18 54 S 0 2 5 0 2 I 0 67690 3 0 2 S 1 1 M 18 54 S 0 2 5 0 2 I 0 9847 3 0 2 S 1 1 M 12 36 5 0 2 I 0 91969 3 0 2 M 9 27 S 0 2 5 0 2 I 0 48331 3 0 2 S 1 1 M 1 3 S 0 2 5 0 2 I 0 1314 3 0 2 S 1 1 M 11 33 5 0 2 I 0 7680 3 0 2 M 7 21 S 0 1 5 0 2 I 0 53057 3 0 2 S 1 2 M 5 15 S 0 1 5 0 2 I 0 60088 3 0 2 S 1 2 M 4 12 5 0 2 I 0 77057 3 0 2 M 7 21 S 0 1 5 0 2 I 0 62630 3 0 2 S 1 2 M 7 21 5 0 2 I 0 74359 3 0 2 M 10 30 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-17 ##type DNA # # # seqname source feature start end score strand frame attributes # NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local gene 66868 717087 111 + . gene_id 5 ; sequence SPP00000017_1.0 ; gene_orientation + NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 66868 66922 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 66868 66922 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 66923 66924 . + . intron_id 1 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 66923 107321 . + . intron_id 1 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 107320 107321 . + . intron_id 0 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 107322 107340 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 107322 107340 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 107341 107342 . + . intron_id 2 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 107341 162672 . + . intron_id 2 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 162671 162672 . + . intron_id 1 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 162673 162729 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 162673 162729 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 162730 162731 . + . intron_id 3 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 162730 230423 . + . intron_id 3 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 230422 230423 . + . intron_id 2 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 230424 230480 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 230424 230480 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 230481 230482 . + . intron_id 4 ; splice_site "GC" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 230481 240331 . + . intron_id 4 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 240330 240331 . + . intron_id 3 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 240332 240368 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 240332 240368 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 240369 240370 . + . intron_id 5 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 240369 332341 . + . intron_id 5 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 332340 332341 . + . intron_id 4 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 332342 332370 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 332342 332370 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 332371 332372 . + . intron_id 6 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 332371 380705 . + . intron_id 6 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 380704 380705 . + . intron_id 5 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 380706 380711 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 380706 380711 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 380712 380713 . + . intron_id 7 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 380712 382029 . + . intron_id 7 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 382028 382029 . + . intron_id 6 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 382030 382063 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 382030 382063 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 382064 382065 . + . intron_id 8 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 382064 389747 . + . intron_id 8 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 389746 389747 . + . intron_id 7 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 389748 389769 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 389748 389769 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 389770 389771 . + . intron_id 9 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 389770 442830 . + . intron_id 9 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 442829 442830 . + . intron_id 8 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 442831 442848 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 442831 442848 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 442849 442850 . + . intron_id 10 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 442849 502940 . + . intron_id 10 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 502939 502940 . + . intron_id 9 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 502941 502954 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 502941 502954 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 502955 502956 . + . intron_id 11 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 502955 580015 . + . intron_id 11 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 580014 580015 . + . intron_id 10 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 580016 580037 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 580016 580037 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 580038 580039 . + . intron_id 12 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 580038 642671 . + . intron_id 12 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 642670 642671 . + . intron_id 11 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 642672 642694 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 642672 642694 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 642695 642696 . + . intron_id 13 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 642695 717057 . + . intron_id 13 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 717056 717057 . + . intron_id 12 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 717058 717087 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 717058 717087 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local similarity 66868 717087 111 + . alignment_id 5 ; Query SPP00000017_1.0 ; Align 66868 2 54 ; Align 107324 21 15 ; Align 162674 27 54 ; Align 230425 46 54 ; Align 240333 65 36 ; Align 332342 77 27 ; Align 380707 87 3 ; Align 382031 89 33 ; Align 389748 100 21 ; Align 442833 108 15 ; Align 502943 114 12 ; Align 580016 118 21 ; Align 642674 126 21 ; Align 717058 133 30 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000017_1.0 # Protein # Selenoprotein M (SelM) # Homo sapiens # Complete Target: NIVO01044519.1:subseq(733635,745166) Ammotragus lervia isolate NAZ scaffold2533_len1482783_cov71, whole genome shotgun sequence Model: protein2genome:local Raw score: 106 Query range: 3 -> 132 Target range: 181198 -> 668407 4 : LeuLeuProProLeu{A} >>>> Target Intron 1 >>>> {la}LeuLeuL : 12 |||||||||||| !{!} 45253 bp {.!}|||...| LeuLeuProProAla{V}++ ++{al}LeuPheL 181199 : CTCCTTCCTCCTGCA{G}gt.........................ag{tt}ctttttt : 226476 13 : euLeuLeu >>>> Target Intron 2 >>>> AlaAlaLeuValAlaProAla : 21 ||:::::: 154030 bp ||||||! ! ! !|||::! euIleMet++ ++AlaAlaSerSerMetProSer 226477 : taatcatggt.........................agGCAGCTTCCTCGATGCCCAGC : 380533 22 : ThrAlaAlaThrAlaTyrArgProAspTrpAsnArgLeuSer{Gl} >>>> Targe : 36 ! !||| ! ! ! !!|||..!|||!.. !!:!!!!!{||} LeuArgAlaGlyArgAlaGlyProSerTrpArgGlyIleArg{Gl}++ 380534 : CTCAGGGCAGGCAGGGCCGGACCCAGCTGGAGAGGGATCAGA{GG}gt.......... : 380582 37 : t Intron 3 >>>> {y}Leu{Th} >>>> Target Intron 4 >>>> {r : 38 126 bp {|}! !{!:} 86054 bp {! ++{y}Arg{Se}++ ++{r 380583 : ...............ag{G}CGA{AG}gt.........................ag{C : 466766 39 : }ArgAlaArgValGluThrCys{Gl} >>>> Target Intron 5 >>>> {y} : 46 }||| ! !!:!!..!!:!|||{||} 5738 bp {|} }ArgLysGlyLeuArgSerCys{Gl}++ ++{y} 466767 : }AGGAAGGGGCTCCGGAGCTGC{GG}gt.........................ag{G} : 472528 47 : GlyUnkGlnLeuAsnArgLeuLysGluVal >>>> Target Intron 6 >>>> : 57 ..!...!!.|||!..|||:!! ..! ! 12451 bp SerSerHisLeuArgArgIleCysArgLys++ + 472529 : TCAAGTCACTTAAGGAGGATTTGCAGAAAGgt.........................a : 485008 58 : LysAlaPheValThrGlnAspIleProPheTyrHisAsnLeuVal{Me} >>>> T : 72 ...||| |||||| ::: ||| {! } +GlyThrPheSerThrGlnGlySerAsnProHisLeuLeuLeuGly{Se}++ 485009 : ggggaccttctccacccagggatcgaacccccatctcctgcttggc{ag}gt...... : 485059 73 : arget Intron 7 >>>> {t}LysHisLeuProGlyAlaAspProGluLeu{Va} : 83 10692 bp { } |||:!!|||!.!|||! !||| !{||} ++{r}AlaHisValProAlaAlaGlyArgGluAla{Va} 485060 : ...................ag{C}GCTCATGTCCCAGCAGCAGGAAGAGAGGCA{GT} : 495780 84 : >>>> Target Intron 8 >>>> {l}LeuLeuGlyArgArgTyrGluGluLe : 92 91578 bp {|} ! !|||||||||! ! ! ! ++ ++{l}AlaGlyGlyArgArgCysLeuTyrCy 495781 : gt.........................ag{A}GCAGGGGGCAGACGATGCCTCTATTG : 587385 93 : uGluArgIle{Pr} >>>> Target Intron 9 >>>> {o}LeuSerGluMet : 100 ! !|||:!!{ } 80900 bp {!}|||||| sProArgLeu{Se}++ ++{r}LeuSerCysSer 587386 : CCCGAGGCTC{AG}gt.........................ag{c}CTTAGCTGCTCC : 668309 101 : ThrArgGluGluIleAsnAlaLeuValGlnGluLeuGlyPheTyrArgLysAlaAlaP : 120 ! !|||:!!! ! !!..!.!||| !! ! ! !|||.!. ! !..!|||||| ArgArgGlnGlyArgArgGlyLeuArgProGlyArgGlyMetLeuSerSerAlaAlaA 668310 : AGAAGGCAAGGTAGAAGAGGTCTCAGACCTGGGAGGGGAATGCTTTCCTCAGCTGCAG : 668369 121 : roAspAlaGlnValProProGluTyrValTrpAlaPro : 132 ! ! !||||||! !||| ! :!! ::!||| spProLeuGlnValGlnProLeuArgIleThrSerPro 668370 : ATCCTCTCCAGGTCCAGCCACTAAGAATCACAAGCCCC : 668407 vulgar: SPP00000017_1.0 3 132 . NIVO01044519.1:subseq(733635,745166) 181198 668407 + 106 M 5 15 S 0 1 5 0 2 I 0 45249 3 0 2 S 1 2 M 5 15 5 0 2 I 0 154026 3 0 2 M 21 63 S 0 2 5 0 2 I 0 122 3 0 2 S 1 1 M 1 3 S 0 2 5 0 2 I 0 86050 3 0 2 S 1 1 M 7 21 S 0 2 5 0 2 I 0 5734 3 0 2 S 1 1 M 10 30 5 0 2 I 0 12447 3 0 2 M 15 45 S 0 2 5 0 2 I 0 10688 3 0 2 S 1 1 M 10 30 S 0 2 5 0 2 I 0 91574 3 0 2 S 1 1 M 12 36 S 0 2 5 0 2 I 0 80896 3 0 2 S 1 1 M 36 108 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-17 ##type DNA # # # seqname source feature start end score strand frame attributes # NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local gene 181199 668407 106 + . gene_id 6 ; sequence SPP00000017_1.0 ; gene_orientation + NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 181199 181214 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 181199 181214 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 181215 181216 . + . intron_id 1 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 181215 226467 . + . intron_id 1 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 226466 226467 . + . intron_id 0 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 226468 226484 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 226468 226484 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 226485 226486 . + . intron_id 2 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 226485 380514 . + . intron_id 2 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 380513 380514 . + . intron_id 1 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 380515 380579 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 380515 380579 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 380580 380581 . + . intron_id 3 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 380580 380705 . + . intron_id 3 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 380704 380705 . + . intron_id 2 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 380706 380711 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 380706 380711 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 380712 380713 . + . intron_id 4 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 380712 466765 . + . intron_id 4 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 466764 466765 . + . intron_id 3 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 466766 466789 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 466766 466789 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 466790 466791 . + . intron_id 5 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 466790 472527 . + . intron_id 5 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 472526 472527 . + . intron_id 4 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 472528 472558 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 472528 472558 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 472559 472560 . + . intron_id 6 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 472559 485009 . + . intron_id 6 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 485008 485009 . + . intron_id 5 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 485010 485056 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 485010 485056 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 485057 485058 . + . intron_id 7 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 485057 495748 . + . intron_id 7 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 495747 495748 . + . intron_id 6 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 495749 495781 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 495749 495781 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 495782 495783 . + . intron_id 8 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 495782 587359 . + . intron_id 8 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 587358 587359 . + . intron_id 7 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 587360 587398 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 587360 587398 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 587399 587400 . + . intron_id 9 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 587399 668298 . + . intron_id 9 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 668297 668298 . + . intron_id 8 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 668299 668407 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 668299 668407 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local similarity 181199 668407 106 + . alignment_id 6 ; Query SPP00000017_1.0 ; Align 181199 4 15 ; Align 226470 10 15 ; Align 380515 15 63 ; Align 380707 37 3 ; Align 466767 39 21 ; Align 472529 47 30 ; Align 485010 57 45 ; Align 495750 73 30 ; Align 587361 84 36 ; Align 668300 97 108 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000017_1.0 # Protein # Selenoprotein M (SelM) # Homo sapiens # Complete Target: NIVO01044519.1:subseq(733635,745166) Ammotragus lervia isolate NAZ scaffold2533_len1482783_cov71, whole genome shotgun sequence Model: protein2genome:local Raw score: 104 Query range: 8 -> 142 Target range: 7318 -> 509842 9 : AlaLeuLeuLeuLeuLeuAlaAlaLeuValAlaProAlaThrAlaAla{Th} >>>> : 25 ::!