Command line: [exonerate --exhaustive yes -m p2g --showtargetgff -q ../TR2-human.fa -t TR2-NIVO01019577.1.subseq] Hostname: [sitdoc] C4 Alignment: ------------ Query: SPP00000035_1.0 # Protein # Thioredoxin reductase 2 (TR2) # Homo sapiens # Complete Target: NIVO01019577.1:subseq(189524,120883) Ammotragus lervia isolate NAZ scaffold5500_len738321_cov71, whole genome shotgun sequence Model: protein2genome:local Raw score: 2116 Query range: 2 -> 524 Target range: 1188 -> 70883 3 : AlaMetAlaValAlaLeuArgGlyLeuGlyGly{A} >>>> Target Intron 1 > : 14 ||| !.!!.!::!||||||! !|||||||||{ } 2357 bp AlaAspGlyAlaSerLeuArgGluLeuGlyGly{G}++ 1189 : GCGGATGGGGCCAGCCTCAGGGAACTTGGGGGA{G}gt...................... : 1225 15 : >>> {rg}PheArgTrpArgThrGlnAlaValAlaGlyGly{Va} >>>> Target : 26 {!!} !|||||| !! !||||||! !|||!.!{! } 815 ++{ly}ArgAlaTrpArgProAlaAlaValAspGlyAla{As}++ 1226 : ...ag{GG}AGGGCCTGGCGCCCCGCGGCCGTGGATGGGGCC{GA}gt............ : 3619 27 : Intron 2 >>>> {l}ArgGlyAlaAlaArgGlyAlaAla >>>> Target Intr : 35 3 bp {!}||| !||||||||| !||| ! 12582 b ++{p}ArgProAlaAlaArgLysAlaGln++ 3620 : .............ag{C}AGGCCAGCTGCCAGAAAGGCTCAGgt................ : 11797 36 : on 3 >>>> Ala{G} >>>> Target Intron 4 >>>> {ly}GlnArgAspT : 40 p |||{|} 22303 bp {||}!:!!:! | ++Ala{G}-+ ++{ly}ArgGlnArgT 11798 : .........agGCA{G}ct.........................ag{GC}CGGCAACGGT : 46695 41 : yrAspLeuLeuValValGlyGlyGlySerGlyGlyLeuAlaCysAlaLysGlu{A} >> : 58 ||||||||||||||:!!||||||||||||||||||||||||||||||||||||{|} yrAspLeuLeuValIleGlyGlyGlySerGlyGlyLeuAlaCysAlaLysGlu{A}++ 46696 : ATGACCTCCTGGTGATCGGCGGTGGATCCGGCGGCCTGGCCTGCGCCAAGGAA{G}gt.. : 46752 59 : >> Target Intron 5 >>>> {la}AlaGlnLeuGlyArgLysValAlaValValA : 69 3251 bp {||}||||||||||||!:!||||||||||||:!!| ++{la}AlaGlnLeuGlyLysLysValAlaValLeuA 46753 : .......................ag{CT}GCCCAGCTGGGGAAGAAGGTGGCCGTGCTGG : 50033 70 : spTyrValGluProSerProGln{G} >>>> Target Intron 6 >>>> {ly}T : 78 ||||||||||||||||||||!:!{|} 118 bp {||}| spTyrValGluProSerProArg{G}++ ++{ly}T 50034 : ACTACGTGGAGCCTTCCCCCCGA{G}gt.........................ag{gc}a : 50178 79 : hrArgTrpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetH : 98 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| hrArgTrpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetH 50179 : cCAGGTGGGGCCTCGGCGGCACCTGCGTGAATGTCGGCTGCATCCCCAAGAAGCTGATGC : 50238 99 : isGlnAlaAlaLeuLeuGlyGlyLeuIleGlnAspAlaProAsnTyrGlyTrpGluValA : 118 |||||||||||||||||||||||:!!|||!::|||||||||:!!|||||||||...