||| !|||:!!! !!.! !:!!||||||||||||..! !..!{! } SerLeuLysLeuIleCysValTyrMetValAlaProAlaValLeuCys{Me}++ 7319 : AGCTTGAAACTCATCTGTGTGTACATGGTGGCTCCTGCAGTGCTTTGC{AT}gt.... : 7371 26 : Target Intron 1 >>>> {r}AlaTyrArgProAspTrpAsnArgLeuSerGl : 36 5717 bp {!}||| ! ! ! !!||| !! !!.!|| ++{t}AlaGluValLysHisTrp***Ser***LysGl 7372 : .....................ag{G}GCTGAGGTGAAACACTGGTGATCTTGAAAAGG : 13117 37 : yLeuThrArgAlaArgValGluThrCysGlyGlyUnkGlnLeuAsnArgLeuLysGlu : 55 |||| !||| ! !!! !! !|||||| ...|||:::......... yLeuCysArgLeu***AspGlyThrCysThrLeuCysMetLeuSerHisPheSerLeu 13118 : ACTTTGTAGGCTCTGAGATGGGACGTGCAcgctatgcatgctaagtcacttcagtctt : 13174 56 : ValLysAlaPhe >>>> Target Intron 2 >>>> ValThrGlnAspIlePr : 65 |||::: ||| 7095 bp ||||||....!.||| ! ValGlnLeuPhe++ ++ValThrSerGlnIleSe 13175 : gtccaactctttgt.........................agGTCACAAGCCAGATTTC : 20299 66 : oPheTyrHisAsnLeu{V} >>>> Target Intron 3 >>>> {al}MetLys : 73 ! !|||...|||{ } 4781 bp { !} !||| rGlnAlaHisArgLeu{H}++ ++{is}GlyLys 20300 : CCAAGCCCATCGGCTA{C}gt.........................ag{AT}GGGAAG : 25104 74 : >>>> Target Intron 4 >>>> HisLeuProGlyAlaAspPro{G} >>> : 81 7629 bp ...|||! !|||...||| {!} +- ++ArgLeuArgGlyGlyAspGlu{A}++ 25105 : gg.........................agaggcTCCGTGgaggggatgag{g}gt... : 32760 82 : > Target Intron 5 >>>> {lu}LeuValLeuLeuGlyArgArgTyr{G} > : 90 1705 bp { } !..!||| !||||||! !|||{.} ++{la}AlaThrLeuAlaGlyArgLeuTyr{A}++ 32761 : ......................ag{cc}GCCACCTTGGCTGGAAGGCTTTAC{A}gt. : 34492 91 : >>> Target Intron 6 >>>> {lu}GluLeuGluArgIleProLeuSerGluM : 100 25760 bp {!.}!!:||||||!:!:!!|||||| !!... ++{sn}AspLeuGluLysValProLeuProSerH 34493 : ........................ag{AT}GACCTTGAGAAAGTCCCTCTCCCAAGCC : 60279 101 : etThr{Ar} >>>> Target Intron 7 >>>> {g}GluGlu{I} >>>> T : 105 |||{!:} 58006 bp {!}||||||{:} isThr{Gl}++ ++{n}GluGlu{V}++ 60280 : ACACC{CA}gt.........................ag{a}gaggaa{g}gt...... : 118303 106 : arget Intron 8 >>>> {le}AsnAlaLeuValGlnGluLeu{G} >>>> Ta : 113 11335 bp {!:}::: ||| |||||| !{|} ++{al}HisPheLeuPheGlnGluGln{G}++ 118304 : ...................ag{tg}catttcctctttcaggagcAA{G}gt....... : 129662 114 : rget Intron 9 >>>> {ly}PheTyr{Ar} >>>> Target Intron 10 : 116 120549 bp {||}|||:::{||} 22787 bp ++{ly}PhePhe{Ar}+- 129663 : ..................ag{ga}tttttc{ag}gc...................... : 250221 117 : >>>> {g}LysAla{A} >>>> Target Intron 11 >>>> {la}ProAsp : 121 {|}||||||{!} 43666 bp {.!}|||||| ++{g}LysAla{G}+- ++{ly}ProAsp 250222 : ....ag{A}AAGGCT{G}ga..........................ag{GC}CCGGAC : 316685 122 : AlaGlnValProProGluTyrValTrpAlaPro >>>> Target Intron 12 > : 133 !!:!!! !||| !!:!! ..! !..!! ! 63985 bp ProLysGlyProAlaLysArgThrAlaCysGln++ 316686 : CCGAAGGGACCGGCTAAGAGAACTGCGTGTCAGgt....................... : 316723 134 : >>> AlaLys >>>> Target Intron 13 >>>> ProProGluGluThrSe : 140 |||||| 129107 bp |||:::::: || ++AlaLys++ ++SerProLysAspCysSe 316724 : ...agGCGAAGgt..........................agagtccaaaagactgttc : 509834 141 : rAspHis : 142 | ||| rThrHis 509835 : tacacat : 509842 vulgar: SPP00000017_1.0 8 142 . NIVO01044519.1:subseq(733635,745166) 7318 509842 + 104 M 16 48 S 0 2 5 0 2 I 0 5713 3 0 2 S 1 1 M 34 102 5 0 2 I 0 7091 3 0 2 M 11 33 S 0 1 5 0 2 I 0 4777 3 0 2 S 1 2 M 2 6 5 0 2 I 0 7625 3 0 2 M 7 21 S 0 1 5 0 2 I 0 1701 3 0 2 S 1 2 M 8 24 S 0 1 5 0 2 I 0 25756 3 0 2 S 1 2 M 11 33 S 0 2 5 0 2 I 0 58002 3 0 2 S 1 1 M 2 6 S 0 1 5 0 2 I 0 11331 3 0 2 S 1 2 M 7 21 S 0 1 5 0 2 I 0 120545 3 0 2 S 1 2 M 2 6 S 0 2 5 0 2 I 0 22783 3 0 2 S 1 1 M 2 6 S 0 1 5 0 2 I 0 43662 3 0 2 S 1 2 M 13 39 5 0 2 I 0 63981 3 0 2 M 2 6 5 0 2 I 0 129103 3 0 2 M 8 24 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-17 ##type DNA # # # seqname source feature start end score strand frame attributes # NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local gene 7319 509842 104 + . gene_id 7 ; sequence SPP00000017_1.0 ; gene_orientation + NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 7319 7368 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 7319 7368 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 7369 7370 . + . intron_id 1 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 7369 13085 . + . intron_id 1 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 13084 13085 . + . intron_id 0 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 13086 13188 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 13086 13188 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 13189 13190 . + . intron_id 2 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 13189 20283 . + . intron_id 2 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 20282 20283 . + . intron_id 1 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 20284 20317 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 20284 20317 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 20318 20319 . + . intron_id 3 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 20318 25098 . + . intron_id 3 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 25097 25098 . + . intron_id 2 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 25099 25106 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 25099 25106 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 25107 25108 . + . intron_id 4 ; splice_site "GG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 25107 32735 . + . intron_id 4 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 32734 32735 . + . intron_id 3 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 32736 32757 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 32736 32757 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 32758 32759 . + . intron_id 5 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 32758 34462 . + . intron_id 5 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 34461 34462 . + . intron_id 4 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 34463 34489 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 34463 34489 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 34490 34491 . + . intron_id 6 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 34490 60249 . + . intron_id 6 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 60248 60249 . + . intron_id 5 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 60250 60286 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 60250 60286 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 60287 60288 . + . intron_id 7 ; splice_site "Gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 60287 118292 . + . intron_id 7 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 118291 118292 . + . intron_id 6 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 118293 118300 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 118293 118300 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 118301 118302 . + . intron_id 8 ; splice_site "gT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 118301 129635 . + . intron_id 8 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 129634 129635 . + . intron_id 7 ; splice_site "Ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 129636 129659 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 129636 129659 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 129660 129661 . + . intron_id 9 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 129660 250208 . + . intron_id 9 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 250207 250208 . + . intron_id 8 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 250209 250218 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 250209 250218 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 250219 250220 . + . intron_id 10 ; splice_site "gc" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 250219 273005 . + . intron_id 10 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 273004 273005 . + . intron_id 9 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 273006 273013 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 273006 273013 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 273014 273015 . + . intron_id 11 ; splice_site "GA" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 273014 316679 . + . intron_id 11 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 316678 316679 . + . intron_id 10 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 316680 316720 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 316680 316720 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 316721 316722 . + . intron_id 12 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 316721 380705 . + . intron_id 12 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 380704 380705 . + . intron_id 11 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 380706 380711 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 380706 380711 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 380712 380713 . + . intron_id 13 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 380712 509818 . + . intron_id 13 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 509817 509818 . + . intron_id 12 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 509819 509842 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 509819 509842 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local similarity 7319 509842 104 + . alignment_id 7 ; Query SPP00000017_1.0 ; Align 7319 9 48 ; Align 13087 26 102 ; Align 20284 60 33 ; Align 25101 72 6 ; Align 32736 74 21 ; Align 34465 82 24 ; Align 60252 91 33 ; Align 118294 103 6 ; Align 129638 106 21 ; Align 250211 114 6 ; Align 273007 117 6 ; Align 316682 120 39 ; Align 380706 133 6 ; Align 509819 135 24 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000017_1.0 # Protein # Selenoprotein M (SelM) # Homo sapiens # Complete Target: NIVO01044519.1:subseq(733635,745166) Ammotragus lervia isolate NAZ scaffold2533_len1482783_cov71, whole genome shotgun sequence Model: protein2genome:local Raw score: 102 Query range: 5 -> 141 Target range: 3163 -> 668621 6 : ProProLeuAlaLeuLeuLeuLeu >>>> Target Intron 1 >>>> LeuAl : 15 |||! !||||||!!!||||||:!! 26581 bp ||| ProHisLeuAlaPheLeuLeuMet+- ++LeuLe 3164 : CCCCACCTGGCTTTCCTTTTGATGga.........................agCTTCT : 29772 16 : aAlaLeuValAlaProAlaThrAlaAlaThrAlaTyrArgProAspTrpAsnArgLeu : 34 ! ! !!.! !!||| !!|||:!!!.! !!..! ..! !.!.|||..!!.!! ! uLeuGluAlaProProProThrSerValProCysThrGluArgGlnTrpGlyAsnArg 29773 : TCTTGAAGCCCCTCCCCCAACATCCGTACCATGCACAGAGAGGCAGTGGGGCAATCGA : 29829 35 : SerGlyLeu >>>> Target Intron 2 >>>> ThrArgAlaArgValGluTh : 44 :!!|||! ! 8678 bp ..! !!.!! !..!! AlaGlyGln++ ++ValGlyThr***ThrAlaLe 29830 : GCAGGGCAAgt.........................agGTTGGCACTTAAACCGCTCT : 38537 45 : rCysGlyGly{U} >>>> Target Intron 3 >>>> {nk}GlnLeuAsnArg : 52 !||| !|||{ } 23236 bp { }:!!:!!!..||| uCysGlnGly{G}++ ++{ly}GluValThrArg 38538 : CTGCCAAGGA{G}gt.........................ag{GT}GAAGTGACGAGG : 61797 53 : >>>> Target Intron 4 >>>> LeuLysGluValLys >>>> Target : 58 32073 bp |||:::... !:!! 175 ++ -+LeuArgSerCysGlu++ 61798 : gt.........................tgcttcgTTCCTGTGAGgt............ : 93890 59 : Intron 5 >>>> AlaPheValThrGlnAspIlePro >>>> Target Intro : 66 30 bp :::||| ||||||||| ||| 69773 bp ++SerPheGlyThrGlnAspGlnPro-+ 93891 : .............agagctttggaaCTCAAGACCAGCCGtt................. : 111444 67 : n 6 >>>> >>>> Target Intron 7 >>>> PheTyrHisAsnLeuValM : 72 37323 bp ..! |||::!! ! !!: ++++ ++IleValHisSerSerPheV 111445 : ........aggt.........................agatCGTGCACTCTTCTTTCG : 218556 73 : etLysHisLeuProGlyAlaAspProGluLeuValLeuLeuGlyArgArgTyrGluGl : 91 ::... ||| |||...|||...||| !! !||| !! ! !|||:! alSerAlaArgProProAlaSerProSerLeuSerThrSerGlyGlyValArgGluGl 218557 : tctccgcccgcccgcccgcctccccttctctttctacCTCCGGGGGGGTACGCGAGCA : 218613 92 : uLeu{G} >>>> Target Intron 8 >>>> {lu}ArgIleProLeu{S} > : 98 ! !{!} 146268 bp {!:}||||||||||||{.} nArg{A}++ -+{sp}ArgIleProLeu{G}++ 218614 : AAGA{G}gt.........................cg{at}cgcatccctcta{g}gt. : 364905 99 : >>> Target Intron 9 >>>> {er}Glu{M} >>>> Target Intron 1 : 100 15803 bp {!!}|||{ } 34862 bp ++{ly}Glu{G}++ 364906 : ........................ag{GC}GAA{G}gt.................... : 380714 101 : 0 >>>> {et}ThrArgGluGluIleAsnAlaLeuValGln >>>> Target In : 111 { }:::...||||||:::...:::|||:::::: 16139 ++{lu}SerGluGluGluLeuLysSerLeuLeuLys++ 380715 : ......ag{aa}agtgaagaagaactaaagagcctcttgaaggt.............. : 415608 112 : tron 11 >>>> GluLeuGlyPheTyrArgLysAlaAlaPro{As} >>>> Tar : 121 bp :::||| ||| ...|||||||||{.!} ++GlnLeuGlnPheAlaGlySerAlaAlaPro{Gl}++ 415609 : ............agcagctgcagtttgcaggctcagctgctcca{ca}gt........ : 431779 122 : get Intron 12 >>>> {p}AlaGlnValProProGluTyrValTrp{A} >>> : 131 127522 bp {.}|||:!!:!!||| !:!! :::|||{!} ++{n}AlaLysLeuPro***LysSerLeuTrp{G}+- 431780 : ..................ag{A}GCCAAGCTCCCCTGAAAAAGcttgtgg{g}gg... : 559330 132 : > Target Intron 13 >>>> {la}ProAlaLysProPro{Gl} >>>> Tar : 137 9695 bp {.!}|||||| !!|||{ } ++{ly}ProAlaAlaSerPro{Tr}++ 559331 : .......................ag{GA}CCTGCAGCTTCTCCC{TG}gt........ : 569044 138 : get Intron 14 >>>> {u}GluThrSerAsp : 141 99567 bp {!}||| |||||| ++{p}GluAspSerAsp 569045 : ..................ag{g}gaagacAGTGAC : 668621 vulgar: SPP00000017_1.0 5 141 . NIVO01044519.1:subseq(733635,745166) 3163 668621 + 102 M 8 24 5 0 2 I 0 26577 3 0 2 M 24 72 5 0 2 I 0 8674 3 0 2 M 10 30 S 0 1 5 0 2 I 0 23232 3 0 2 S 1 2 M 4 12 5 0 2 I 0 32069 3 0 2 M 5 15 5 0 2 I 0 17526 3 0 2 M 8 24 5 0 2 I 0 69769 3 0 2 5 0 2 I 0 37319 3 0 2 M 27 81 S 0 1 5 0 2 I 0 146264 3 0 2 S 1 2 M 4 12 S 0 1 5 0 2 I 0 15799 3 0 2 S 1 2 M 1 3 S 0 1 5 0 2 I 0 34858 3 0 2 S 1 2 M 10 30 5 0 2 I 0 16135 3 0 2 M 10 30 S 0 2 5 0 2 I 0 127518 3 0 2 S 1 1 M 9 27 S 0 1 5 0 2 I 0 9691 3 0 2 S 1 2 M 5 15 S 0 2 5 0 2 I 0 99563 3 0 2 S 1 1 M 4 12 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-17 ##type DNA # # # seqname source feature start end score strand frame attributes # NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local gene 3164 668621 102 + . gene_id 8 ; sequence SPP00000017_1.0 ; gene_orientation + NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 3164 3187 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 3164 3187 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 3188 3189 . + . intron_id 1 ; splice_site "GA" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 3188 29768 . + . intron_id 1 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 29767 29768 . + . intron_id 0 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 29769 29840 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 29769 29840 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 29841 29842 . + . intron_id 2 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 29841 38518 . + . intron_id 2 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 38517 38518 . + . intron_id 1 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 38519 38549 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 38519 38549 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 38550 38551 . + . intron_id 3 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 38550 61785 . + . intron_id 3 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 61784 61785 . + . intron_id 2 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 61786 61799 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 61786 61799 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 61800 61801 . + . intron_id 4 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 61800 93872 . + . intron_id 4 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 93871 93872 . + . intron_id 3 ; splice_site "tg" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 93873 93887 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 93873 93887 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 93888 93889 . + . intron_id 5 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 93888 111417 . + . intron_id 5 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 111416 111417 . + . intron_id 4 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 111418 111441 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 111418 111441 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 111442 111443 . + . intron_id 6 ; splice_site "TT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 111442 181214 . + . intron_id 6 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 181213 181214 . + . intron_id 5 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 181215 181216 . + . intron_id 7 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 181215 218537 . + . intron_id 7 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 218536 218537 . + . intron_id 6 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 218538 218619 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 218538 218619 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 218620 218621 . + . intron_id 8 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 218620 364887 . + . intron_id 8 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 364886 364887 . + . intron_id 7 ; splice_site "cg" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 364888 364902 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 364888 364902 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 364903 364904 . + . intron_id 9 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 364903 380705 . + . intron_id 9 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 380704 380705 . + . intron_id 8 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 380706 380711 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 380706 380711 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 380712 380713 . + . intron_id 10 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 380712 415573 . + . intron_id 10 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 415572 415573 . + . intron_id 9 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 415574 415605 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 415574 415605 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 415606 415607 . + . intron_id 11 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 415606 431744 . + . intron_id 11 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 431743 431744 . + . intron_id 10 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 431745 431776 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 431745 431776 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 431777 431778 . + . intron_id 12 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 431777 559298 . + . intron_id 12 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 559297 559298 . + . intron_id 11 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 559299 559327 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 559299 559327 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 559328 559329 . + . intron_id 13 ; splice_site "gg" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 559328 569022 . + . intron_id 13 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 569021 569022 . + . intron_id 12 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 569023 569041 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 569023 569041 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 569042 569043 . + . intron_id 14 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 569042 668608 . + . intron_id 14 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 668607 668608 . + . intron_id 13 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 668609 668621 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 668609 668621 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local similarity 3164 668621 102 + . alignment_id 8 ; Query SPP00000017_1.0 ; Align 3164 6 24 ; Align 29769 14 72 ; Align 38519 38 30 ; Align 61788 49 12 ; Align 93873 53 15 ; Align 111418 58 24 ; Align 218538 66 81 ; Align 364890 94 12 ; Align 380708 99 3 ; Align 415576 101 30 ; Align 431745 111 30 ; Align 559300 122 27 ; Align 569025 132 15 ; Align 668610 138 12 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000017_1.0 # Protein # Selenoprotein M (SelM) # Homo sapiens # Complete Target: NIVO01044519.1:subseq(733635,745166) Ammotragus lervia isolate NAZ scaffold2533_len1482783_cov71, whole genome shotgun sequence Model: protein2genome:local Raw score: 100 Query range: 0 -> 129 Target range: 157646 -> 726708 1 : MetSerLeuLeuLeuProProLeuAlaLeuLeuLeuLeuLeuAlaAlaLeu{Va} > : 18 |||.!!! !! ! !|||||||||! ! !! !|||||||||!.!|||! !{ } MetGlyProCysAlaProProLeuGluGlySerLeuLeuLeuGlyAlaSer{Ar}++ 157647 : ATGGGGCCATGCGCTCCGCCGCTGGAAGGCTCCTTGTTGCTGGGGGCTTCC{AG}gt. : 157702 19 : >>> Target Intron 1 >>>> {l}AlaProAlaThrAlaAlaThrAlaTyrAr : 28 147135 bp {!} ...:::!.! !!|||:!!|| +-{g}ArgAlaArgAlaSerValProAlaHisAr 157703 : ........................ac{g}cgcgcgcgcgcgtcgGTACCGGCTCACCG : 304863 29 : gProAspTrpAsnArgLeuSerGlyLeuThrArgAlaArgValGlu >>>> Targe : 44 | ! |||!.. !! !||||||! ! !||||||||| !||| 2 gGluProTrpArgAlaGlnSerGlyProLeuArgAlaArgProGlu++ 304864 : GGAACCGTGGAGAGCCCAGAGCGGCCCATTACGCGCGAGGCCGGAGgt.......... : 304913 45 : t Intron 2 >>>> ThrCys{G} >>>> Target Intron 3 >>>> {ly : 46 8307 bp !|||{|} 3341 bp {|| ++***Cys{G}++ ++{ly 304914 : ...............agtAATGT{G}gt.........................ag{GA : 336566 47 : }GlyUnkGlnLeuAsn >>>> Target Intron 4 >>>> ArgLeu >>>> : 54 }|||......|||.!. 44123 bp ! ! }GlyAlaSerLeuGln++ ++AlaLys++ 336567 : }GGCGCCAGTTTGCAGgt.........................agGCGAAGgt..... : 380714 55 : Target Intron 5 >>>> LysGluValLysAlaPheValThrGlnAspIle{Pr : 65 14192 bp ||| !:::...|||::: ::: !{ ++LeuGluCysArgThrPheLeuLeuLysThrPro{Ly 380715 : ....................agctggaATGCCGcaccttccttttaaaaacaccA{AA : 394937 66 : } >>>> Target Intron 6 >>>> {o}PheTyrHisAsnLeuValMetLysH : 74 } 49252 bp {!} !! !|||.!.|||||||||! . }++ ++{s}ValGlyHisGluLeuValMetIleG 394938 : }gt.........................ag{G}GTCGGTCATGAGTTGGTAATGATTG : 444216 75 : is{L} >>>> Target Intron 7 >>>> {eu}ProGlyAla{A} >>>> T : 79 !.{:} 41800 bp {!!}|||.!!|||{|} lu{V}++ ++{al}ProSerAla{A}++ 444217 : AA{G}gt.........................ag{TA}CCCAGTGCT{G}gt...... : 486034 80 : arget Intron 8 >>>> {sp}Pro{G} >>>> Target Intron 9 >>>> : 81 13487 bp {||}|||{.} 35894 bp ++{sp}Pro{S}++ 486035 : ...................ag{AC}CCA{A}gt......................... : 499527 82 : {lu}LeuValLeuLeuGlyArgArgTyr{G} >>>> Target Intron 10 > : 90 {..}||| !!||| !||||||!:!:!!{|} 119838 bp ++{er}LeuPheLeuAlaGlyArgLysHis{G}+- 499528 : ag{GT}TTGTTCTTAGCAGGAAGGAAGCAT{G}gg....................... : 535448 91 : >>> {lu}GluLeuGluArgIleProLeuSerGluMetThrArgGluGluIleAsnA : 107 {||}..!:!! !!:!:!: !!|||..!|||..!|||!.!|||:!!! !!!. ++{lu}ArgValThrLysValAlaLeuGluGluGlnThrHisGluLysThrLysL 535449 : ...ag{AG}AGAGTGACAAAGGTGGCTCTTGAGGAGCAGACACATGAGAAGACAAAGC : 655334 108 : laLeuValGlnGlu{Le} >>>> Target Intron 11 >>>> {u}GlyPheT : 115 ! !:!!|||:!!{:!} 51693 bp {!}||| ! euSerLeuGlnLys{Me}++ -+{t}GlyArgP 655335 : TTAGCCTACAGAAG{AT}gt..........................gg{G}GGCAGAT : 707051 116 : yrArgLysAlaAlaProAsp{Al} >>>> Target Intron 12 >>>> {a}G : 123 :!||||||!.!!.!|||:!!{ } 19613 bp {!}| heArgLysValGlyProAsn{Ar}++ -+{g}G 707052 : TCAGAAAAGTGGGGCCAAAC{AG}gt..........................tg{a}c : 726688 124 : lnValProProGluTyrVal : 129 |||||||||||::::::::: lnValProProAspPheLeu 726689 : aggttcccccggactttttg : 726708 vulgar: SPP00000017_1.0 0 129 . NIVO01044519.1:subseq(733635,745166) 157646 726708 + 100 M 17 51 S 0 2 5 0 2 I 0 147131 3 0 2 S 1 1 M 25 75 5 0 2 I 0 28303 3 0 2 M 2 6 S 0 1 5 0 2 I 0 3337 3 0 2 S 1 2 M 5 15 5 0 2 I 0 44119 3 0 2 M 2 6 5 0 2 I 0 14188 3 0 2 M 11 33 S 0 2 5 0 2 I 0 49248 3 0 2 S 1 1 M 9 27 S 0 1 5 0 2 I 0 41796 3 0 2 S 1 2 M 3 9 S 0 1 5 0 2 I 0 13483 3 0 2 S 1 2 M 1 3 S 0 1 5 0 2 I 0 35890 3 0 2 S 1 2 M 8 24 S 0 1 5 0 2 I 0 119834 3 0 2 S 1 2 M 21 63 S 0 2 5 0 2 I 0 51689 3 0 2 S 1 1 M 9 27 S 0 2 5 0 2 I 0 19609 3 0 2 S 1 1 M 7 21 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-17 ##type DNA # # # seqname source feature start end score strand frame attributes # NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local gene 157647 726708 100 + . gene_id 9 ; sequence SPP00000017_1.0 ; gene_orientation + NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 157647 157699 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 157647 157699 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 157700 157701 . + . intron_id 1 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 157700 304834 . + . intron_id 1 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 304833 304834 . + . intron_id 0 ; splice_site "ac" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 304835 304910 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 304835 304910 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 304911 304912 . + . intron_id 2 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 304911 333217 . + . intron_id 2 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 333216 333217 . + . intron_id 1 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 333218 333224 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 333218 333224 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 333225 333226 . + . intron_id 3 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 333225 336565 . + . intron_id 3 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 336564 336565 . + . intron_id 2 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 336566 336582 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 336566 336582 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 336583 336584 . + . intron_id 4 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 336583 380705 . + . intron_id 4 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 380704 380705 . + . intron_id 3 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 380706 380711 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 380706 380711 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 380712 380713 . + . intron_id 5 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 380712 394903 . + . intron_id 5 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 394902 394903 . + . intron_id 4 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 394904 394938 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 394904 394938 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 394939 394940 . + . intron_id 6 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 394939 444190 . + . intron_id 6 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 444189 444190 . + . intron_id 5 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 444191 444219 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 444191 444219 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 444220 444221 . + . intron_id 7 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 444220 486019 . + . intron_id 7 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 486018 486019 . + . intron_id 6 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 486020 486031 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 486020 486031 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 486032 486033 . + . intron_id 8 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 486032 499518 . + . intron_id 8 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 499517 499518 . + . intron_id 7 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 499519 499524 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 499519 499524 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 499525 499526 . + . intron_id 9 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 499525 535418 . + . intron_id 9 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 535417 535418 . + . intron_id 8 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 535419 535445 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 535419 535445 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 535446 535447 . + . intron_id 10 ; splice_site "GG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 535446 655283 . + . intron_id 10 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 655282 655283 . + . intron_id 9 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 655284 655350 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 655284 655350 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 655351 655352 . + . intron_id 11 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 655351 707043 . + . intron_id 11 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 707042 707043 . + . intron_id 10 ; splice_site "GG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 707044 707073 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 707044 707073 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 707074 707075 . + . intron_id 12 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 707074 726686 . + . intron_id 12 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 726685 726686 . + . intron_id 11 ; splice_site "tg" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 726687 726708 . + . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 726687 726708 . + . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local similarity 157647 726708 100 + . alignment_id 9 ; Query SPP00000017_1.0 ; Align 157647 1 51 ; Align 304836 19 75 ; Align 333218 44 6 ; Align 336568 47 15 ; Align 380706 52 6 ; Align 394904 54 33 ; Align 444192 66 27 ; Align 486022 76 9 ; Align 499521 80 3 ; Align 535421 82 24 ; Align 655286 91 63 ; Align 707045 113 27 ; Align 726688 123 21 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000017_1.0 # Protein # Selenoprotein M (SelM) # Homo sapiens # Complete Target: NIVO01044519.1:subseq(733635,745166) Ammotragus lervia isolate NAZ scaffold2533_len1482783_cov71, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 530 Query range: 0 -> 145 Target range: 125261 -> 49999 1 : MetSerLeuLeuLeuProPro{L} >>>> Target Intron 1 >>>> {eu}A : 9 ||||||||| !|||||||||{ } 68287 bp { !}: MetSerLeuGlyLeuProPro{G}++ ++{ly}S 125261 : ATGTCCTTGGGACTACCTCCA{G}gt.........................ag{gc}a : 56950 10 : laLeuLeuLeuLeuLeuAlaAlaLeu{Va} >>>> Target Intron 2 >>>> : 18 :!||| !||||||! !|||||||||{ } 4428 bp erLeuAlaLeuLeuSerAlaAlaLeu{Ly}++ - 56949 : GCCTGGCACTGCTGTCAGCTGCTCTG{AA}gt.........................g : 52495 19 : {l}AlaProAlaThrAlaAlaThrAlaTyrArgProAspTrpAsnArgLeuSerGly : 36 {!}||| !|||.!!|||.!!|||.!!!:!|||||||||||||||||||||..!||| -{s}AlaValAlaAlaAlaThrThrThrPheArgProAspTrpAsnArgLeuGlnGly 52494 : c{G}GCAGTCGCGGCCGCCACCACCACCTTCCGGCCCGACTGGAACCGTCTACAAGGC : 52441 37 : LeuThrArgAlaArgValGlu >>>> Target Intron 3 >>>> ThrCysGl : 46 |||.!!||||||||||||||| 1479 bp |||||||| LeuAlaArgAlaArgValGlu++ ++ThrCysGl 52440 : CTGGCCCGAGCCCGGGTAGAGgt.........................agACATGTGG : 50932 47 : yGlyUnkGlnLeuAsnArgLeuLysGlu >>>> Target Intron 4 >>>> V : 56 |||| ||||||||||||||||||||| 197 bp | yGly***GlnLeuAsnArgLeuLysGlu++ ++V 50931 : AGGATGACAGCTTAATCGCCTCAAGGAGgt.........................agg : 50705 57 : alLysAlaPheValThrGlnAspIleProPhe{Ty} >>>> Target Intron 5 : 67 |||||||||||||||||||||||||||||...{||} 359 bp alLysAlaPheValThrGlnAspIleProLeu{Ty}++ 50704 : TGAAGGCCTTCGTCACCCAGGacatcccactc{ta}gt.................... : 50668 68 : >>>> {r}HisAsnLeuValMetLysHisLeuProGlyAlaAspProGluLeuVal : 83 {|}|||||||||||||||||||||||||||||||||||||||||||||||| ++{r}HisAsnLeuValMetLysHisLeuProGlyAlaAspProGluLeuVal 50667 : .....ag{C}CACAACCTGGTGATGAAACACCTTCCGGGGGCCGACCCAGAGCTCGTG : 50265 84 : LeuLeuGlyArgArgTyrGluGluLeuGlu >>>> Target Intron 6 >>>> : 94 |||||||||!.!|||!:!|||||||||||| 77 bp LeuLeuGlyHisArgPheGluGluLeuGlu++ + 50264 : TTGCTGGGCCATCGCTTTGAGGAACTGGAGgt.........................a : 50157 95 : ArgIleProLeuSerGluMetThrArgGluGluIleAsnAlaLeuValGlnGluLeu : 112 |||||||||||||||!!:||||||||||||||||||||||||||||||||||||||| +ArgIleProLeuSerAspMetThrArgGluGluIleAsnAlaLeuValGlnGluLeu 50156 : gCGAATTCCACTCAGCGACATGACCCGCGAGGAGATCAACGCGCTGGTGCAGGAGCTC : 50101 113 : GlyPheTyrArgLysAlaAlaProAspAlaGlnValProProGluTyrValTrpAlaP : 132 ||||||||||||||||||:!!||||||! !! |||||||||||||||:!! !!|||| GlyPheTyrArgLysAlaSerProAspAspProValProProGluTyrLeuArgAlaP 50100 : GGCTTCTACCGCAAGGCGTCTCCCGACGACCCTGTGCCCCCGGAGTACCTTCGGGCTC : 50041 133 : roAlaLysProProGluGluThrSerAspHisAlaAspLeu : 145 |||||!:!||| !!! !! ||| !!||||||||||||||| roAlaArgProAlaGlyGlyThrProAspHisAlaAspLeu 50040 : CCGCTAGGCCCGCCGGAGGCACTCCTGACCACGCAGACCTG : 50000 vulgar: SPP00000017_1.0 0 145 . NIVO01044519.1:subseq(733635,745166) 125261 49999 - 530 M 7 21 S 0 1 5 0 2 I 0 68283 3 0 2 S 1 2 M 9 27 S 0 2 5 0 2 I 0 4424 3 0 2 S 1 1 M 25 75 5 0 2 I 0 1475 3 0 2 M 12 36 5 0 2 I 0 193 3 0 2 M 11 33 S 0 2 5 0 2 I 0 355 3 0 2 S 1 1 M 26 78 5 0 2 I 0 73 3 0 2 M 52 156 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-17 ##type DNA # # # seqname source feature start end score strand frame attributes # NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local gene 50000 125261 530 - . gene_id 1 ; sequence SPP00000017_1.0 ; gene_orientation + NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 125240 125261 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 125240 125261 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 125238 125239 . - . intron_id 1 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 56953 125239 . - . intron_id 1 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 56953 56954 . - . intron_id 0 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 56922 56952 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 56922 56952 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 56920 56921 . - . intron_id 2 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 52494 56921 . - . intron_id 2 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 52494 52495 . - . intron_id 1 ; splice_site "GC" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 52418 52493 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 52418 52493 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 52416 52417 . - . intron_id 3 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 50939 52417 . - . intron_id 3 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 50939 50940 . - . intron_id 2 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 50903 50938 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 50903 50938 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 50901 50902 . - . intron_id 4 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 50706 50902 . - . intron_id 4 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 50706 50707 . - . intron_id 3 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 50671 50705 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 50671 50705 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 50669 50670 . - . intron_id 5 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 50312 50670 . - . intron_id 5 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 50312 50313 . - . intron_id 4 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 50233 50311 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 50233 50311 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 50231 50232 . - . intron_id 6 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 50156 50232 . - . intron_id 6 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 50156 50157 . - . intron_id 5 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 50000 50155 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 50000 50155 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local similarity 50000 125261 530 - . alignment_id 1 ; Query SPP00000017_1.0 ; Align 125262 1 21 ; Align 56951 9 27 ; Align 52493 19 75 ; Align 50939 44 36 ; Align 50706 56 33 ; Align 50311 68 78 ; Align 50156 94 156 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000017_1.0 # Protein # Selenoprotein M (SelM) # Homo sapiens # Complete Target: NIVO01044519.1:subseq(733635,745166) Ammotragus lervia isolate NAZ scaffold2533_len1482783_cov71, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 135 Query range: 1 -> 142 Target range: 702033 -> 16011 2 : SerLeuLeuLeuProProLeuAlaLeuLeuLeuLeuLeuAlaAlaLeuValAlaProA : 21 |||! !||| !||||||:!!||| !:!!!!!||||||||| !||| ! ! !! SerTyrLeuGlyProProIleAlaAlaValPheLeuLeuAlaIleLeuCysLysArgV 702033 : AGCTACCTTGGGCCTCCAATTGCAGCTGTCTTCCTGCTTGCCATCCTCTGTAAAAGAG : 701976 22 : laThrAlaAla >>>> Target Intron 1 >>>> >>>> Target Intr : 25 .!!.!! ! ! 85221 bp 92397 b alAsnGluGln++ ++++ 701975 : TCAACGAACAGgt.........................aggt................ : 616741 26 : on 2 >>>> ThrAlaTyrArgProAspTrpAsnArgLeuSerGlyLeuThrArgAl : 40 p ..! !! ||| !!||||||::!|||||| !!! !:!!||||||:: ++ValProValArgThrAspTrpSerArgLeuProAspIleThrArgSe 616740 : .........agGTGCCAGTGAGGACTGACTGGTCTAGGCTCCCAGACATAACTCGTAG : 524301 41 : aArg >>>> Target Intron 3 >>>> {Va} >>>> Target Intron : 42 !||| 34287 bp { } 13658 bp rArg++ ++{Ar}++ 524300 : CCGAgt.........................ag{AG}gt................... : 490004 43 : 4 >>>> {l}GluThrCysGlyGly{Un} >>>> Target Intron 5 >>>> : 48 {!}||||||||| !!|||{ } 29902 bp ++{g}GluThrCysTrpGly{Gl}++ + 490003 : ......ag{G}GAAACCTGCTGGGGC{GG}gt.........................a : 446430 49 : {k}GlnLeuAsnArgLeuLysGlu >>>> Target Intron 6 >>>> ValL : 57 { }::! !::!|||! !!:!:!! 25865 bp |||! +{y}ArgThrSerArgCysArgGln++ ++ValT 446429 : g{G}AGGACCTCCAGATGCAGGCAAgt.........................agGTAA : 420538 58 : ysAlaPheValThr{G} >>>> Target Intron 7 >>>> {ln}AspIlePr : 65 :!! ||||||{:} 34532 bp {!!}|||:!:|| hrSerArgValThr{G}++ ++{lu}AspLeuPr 420537 : CTTCCAGGGTCACA{G}gt.........................ag{AG}GACCTGCC : 385982 66 : oPheTyrHis{A} >>>> Target Intron 8 >>>> {sn}LeuVal{M} > : 72 |||| !! {.} 108336 bp {.!}:!!!.!{ } oPheProPro{G}++ ++{ly}IleAla{G}++ 385981 : CTTCCCCCCA{G}gt.........................ag{GT}ATAGCT{G}gt. : 277622 73 : >>> Target Intron 9 >>>> {et}LysHisLeuProGlyAlaAspProGluL : 82 73652 bp { } !!. !||||||||| !!||||||! ++{ly}LeuGlnAlaProGlyAlaHisProGluT 277621 : ........................ag{GT}CTCCAGGCACCAGGAGCCCATCCCGAAT : 203943 83 : eu >>>> Target Intron 10 >>>> ValLeuLeuGlyArg >>>> Targ : 88 ! 16989 bp :::|||||| rp+- ++IleLeuLeuPheLeu-+ 203942 : GGgg..........................agattttactttttctgat......... : 186934 89 : et Intron 11 >>>> ArgTyrGluGluLeuGluArg >>>> Target Intr : 95 5842 bp !:! !.!.||| !|||||| 12503 b ++GlnLeuAsnGluAlaGluArg++ 186933 : .................agCAACTTAATGAAGCAGAAAGGgt................ : 181071 96 : on 12 >>>> IlePro{L} >>>> Target Intron 13 >>>> {eu}Ser : 98 p :!!|||{ } 2489 bp { !}..! ++LeuPro{G}+- ++{lu}Asp 181070 : ..........agcTTCCA{G}gc..........................ag{AG}GAC : 166072 99 : GluMetThrArgGluGluIleAsnAlaLeuValGlnGluLeuGlyPheTyrArgLys{ : 118 !!: ! !||||||!!:|||:!! !|||:!! !! |||..!||| !.!! !{ AspProLysArgGluAspIleHisArgLeuIleValAlaLeuSerPheGlyAsnThr{ 166071 : GATCCCAAAAGAGAAGACATCCACCGTCTCATCGTAGCTCTTTCCTTCGGAAACACA{ : 166012 119 : A} >>>> Target Intron 14 >>>> {la}AlaPro{A} >>>> Target : 121 !} 56980 bp {.!}!.!|||{|} 39 G}+- ++{ly}GlyPro{A}-+ 166011 : G}ga..........................ag{GC}GGCCCA{G}ct........... : 109020 122 : Intron 15 >>>> {sp}AlaGlnValProPro{Gl} >>>> Target Intr : 127 844 bp {||} !||| ! !|||{..} 29141 b ++{sp}MetGlnCysAspPro{Ar}++ 109019 : ...............ag{AC}ATGCAGTGTGACCCG{AG}gt................ : 69157 128 : on 16 >>>> {u}TyrValTrpAlaProAlaLys >>>> Target Intron 1 : 135 p {!} ! !|||:!! !!!.!!:! 17899 bp ++{g}AlaProTrpSerAlaValArg++ 69156 : ..........ag{G}GCCCCTTGGTCTGCTGTAAGGgt.................... : 39994 136 : 7 >>>> ProProGlu >>>> Target Intron 18 >>>> GluThrSerAs : 141 !!|||||| 6062 bp !|||||||| ++AlaProGlu++ ++TrpThrSerAs 39993 : ......agGCTCCCGAGgt..........................agTGGACATCAGA : 16017 142 : pHis : 142 |||| pHis 16016 : TCAT : 16012 vulgar: SPP00000017_1.0 1 142 . NIVO01044519.1:subseq(733635,745166) 702033 16011 - 135 M 23 69 5 0 2 I 0 85217 3 0 2 5 0 2 I 0 92393 3 0 2 M 17 51 5 0 2 I 0 34283 3 0 2 S 0 2 5 0 2 I 0 13654 3 0 2 S 1 1 M 5 15 S 0 2 5 0 2 I 0 29898 3 0 2 S 1 1 M 7 21 5 0 2 I 0 25861 3 0 2 M 6 18 S 0 1 5 0 2 I 0 34528 3 0 2 S 1 2 M 6 18 S 0 1 5 0 2 I 0 108332 3 0 2 S 1 2 M 2 6 S 0 1 5 0 2 I 0 73648 3 0 2 S 1 2 M 10 30 5 0 2 I 0 16985 3 0 2 M 5 15 5 0 2 I 0 5838 3 0 2 M 7 21 5 0 2 I 0 12499 3 0 2 M 2 6 S 0 1 5 0 2 I 0 2485 3 0 2 S 1 2 M 20 60 S 0 1 5 0 2 I 0 56976 3 0 2 S 1 2 M 2 6 S 0 1 5 0 2 I 0 39840 3 0 2 S 1 2 M 5 15 S 0 2 5 0 2 I 0 29137 3 0 2 S 1 1 M 7 21 5 0 2 I 0 17895 3 0 2 M 3 9 5 0 2 I 0 6058 3 0 2 M 5 15 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-17 ##type DNA # # # seqname source feature start end score strand frame attributes # NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local gene 16012 702033 135 - . gene_id 2 ; sequence SPP00000017_1.0 ; gene_orientation + NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 701965 702033 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 701965 702033 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 701963 701964 . - . intron_id 1 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 616744 701964 . - . intron_id 1 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 616744 616745 . - . intron_id 0 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 616742 616743 . - . intron_id 2 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 524347 616743 . - . intron_id 2 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 524347 524348 . - . intron_id 1 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 524296 524346 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 524296 524346 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 524294 524295 . - . intron_id 3 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 490009 524295 . - . intron_id 3 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 490009 490010 . - . intron_id 2 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 490007 490008 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 490007 490008 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 490005 490006 . - . intron_id 4 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 476349 490006 . - . intron_id 4 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 476349 476350 . - . intron_id 3 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 476331 476348 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 476331 476348 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 476329 476330 . - . intron_id 5 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 446429 476330 . - . intron_id 5 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 446429 446430 . - . intron_id 4 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 446407 446428 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 446407 446428 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 446405 446406 . - . intron_id 6 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 420542 446406 . - . intron_id 6 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 420542 420543 . - . intron_id 5 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 420523 420541 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 420523 420541 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 420521 420522 . - . intron_id 7 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 385991 420522 . - . intron_id 7 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 385991 385992 . - . intron_id 6 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 385970 385990 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 385970 385990 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 385968 385969 . - . intron_id 8 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 277634 385969 . - . intron_id 8 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 277634 277635 . - . intron_id 7 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 277625 277633 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 277625 277633 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 277623 277624 . - . intron_id 9 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 203973 277624 . - . intron_id 9 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 203973 203974 . - . intron_id 8 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 203941 203972 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 203941 203972 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 203939 203940 . - . intron_id 10 ; splice_site "GG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 186952 203940 . - . intron_id 10 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 186952 186953 . - . intron_id 9 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 186937 186951 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 186937 186951 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 186935 186936 . - . intron_id 11 ; splice_site "aT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 181095 186936 . - . intron_id 11 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 181095 181096 . - . intron_id 10 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 181074 181094 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 181074 181094 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 181072 181073 . - . intron_id 12 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 168571 181073 . - . intron_id 12 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 168571 168572 . - . intron_id 11 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 168564 168570 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 168564 168570 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 168562 168563 . - . intron_id 13 ; splice_site "GC" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 166075 168563 . - . intron_id 13 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 166075 166076 . - . intron_id 12 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 166012 166074 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 166012 166074 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 166010 166011 . - . intron_id 14 ; splice_site "GA" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 109032 166011 . - . intron_id 14 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 109032 109033 . - . intron_id 13 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 109023 109031 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 109023 109031 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 109021 109022 . - . intron_id 15 ; splice_site "CT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 69179 109022 . - . intron_id 15 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 69179 69180 . - . intron_id 14 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 69160 69178 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 69160 69178 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 69158 69159 . - . intron_id 16 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 40019 69159 . - . intron_id 16 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 40019 40020 . - . intron_id 15 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 39997 40018 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 39997 40018 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 39995 39996 . - . intron_id 17 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 22098 39996 . - . intron_id 17 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 22098 22099 . - . intron_id 16 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 22089 22097 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 22089 22097 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 22087 22088 . - . intron_id 18 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 16027 22088 . - . intron_id 18 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 16027 16028 . - . intron_id 17 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 16012 16026 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 16012 16026 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local similarity 16012 702033 135 - . alignment_id 2 ; Query SPP00000017_1.0 ; Align 702034 2 69 ; Align 524347 25 51 ; Align 476348 43 15 ; Align 446428 49 21 ; Align 420542 56 18 ; Align 385989 63 18 ; Align 277632 70 6 ; Align 203971 73 30 ; Align 186952 83 15 ; Align 181095 88 21 ; Align 168571 95 6 ; Align 166073 98 60 ; Align 109030 119 6 ; Align 69177 122 15 ; Align 40018 128 21 ; Align 22098 135 9 ; Align 16027 138 15 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000017_1.0 # Protein # Selenoprotein M (SelM) # Homo sapiens # Complete Target: NIVO01044519.1:subseq(733635,745166) Ammotragus lervia isolate NAZ scaffold2533_len1482783_cov71, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 124 Query range: 9 -> 145 Target range: 743224 -> 6846 10 : LeuLeuLeuLeuLeuAlaAlaLeuValAlaProAlaThrAlaAlaThrAlaTyrArgP : 29 ||||||||| ! !!.! !||||||||| !! !|||!.!||||||||| ! !! LeuLeuLeuGluThrGlyHisLeuValAlaThrAsnThrValAlaThrAlaGlnGlyA 743224 : CTTCTGCTGGAAACAGGACATTTGGTAGCTACCAACACTGTAGCCACTGCTCAGGGTG : 743167 30 : ro{A} >>>> Target Intron 1 >>>> {sp}TrpAsnArgLeuSerGlyLe : 37 !!{!} 63199 bp {!:}|||... ||||| la{G}++ ++{lu}TrpLysAspAlaCysGlyLe 743166 : CA{G}gt.........................ag{aa}tggaaagacgcctgtggcct : 679944 38 : uThrArg{Al} >>>> Target Intron 2 >>>> {a}ArgValGluThrCys : 45 | |||{..} 46666 bp {!}!:!|||!!:!:! uHisArg{Cy}++ ++{s}LysValAspSerLeu 679943 : acatagg{tg}gt.........................ag{T}AAAGTCGACAGCCTA : 633254 46 : GlyGlyUnkGln >>>> Target Intron 3 >>>> >>>> Target Int : 50 |||||| 16496 bp 5921 b GlyGlyGluAla++ ++++ 633253 : GGTGGGGAGGCCgt.........................aggt............... : 616741 51 : ron 4 >>>> LeuAsnArg >>>> Target Intron 5 >>>> LeuLysGl : 55 p |||!:!!:! 181656 bp :::||||| ++LeuSerGln++ ++ValLysGl 616740 : ..........agCTGAGTCAGgt.........................aggttaaaga : 429151 56 : uValLys{A} >>>> Target Intron 6 >>>> {la}Phe{Va} >>>> T : 60 | :::{!} 23265 bp { !}|||{ } uLysArg{A}-+ ++{sp}Phe{Se}++ 429150 : aaaaaga{g}tt.........................ag{AT}TTC{AG}gt...... : 405867 61 : arget Intron 7 >>>> {l}ThrGln{A} >>>> Target Intron 8 >> : 63 14498 bp {!}:!!|||{|} 46154 bp ++{r}SerGln{A}++ 405866 : ...................ag{C}TCGCAG{G}gt....................... : 391361 64 : >> {sp}IleProPheTyrHisAsnLeuValMetLysHis{Le} >>>> Target : 75 {||}:!! !!.!.||||||.!.||| !... |||{ } 166 +-{sp}LeuSerIleTyrHisGluLeuHisGlnValHis{Ar}++ 391360 : ..ac{AC}TTATCAATATATCATGAGCTACATCAAGTTCAC{AG}gt........... : 345170 76 : Intron 9 >>>> {u}ProGlyAlaAspProGluLeuValLeuLeuGlyArgArg : 88 978 bp {!} !|||:!!.!.||| !|||:!!! !||||||! !..! ++{g}LysGlySerGlnProLeuLeuLeuGlnLeuGlyLeuGlu 345169 : ..............ag{A}AAAGGTTCCCAGCCACTGCTTTTGCAGTTGGGGCTTGAA : 178157 89 : TyrGluGlu{Le} >>>> Target Intron 10 >>>> {u}GluArgIlePro : 96 ||| |||{||} 2021 bp {|} !:!||| !! TyrProGlu{Le}++ ++{u}CysLysIleAla 178156 : TATCCTGAG{CT}gt..........................ag{G}TGTAAAATAGCA : 176112 97 : LeuSerGlu >>>> Target Intron 11 >>>> MetThrArgGluGluIleA : 106 ! !.!!:!! 38432 bp ||| ::::::... !. TrpGlyGln++ ++MetLysLysGlnSerThrG 176111 : TGGGGGCAGgt..........................agatgaagaaacaaagcaCAG : 137650 107 : snAla >>>> Target Intron 12 >>>> LeuValGlnGluLeuGlyPheTy : 115 !. ! 61786 bp ::: ...||||||||| luArg++ ++AlaLeuProSerLeuGlyPheSe 137649 : AGAGGgt..........................aggctctgccgtccctgggattttc : 75837 116 : r{Ar} >>>> Target Intron 13 >>>> {g}LysAlaAlaProAspAlaGl : 123 {||} 10960 bp {|} ! !!||| !!!!:||||| r{Ar}++ ++{g}AspProAlaThrGluAlaGl 75836 : c{ag}gt..........................ag{G}GACCCGGCCACAGAGGCTCA : 64853 124 : nValProPro{Gl} >>>> Target Intron 14 >>>> {u}TyrValTrp : 131 | ! !!|||{:!} 4546 bp {!} !||| nArgAlaPro{Gl}++ ++{n}ThrHisTrp++ 64852 : GCGGGCCCCG{CA}gt..........................ag{g}actcaCTGGgt : 60283 132 : >>>> Target Intron 15 >>>> AlaProAlaLysProProGluGluThrSer : 140 53392 bp ||| ! !||| !! !!..!... !!||| ++AlaValArgLysAlaThrArgSerProSer 60282 : ..........................aggcAGTGAGGAAGGCGACGCGGAGTCCCTCA : 6864 141 : AspHisAlaAspLeu : 145 :!!|||:!!:!!:!! AsnHisSerAsnIle 6863 : AACCATTCAAACATC : 6847 vulgar: SPP00000017_1.0 9 145 . NIVO01044519.1:subseq(733635,745166) 743224 6846 - 124 M 20 60 S 0 1 5 0 2 I 0 63195 3 0 2 S 1 2 M 9 27 S 0 2 5 0 2 I 0 46662 3 0 2 S 1 1 M 9 27 5 0 2 I 0 16492 3 0 2 5 0 2 I 0 5917 3 0 2 M 3 9 5 0 2 I 0 181652 3 0 2 M 5 15 S 0 1 5 0 2 I 0 23261 3 0 2 S 1 2 M 1 3 S 0 2 5 0 2 I 0 14494 3 0 2 S 1 1 M 2 6 S 0 1 5 0 2 I 0 46150 3 0 2 S 1 2 M 11 33 S 0 2 5 0 2 I 0 166974 3 0 2 S 1 1 M 16 48 S 0 2 5 0 2 I 0 2017 3 0 2 S 1 1 M 7 21 5 0 2 I 0 38428 3 0 2 M 8 24 5 0 2 I 0 61782 3 0 2 M 8 24 S 0 2 5 0 2 I 0 10956 3 0 2 S 1 1 M 10 30 S 0 2 5 0 2 I 0 4542 3 0 2 S 1 1 M 3 9 5 0 2 I 0 53388 3 0 2 M 15 45 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-17 ##type DNA # # # seqname source feature start end score strand frame attributes # NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local gene 6847 743224 124 - . gene_id 3 ; sequence SPP00000017_1.0 ; gene_orientation + NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 743164 743224 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 743164 743224 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 743162 743163 . - . intron_id 1 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 679965 743163 . - . intron_id 1 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 679965 679966 . - . intron_id 0 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 679934 679964 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 679934 679964 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 679932 679933 . - . intron_id 2 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 633268 679933 . - . intron_id 2 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 633268 633269 . - . intron_id 1 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 633240 633267 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 633240 633267 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 633238 633239 . - . intron_id 3 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 616744 633239 . - . intron_id 3 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 616744 616745 . - . intron_id 2 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 616742 616743 . - . intron_id 4 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 610823 616743 . - . intron_id 4 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 610823 610824 . - . intron_id 3 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 610814 610822 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 610814 610822 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 610812 610813 . - . intron_id 5 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 429158 610813 . - . intron_id 5 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 429158 429159 . - . intron_id 4 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 429142 429157 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 429142 429157 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 429140 429141 . - . intron_id 6 ; splice_site "tt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 405877 429141 . - . intron_id 6 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 405877 405878 . - . intron_id 5 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 405870 405876 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 405870 405876 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 405868 405869 . - . intron_id 7 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 391372 405869 . - . intron_id 7 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 391372 391373 . - . intron_id 6 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 391364 391371 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 391364 391371 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 391362 391363 . - . intron_id 8 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 345210 391363 . - . intron_id 8 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 345210 345211 . - . intron_id 7 ; splice_site "AC" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 345173 345209 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 345173 345209 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 345171 345172 . - . intron_id 9 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 178195 345172 . - . intron_id 9 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 178195 178196 . - . intron_id 8 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 178144 178194 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 178144 178194 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 178142 178143 . - . intron_id 10 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 176123 178143 . - . intron_id 10 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 176123 176124 . - . intron_id 9 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 176101 176122 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 176101 176122 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 176099 176100 . - . intron_id 11 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 137669 176100 . - . intron_id 11 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 137669 137670 . - . intron_id 10 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 137645 137668 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 137645 137668 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 137643 137644 . - . intron_id 12 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 75859 137644 . - . intron_id 12 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 75859 75860 . - . intron_id 11 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 75833 75858 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 75833 75858 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 75831 75832 . - . intron_id 13 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 64873 75832 . - . intron_id 13 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 64873 64874 . - . intron_id 12 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 64840 64872 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 64840 64872 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 64838 64839 . - . intron_id 14 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 60294 64839 . - . intron_id 14 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 60294 60295 . - . intron_id 13 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 60284 60293 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 60284 60293 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 60282 60283 . - . intron_id 15 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 6892 60283 . - . intron_id 15 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 6892 6893 . - . intron_id 14 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 6847 6891 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 6847 6891 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local similarity 6847 743224 124 - . alignment_id 3 ; Query SPP00000017_1.0 ; Align 743225 10 60 ; Align 679963 31 27 ; Align 633267 41 27 ; Align 610823 50 9 ; Align 429158 53 15 ; Align 405875 59 3 ; Align 391371 61 6 ; Align 345208 64 33 ; Align 178194 76 48 ; Align 176122 93 21 ; Align 137669 100 24 ; Align 75859 108 24 ; Align 64872 117 30 ; Align 60293 128 9 ; Align 6892 131 45 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000017_1.0 # Protein # Selenoprotein M (SelM) # Homo sapiens # Complete Target: NIVO01044519.1:subseq(733635,745166) Ammotragus lervia isolate NAZ scaffold2533_len1482783_cov71, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 111 Query range: 2 -> 143 Target range: 649886 -> 5923 3 : LeuLeuLeuProProLeuAlaLeuLeuLeuLeuLeuAlaAlaLeuValAlaProAlaT : 22 ||||||||| !|||!!!|||! !|||||||||!!! !:!!|||:!!::! !! ! LeuLeuLeuCysProPheAlaSerLeuLeuLeuPheLeuSerLeuMetSerSerHisL 649886 : CTTCTCCTGTGTCCATTCGCTTCACTCCTGCTTTTCCTCTCACTCATGAGTTCCCACT : 649829 23 : hr{A} >>>> Target Intron 1 >>>> {la}AlaThrAlaTyrArgProAs : 30 !{!} 86464 bp {.!}!.! !.!! ! |||||| eu{G}++ ++{ly}GlyGlyThrGluArgProAr 649828 : TA{G}gt.........................ag{GA}GGAGGGACTGAGAGGCCCCG : 563341 31 : pTrpAsn{Ar} >>>> Target Intron 2 >>>> {g}LeuSerGlyLeuThr : 38 !||||||{||} 99094 bp {|} !!!!.!! !||| gTrpAsn{Ar}++ ++{g}AlaArgSerLysThr 563340 : CTGGAAC{AG}gt.........................ag{A}GCTAGAAGCAAGACT : 464223 39 : ArgAlaArgVal{Gl} >>>> Target Intron 3 >>>> {u}ThrCys{G} : 46 |||.!!||||||{..} 9694 bp {!} !|||{|} ArgThrArgVal{Ar}++ ++{g}LeuCys{G}+ 464222 : AGGACTAGGGTG{AG}gt.........................ag{G}CTGTGT{G}g : 454504 47 : >>>> Target Intron 4 >>>> {ly}GlyUnkGlnLeuAsn{Ar} >>>> : 52 33963 bp {||}..! ||| !:!!{||} + ++{ly}AsnPheGlnGlyHis{Ar}++ 454503 : t.........................ag{GT}AACTTCCAGGGTCAC{AG}gt..... : 420520 53 : Target Intron 5 >>>> {g}LeuLysGluValLysAlaPheValThrGlnAsp : 63 9995 bp {|}||| |||!:!.!!|||:!!! !!:!:!! ++{g}LeuProThrValArgThrPheIleIleArgAsn 420519 : ....................ag{G}CTGCCCACCGTGAGGACATTCATTATTCGAAAT : 410496 64 : IlePro{P} >>>> Target Intron 6 >>>> {he}TyrHisAsnLeuValM : 72 ! ! !{!} 39837 bp {:!} ! ! :!!|||:!!: SerLeu{T}++ ++{yr}GlyLysHisLeuLeuL 410495 : AGCTTA{T}gt.........................ag{AT}GGCAAACACCTGCTTC : 370632 73 : etLysHisLeuPro >>>> Target Intron 7 >>>> GlyAlaAspProGlu : 81 !: !!||||||||| 35436 bp |||... !:!! eu***HisLeuPro+- ++GlyThrProAsnLys 370631 : TCTAACATCTCCCTga.........................agggaactcccAATAAA : 335169 82 : LeuValLeuLeuGlyArgArgTyrGluGlu >>>> Target Intron 8 >>>> : 92 :!!:!!:!! !||| !!||| ! :!!:!! 47164 bp ValLeuIleLysGlyGlyArgGlnLysGln++ + 335168 : GTCTTAATAAAGGGGGGGAGGCAAAAACAAgt.........................a : 287974 93 : LeuGluArgIleProLeuSerGluMetThrArg >>>> Target Intron 9 > : 103 |||::: ...||| |||||| ::: 20160 bp -LeuGlnSerPheProAlaSerGluSerPheGln-+ 287973 : ccttcaatctttcccagcatcagagtcttttcaaat...................... : 287937 104 : >>> GluGluIleAsnAlaLeuValGlnGluLeu{G} >>>> Target Intron : 113 !|||:!!:::|||||| !::!:!!|||{ } 97338 bp ++IleGluValSerAlaLeuLysArgGlnLeu{T}++ 287936 : ...agATAGAGGTCTCGGCTCTGAAGAGACAGCTT{A}gt.................. : 267746 114 : 10 >>>> {ly}PheTyrArg{L} >>>> Target Intron 11 >>>> {y : 117 { !}|||!:!|||{ } 38202 bp {! ++{hr}PhePheArg{A}++ ++{s 267745 : ........ag{CA}TTCTTTAGA{G}gt..........................ag{a : 132196 118 : s}AlaAlaProAspAlaGln >>>> Target Intron 12 >>>> ValProPr : 126 } ...|||!!:|||||| 18897 bp :!!! ! ! p}GluValProGluAlaGln+- ++LeuArgAl 132195 : t}gaggtaccTGAAGCTCAGgg..........................agCTCCGGGC : 113273 127 : oGluTyrValTrpAlaProAla{Ly} >>>> Target Intron 13 >>>> {s : 134 !||| !! !|||!.!||||||{!:} 107296 bp {! aGluGlyGluTrpGlyProAla{Ar}++ ++{g 113272 : AGAGGGTGAGTGGGGACCTGCA{AG}gt..........................ag{G : 5951 135 : }ProProGluGluThrSerAspHisAla : 143 }||||||..! ! !!!!..!|||||| }ProProSerProLeuThrSerHisAla 5950 : }CCCCCGTCACCACTTACTTCTCATGCT : 5924 vulgar: SPP00000017_1.0 2 143 . NIVO01044519.1:subseq(733635,745166) 649886 5923 - 111 M 20 60 S 0 1 5 0 2 I 0 86460 3 0 2 S 1 2 M 9 27 S 0 2 5 0 2 I 0 99090 3 0 2 S 1 1 M 9 27 S 0 2 5 0 2 I 0 9690 3 0 2 S 1 1 M 2 6 S 0 1 5 0 2 I 0 33959 3 0 2 S 1 2 M 5 15 S 0 2 5 0 2 I 0 9991 3 0 2 S 1 1 M 13 39 S 0 1 5 0 2 I 0 39833 3 0 2 S 1 2 M 10 30 5 0 2 I 0 35432 3 0 2 M 15 45 5 0 2 I 0 47160 3 0 2 M 11 33 5 0 2 I 0 20156 3 0 2 M 10 30 S 0 1 5 0 2 I 0 97334 3 0 2 S 1 2 M 3 9 S 0 1 5 0 2 I 0 38198 3 0 2 S 1 2 M 6 18 5 0 2 I 0 18893 3 0 2 M 10 30 S 0 2 5 0 2 I 0 107292 3 0 2 S 1 1 M 9 27 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-17 ##type DNA # # # seqname source feature start end score strand frame attributes # NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local gene 5924 649886 111 - . gene_id 4 ; sequence SPP00000017_1.0 ; gene_orientation + NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 649826 649886 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 649826 649886 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 649824 649825 . - . intron_id 1 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 563362 649825 . - . intron_id 1 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 563362 563363 . - . intron_id 0 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 563331 563361 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 563331 563361 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 563329 563330 . - . intron_id 2 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 464237 563330 . - . intron_id 2 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 464237 464238 . - . intron_id 1 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 464207 464236 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 464207 464236 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 464205 464206 . - . intron_id 3 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 454513 464206 . - . intron_id 3 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 454513 454514 . - . intron_id 2 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 454505 454512 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 454505 454512 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 454503 454504 . - . intron_id 4 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 420542 454504 . - . intron_id 4 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 420542 420543 . - . intron_id 3 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 420523 420541 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 420523 420541 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 420521 420522 . - . intron_id 5 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 410528 420522 . - . intron_id 5 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 410528 410529 . - . intron_id 4 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 410487 410527 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 410487 410527 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 410485 410486 . - . intron_id 6 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 370650 410486 . - . intron_id 6 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 370650 370651 . - . intron_id 5 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 370618 370649 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 370618 370649 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 370616 370617 . - . intron_id 7 ; splice_site "GA" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 335182 370617 . - . intron_id 7 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 335182 335183 . - . intron_id 6 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 335137 335181 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 335137 335181 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 335135 335136 . - . intron_id 8 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 287973 335136 . - . intron_id 8 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 287973 287974 . - . intron_id 7 ; splice_site "ac" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 287940 287972 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 287940 287972 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 287938 287939 . - . intron_id 9 ; splice_site "at" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 267780 287939 . - . intron_id 9 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 267780 267781 . - . intron_id 8 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 267749 267779 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 267749 267779 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 267747 267748 . - . intron_id 10 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 170411 267748 . - . intron_id 10 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 170411 170412 . - . intron_id 9 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 170399 170410 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 170399 170410 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 170397 170398 . - . intron_id 11 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 132197 170398 . - . intron_id 11 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 132197 132198 . - . intron_id 10 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 132177 132196 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 132177 132196 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 132175 132176 . - . intron_id 12 ; splice_site "GG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 113280 132176 . - . intron_id 12 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 113280 113281 . - . intron_id 11 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 113248 113279 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 113248 113279 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 113246 113247 . - . intron_id 13 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 5952 113247 . - . intron_id 13 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 5952 5953 . - . intron_id 12 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 5924 5951 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 5924 5951 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local similarity 5924 649886 111 - . alignment_id 4 ; Query SPP00000017_1.0 ; Align 649887 3 60 ; Align 563360 24 27 ; Align 464236 34 27 ; Align 454512 44 6 ; Align 420540 47 15 ; Align 410527 53 39 ; Align 370648 67 30 ; Align 335182 77 45 ; Align 287973 92 33 ; Align 267780 103 30 ; Align 170409 114 9 ; Align 132195 118 18 ; Align 113280 124 30 ; Align 5951 135 27 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000017_1.0 # Protein # Selenoprotein M (SelM) # Homo sapiens # Complete Target: NIVO01044519.1:subseq(733635,745166) Ammotragus lervia isolate NAZ scaffold2533_len1482783_cov71, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 109 Query range: 9 -> 135 Target range: 693396 -> 60379 10 : LeuLeuLeuLeuLeuAlaAlaLeuValAlaProAlaThrAlaAlaThrAlaTyrArgP : 29 |||||||||||||||:::...... ...|||||| | LeuLeuLeuLeuLeuSerCysPheSerArgValArgLeuCysAlaThrAspSerSerP 693396 : ctgctgctgctgctaagttgcttcagtcgtgtccgactctgtgcaaccgacagcagcc : 693339 30 : roAspTrpAsnArgLeuSerGlyLeuThrArgAlaArgValGlu >>>> Target : 44 || ::: ::: |||::: :::||||||:::::: 187 roLeuGlySerSerValProGlyIleLeuGlnAlaArgIleGln+- 693338 : cattaggctcctctgtccctgggattctccaggcaagaatacagga............ : 693292 45 : Intron 1 >>>> ThrCysGlyGlyUnkGlnLeuAsn{Ar} >>>> Target I : 52 28 bp !||||||||| :!! !:!!{ !} 3170 ++GlnCysGlyGlyMetGluGluAsp{Gl}++ 693291 : .............agCAGTGTGGTGGGATGGAAGAGGAT{GG}gt............. : 674538 53 : ntron 2 >>>> {g}LeuLysGluValLysAlaPhe >>>> Target Intron : 60 2 bp {!}|||!:! !:!! ! !.!. 26073 bp ++{y}LeuArg***IleGlyAspLeu++ 674537 : ............ag{A}TTAAGGTGAATTGGTGACCTGgt.................. : 642814 61 : 3 >>>> >>>> Target Intron 4 >>>> ValThrGln >>>> Targ : 63 5921 bp :!!!:!||| 1 ++++ ++LeuSerGln++ 642813 : .......aggt.........................agCTGAGTCAGgt......... : 610811 64 : et Intron 5 >>>> AspIleProPheTyrHisAsnLeuValMet{Ly} >>>> : 73 36974 bp !!::!! ! !!! !::!|||:!!.!.{!:} ++GluLeuLysThr***SerSerLeuLeuPhe{Ar}++ 610810 : ................agGAACTTAAAACTTAGAGTTCTCTGCTTTTC{AG}gt.... : 473805 74 : Target Intron 6 >>>> {s}HisLeuProGlyAlaAsp >>>> Target : 80 53266 bp {!} ! |||||||||:!!.!. 362 ++{g}***LeuProGlySerGln++ 473804 : .....................ag{G}TAACTTCCAGGGTCACAGgt............ : 420520 81 : Intron 7 >>>> {P} >>>> Target Intron 8 >>>> {ro}GluLeuV : 83 17 bp { } 8562 bp { !}::: . ++{A}++ ++{sp}AspThrT 420519 : .............ag{G}gt.........................ag{at}gatacca : 375734 84 : alLeuLeuGlyArgArgTyrGluGluLeuGluArgIleProLeuSer >>>> Targ : 99 ..|||:::...... |||||||||:::|||::: :::... hrLeuMetAlaGluThrGlnGluGluLeuLysArgLeuLeuMetLys++ 375733 : ctcttatggcagaaacccaagaggaactaaagagactcttgatgaaggt......... : 375684 100 : et Intron 9 >>>> GluMetThrArgGluGluIleAsnAlaLeuValGln{G} : 111 46202 bp .!.:!:|||!:! ! |||...||| :::{ } ++AsnLeuThrLysIleThrAlaAsnThrLeuLysArg{P}+ 375683 : ................agAACCTCACTAAAATAAcagcaaatactttaaaaagg{t}g : 329447 112 : >>>> Target Intron 10 >>>> {lu}LeuGlyPheTyrArg{Ly} >>>> : 117 39102 bp { }||||||.!.! ! !{||} + ++{he}LeuGlyLeuLeuIle{Ly}++ 329446 : t..........................ag{tc}CTTGGCCTGTTAATA{AA}gt.... : 290324 118 : Target Intron 11 >>>> {s}Ala{A} >>>> Target Intron 12 > : 119 192882 bp {|}|||{!} 37010 bp ++{s}Ala{G}++ 290323 : ......................ag{G}GCA{G}gt....................... : 97437 120 : >>> {la}ProAspAlaGlnValProProGluTyrValTrpAlaProAlaLysPro : 135 { !}||||||||||||!.!||| !! !.! !|||:!! ! ||| ++{lu}ProAspAlaGlnAlaProAlaThrGlyAlaLeuLeuProSerHisPro 97436 : ...ag{AG}CCAGACGCTCAGGCTCCAGCAACTGGAGCCCTTTTGCCATCTCACCCT : 60380 vulgar: SPP00000017_1.0 9 135 . NIVO01044519.1:subseq(733635,745166) 693396 60379 - 109 M 34 102 5 0 2 I 0 18724 3 0 2 M 8 24 S 0 2 5 0 2 I 0 31698 3 0 2 S 1 1 M 7 21 5 0 2 I 0 26069 3 0 2 5 0 2 I 0 5917 3 0 2 M 3 9 5 0 2 I 0 136970 3 0 2 M 10 30 S 0 2 5 0 2 I 0 53262 3 0 2 S 1 1 M 6 18 5 0 2 I 0 36213 3 0 2 S 0 1 5 0 2 I 0 8558 3 0 2 S 1 2 M 18 54 5 0 2 I 0 46198 3 0 2 M 12 36 S 0 1 5 0 2 I 0 39098 3 0 2 S 1 2 M 5 15 S 0 2 5 0 2 I 0 192878 3 0 2 S 1 1 M 1 3 S 0 1 5 0 2 I 0 37006 3 0 2 S 1 2 M 16 48 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-17 ##type DNA # # # seqname source feature start end score strand frame attributes # NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local gene 60380 693396 109 - . gene_id 5 ; sequence SPP00000017_1.0 ; gene_orientation + NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 693295 693396 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 693295 693396 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 693293 693294 . - . intron_id 1 ; splice_site "ga" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 674567 693294 . - . intron_id 1 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 674567 674568 . - . intron_id 0 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 674541 674566 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 674541 674566 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 674539 674540 . - . intron_id 2 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 642839 674540 . - . intron_id 2 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 642839 642840 . - . intron_id 1 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 642817 642838 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 642817 642838 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 642815 642816 . - . intron_id 3 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 616744 642816 . - . intron_id 3 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 616744 616745 . - . intron_id 2 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 616742 616743 . - . intron_id 4 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 610823 616743 . - . intron_id 4 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 610823 610824 . - . intron_id 3 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 610814 610822 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 610814 610822 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 610812 610813 . - . intron_id 5 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 473840 610813 . - . intron_id 5 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 473840 473841 . - . intron_id 4 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 473808 473839 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 473808 473839 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 473806 473807 . - . intron_id 6 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 420542 473807 . - . intron_id 6 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 420542 420543 . - . intron_id 5 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 420523 420541 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 420523 420541 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 420521 420522 . - . intron_id 7 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 384306 420522 . - . intron_id 7 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 384306 384307 . - . intron_id 6 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 384305 384305 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 384305 384305 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 384303 384304 . - . intron_id 8 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 375743 384304 . - . intron_id 8 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 375743 375744 . - . intron_id 7 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 375687 375742 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 375687 375742 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 375685 375686 . - . intron_id 9 ; splice_site "gt" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 329485 375686 . - . intron_id 9 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 329485 329486 . - . intron_id 8 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 329448 329484 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 329448 329484 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 329446 329447 . - . intron_id 10 ; splice_site "gT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 290346 329447 . - . intron_id 10 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 290346 290347 . - . intron_id 9 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 290327 290345 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 290327 290345 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 290325 290326 . - . intron_id 11 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 97445 290326 . - . intron_id 11 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 97445 97446 . - . intron_id 10 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 97440 97444 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 97440 97444 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 97438 97439 . - . intron_id 12 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 60430 97439 . - . intron_id 12 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 60430 60431 . - . intron_id 11 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 60380 60429 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 60380 60429 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local similarity 60380 693396 109 - . alignment_id 5 ; Query SPP00000017_1.0 ; Align 693397 10 102 ; Align 674567 44 24 ; Align 642838 53 21 ; Align 610823 60 9 ; Align 473840 63 30 ; Align 420541 74 18 ; Align 375741 81 54 ; Align 329485 99 36 ; Align 290344 112 15 ; Align 97444 118 3 ; Align 60428 120 48 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000017_1.0 # Protein # Selenoprotein M (SelM) # Homo sapiens # Complete Target: NIVO01044519.1:subseq(733635,745166) Ammotragus lervia isolate NAZ scaffold2533_len1482783_cov71, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 102 Query range: 1 -> 140 Target range: 702044 -> 97926 2 : SerLeuLeuLeuProProLeuAlaLeuLeuLeuLeuLeuAlaAlaLeuValAlaProA : 21 !:!|||!!!||| !! !!|||!.!|||! !|||! !|||:!!:!!! !:!! !! !!: AsnLeuPheLeuAlaThrLeuGlyLeuGlnLeuGlnLeuSerSerCysLeuProSerS 702044 : AATCTATTTCTAGCTACCTTGGGCCTCCAATTGCAGCTGTCTTCCTGCTTGCCATCCT : 701987 22 : laThrAlaAlaThrAlaTyr{Ar} >>>> Target Intron 1 >>>> {g}Pr : 29 !!..! !! !:!!.!! !!{||} 24343 bp {|}|| erValLysGluSerThrAsn{Ar}++ ++{g}Pr 701986 : CTGTAAAAGAGTCAACGAAC{AG}gt.........................ag{G}CC : 677620 30 : oAspTrpAsnArg{Le} >>>> Target Intron 2 >>>> {u}SerGlyLeu : 37 |.!.!::::!|||{||} 3037 bp {|}|||! !:!! oGlnPheSerArg{Le}++ ++{u}SerValVal 677619 : TCAATTTTCCCGA{CT}gt.........................ag{C}AGTGTGGTG : 674559 38 : ThrArgAlaArgVal{G} >>>> Target Intron 3 >>>> {lu}ThrCysG : 46 ! !! !|||:!!{|} 22275 bp {||}.!! | GlyTrpLysArgMet{G}++ ++{lu}AlaValG 674558 : GGATGGAAGAGGATG{G}gt.........................ag{AG}GCTGTAG : 652257 47 : ly{Gl} >>>> Target Intron 4 >>>> {y}Unk >>>> Target Int : 49 ||{||} 64964 bp {|} 18300 ly{Gl}++ ++{y}Gly++ 652256 : GT{GG}gt.........................ag{G}GGGgt............... : 587282 50 : ron 5 >>>> Gln >>>> Target Intron 6 >>>> LeuAsnArgLeuLy : 54 bp ||| 2288 bp !!.!||| !:! ++Gln++ ++ArgThrArgArgGl 587281 : ..........agCAGgt.........................agAGGACCAGGAGACA : 566681 55 : sGluValLysAlaPheValThrGlnAspIleProPheTyrHisAsnLeuValMet{Ly : 73 !|||:!! !::!||| !..! !!!: ||| ! ! !! !! ! !:!:{!: nGluIleValSerPheLysValThrGluTrpProHisGlnSerIleProSerLeu{Ar 566680 : AGAAATTGTGAGCTTCAAGGTCACAGAGTGGCCGCATCAGAGCATTCCCTCACTC{AG : 566624 74 : } >>>> Target Intron 7 >>>> {s}HisLeuProGlyAlaAspProGluL : 82 } 48022 bp {!}|||||| !|||!.!||| !!:!! }++ ++{g}HisLeuArgGlyGlyAspThrGlnA 566623 : }gt.........................ag{G}CACCTGAGAGGGGGAGACACACAGG : 518575 83 : euValLeuLeuGlyArgArg >>>> Target Intron 8 >>>> TyrGluGlu : 91 !||||||||| !! !||| 18173 bp ||| :!! laValLeuLeuArgAlaArg+- ++TyrLeuGln 518574 : CGGTTCTGCTCAGAGCCCGGgg.........................agTATCTCCAG : 500375 92 : LeuGluArgIleProLeu{Se} >>>> Target Intron 9 >>>> {r}GluM : 100 ! !! !! ||||||{||} 119426 bp {|} ! AlaLeuProLysProLeu{Se}++ ++{r}CysL 500374 : GCCCTGCCAAAGCCTCTG{AG}gt.........................ag{C}TGCA : 380922 101 : etThrArgGluGluIleAsnAlaLeuValGlnGluLeuGly >>>> Target Int : 114 |||!:!|||! !:!!||||||||| !:!!|||||| ! 8293 ysThrGlnGluAlaLeuAsnAlaLeuProGluGluLeuGln++ 380921 : AAACGCAGGAGGCGCTCAACGCCCTCCCTGAGGAGCTGCAGgt............... : 380878 115 : ron 10 >>>> PheTyrArgLysAlaAlaProAspAlaGlnValProPro{Gl} : 127 bp |||...!.!!.!||| !!::|||||||||{..} ++ProArgArgSerGlyGlyProArgHisArgValProPro{Ar}++ 380877 : ...........agCCGAGGAGGTCTGGGGGACCGCGGCATCGCGTACCCCCC{AG}gt : 372546 128 : >>>> Target Intron 11 >>>> {u}TyrVal{Tr} >>>> Target Int : 130 94913 bp {!}||| !{||} 168593 ++{g}TyrSer{Tr}++ 372545 : ..........................ag{G}TATAGC{TG}gt............... : 277622 131 : ron 12 >>>> {p}AlaPro{Al} >>>> Target Intron 13 >>>> {a : 133 bp {|} !|||{ } 11074 bp {! ++{p}ArgPro{Ar}-+ ++{g 277621 : ...........ag{G}CGGCCC{AG}ct..........................ag{G : 97948 134 : }LysProProGluGluThrSer : 140 }|||! !! !.!.||||||||| }LysLeuGlnHisGluThrSer 97947 : }AAACTGCAGCATGAGACCTCC : 97927 vulgar: SPP00000017_1.0 1 140 . NIVO01044519.1:subseq(733635,745166) 702044 97926 - 102 M 26 78 S 0 2 5 0 2 I 0 24339 3 0 2 S 1 1 M 5 15 S 0 2 5 0 2 I 0 3033 3 0 2 S 1 1 M 8 24 S 0 1 5 0 2 I 0 22271 3 0 2 S 1 2 M 3 9 S 0 2 5 0 2 I 0 64960 3 0 2 S 1 1 M 1 3 5 0 2 I 0 18296 3 0 2 M 1 3 5 0 2 I 0 2284 3 0 2 M 23 69 S 0 2 5 0 2 I 0 48018 3 0 2 S 1 1 M 15 45 5 0 2 I 0 18169 3 0 2 M 9 27 S 0 2 5 0 2 I 0 119422 3 0 2 S 1 1 M 15 45 5 0 2 I 0 8289 3 0 2 M 13 39 S 0 2 5 0 2 I 0 94909 3 0 2 S 1 1 M 2 6 S 0 2 5 0 2 I 0 168589 3 0 2 S 1 1 M 2 6 S 0 2 5 0 2 I 0 11070 3 0 2 S 1 1 M 7 21 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-17 ##type DNA # # # seqname source feature start end score strand frame attributes # NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local gene 97927 702044 102 - . gene_id 6 ; sequence SPP00000017_1.0 ; gene_orientation + NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 701965 702044 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 701965 702044 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 701963 701964 . - . intron_id 1 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 677622 701964 . - . intron_id 1 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 677622 677623 . - . intron_id 0 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 677604 677621 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 677604 677621 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 677602 677603 . - . intron_id 2 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 674567 677603 . - . intron_id 2 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 674567 674568 . - . intron_id 1 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 674541 674566 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 674541 674566 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 674539 674540 . - . intron_id 3 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 652266 674540 . - . intron_id 3 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 652266 652267 . - . intron_id 2 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 652253 652265 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 652253 652265 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 652251 652252 . - . intron_id 4 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 587289 652252 . - . intron_id 4 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 587289 587290 . - . intron_id 3 ; splice_site "ag" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 587285 587288 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 587285 587288 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 587283 587284 . - . intron_id 5 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 568985 587284 . - . intron_id 5 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 568985 568986 . - . intron_id 4 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 568982 568984 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 568982 568984 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 568980 568981 . - . intron_id 6 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 566694 568981 . - . intron_id 6 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 566694 566695 . - . intron_id 5 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 566623 566693 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 566623 566693 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 566621 566622 . - . intron_id 7 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 518601 566622 . - . intron_id 7 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 518601 518602 . - . intron_id 6 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 518555 518600 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 518555 518600 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 518553 518554 . - . intron_id 8 ; splice_site "GG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 500382 518554 . - . intron_id 8 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 500382 500383 . - . intron_id 7 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 500353 500381 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 500353 500381 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 500351 500352 . - . intron_id 9 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 380927 500352 . - . intron_id 9 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 380927 380928 . - . intron_id 8 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 380881 380926 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 380881 380926 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 380879 380880 . - . intron_id 10 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 372588 380880 . - . intron_id 10 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 372588 372589 . - . intron_id 9 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 372547 372587 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 372547 372587 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 372545 372546 . - . intron_id 11 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 277634 372546 . - . intron_id 11 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 277634 277635 . - . intron_id 10 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 277625 277633 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 277625 277633 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 277623 277624 . - . intron_id 12 ; splice_site "GT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 109032 277624 . - . intron_id 12 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 109032 109033 . - . intron_id 11 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 109023 109031 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 109023 109031 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice5 109021 109022 . - . intron_id 13 ; splice_site "CT" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local intron 97949 109022 . - . intron_id 13 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local splice3 97949 97950 . - . intron_id 12 ; splice_site "AG" NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local cds 97927 97948 . - . NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local exon 97927 97948 . - . insertions 0 ; deletions 0 NIVO01044519.1:subseq(733635,745166) exonerate:protein2genome:local similarity 97927 702044 102 - . alignment_id 6 ; Query SPP00000017_1.0 ; Align 702045 2 78 ; Align 677621 29 15 ; Align 674566 35 24 ; Align 652264 44 9 ; Align 587288 48 3 ; Align 568985 49 3 ; Align 566694 50 69 ; Align 518600 74 45 ; Align 500382 89 27 ; Align 380926 99 45 ; Align 372588 114 39 ; Align 277633 128 6 ; Align 109031 131 6 ; Align 97948 134 21 # --- END OF GFF DUMP --- # -- completed exonerate analysis