|||| isGlnAlaAlaLeuLeuGlyGlyMetIleArgAspAlaProHisTyrGlyTrpArgValA 50239 : ACCAGGCGGCGCTGCTGGGGGGCATGATCCGCGACGCCCCCCACTACGGCTGGCGCGTGG : 50298 119 : laGlnProValProHisAsp{Tr} >>>> Target Intron 7 >>>> {p}ArgL : 127 ||||| !.!|||||||||{||} 348 bp {|} !! laGln---AlaProHisAsp{Tr}++ ++{p}AlaT 50299 : CCCAG---GCCCCACACGAC{TG}gt.........................ag{G}GCAA : 50670 128 : ysMetAlaGluAlaValGlnAsnHisValLysSerLeuAsnTrpGlyHisArgValGlnL : 147 !||||||!!:||||||||||||||||||||||||||||||||||||||||||||||||| hrMetAlaAspAlaValGlnAsnHisValLysSerLeuAsnTrpGlyHisArgValGlnL 50671 : CAATGGCGGATGCCGTCCAGAACCACGTGAAGTCCCTGAACTGGGGCCACCGCGTCCAGC : 50730 148 : euGlnAsp{Ar} >>>> Target Intron 8 >>>> {g}LysValLysTyrPheA : 156 ||||||||{||} 617 bp {|}||||||||||||!!.| euGlnAsp{Ar}++ ++{g}LysValLysTyrLeuA 50731 : TGCAGGAC{AG}gt.........................ag{G}AAAGTCAAGTATTTGA : 51374 157 : snIleLysAlaSerPheValAspGluHisThrValCysGlyValAlaLysGlyGlyLysG : 176 ||:!!|||||||||||||||||| !||||||||||||||||||:!:|||||||||:::| snValLysAlaSerPheValAspThrHisThrValCysGlyValSerLysGlyGlyGluG 51375 : ACGTCAAGGCCAGCTTTGTCGACACGCACACGGTTTGCGGTGTCTCcaaaggtggggagg : 51434 177 : lu >>>> Target Intron 9 >>>> IleLeuLeuSerAlaAspHisIleIleIl : 186 || 414 bp ! !||||||||||||!!:||||||:!!|| lu++ ++ThrLeuLeuSerAlaGluHisIleValIl 51435 : aggt.........................agACTCTGCTTTCGGCCGAGCACATTGTCAT : 51878 187 : eAlaThrGlyGlyArgProArgTyrProThrHis >>>> Target Intron 10 >> : 198 |||||||||||||||||||||||||||||||||| 865 bp eAlaThrGlyGlyArgProArgTyrProThrHis++ 51879 : TGCCACCGGAGGTCGGCCGCGGTACCCCACGCACgt........................ : 51916 199 : >> IleGluGlyAlaLeuGluTyrGlyIleThrSerAspAspIlePheTrpLeuLysGl : 216 |||||||||||||||||||||||||||||||||||||||:!!|||||||||||||| ++IleGluGlyAlaLeuGluTyrGlyIleThrSerAspAspLeuPheTrpLeuLysGl 51917 : ..agATCGAAGGTGCCTTGGAATACGGGATCACGAGCGATGACCTCTTCTGGCTGAAGGA : 52833 217 : uSerProGlyLys{Th} >>>> Target Intron 11 >>>> {r}LeuValValG : 225 |||||||||||||{||} 6125 bp {|}|||||||||| uSerProGlyLys{Th}++ ++{r}LeuValValG 52834 : ATCCCCTGGGAAA{AC}gt..........................ag{G}TTGGTGGTCG : 58985 226 : lyAlaSer{T} >>>> Target Intron 12 >>>> {yr}ValAlaLeuGluCys : 233 ||||||||{|} 603 bp {||}||||||||||||||| lyAlaSer{T}++ ++{yr}ValAlaLeuGluCys 58986 : GGGCCAGC{T}gt..........................ag{AC}GTAGCCCTGGAGTGC : 59612 234 : AlaGlyPheLeuThrGlyIleGlyLeuAspThrThrIleMetMetArgSerIleProLeu : 253 ||||||||||||||||||:!!|||||||||||||||:!!|||!!:||||||:!:|||||| AlaGlyPheLeuThrGlyLeuGlyLeuAspThrThrValMetIleArgSerValProLeu 59613 : GCGGGCTTCCTCACCGGGCTCGGCTTGGACACCACCGTCATGATACGCAGCGTGCCCCTC : 59672 254 : ArgGlyPheAspGln >>>> Target Intron 13 >>>> GlnMetSerSerMet : 263 |||!.!||||||||| 1106 bp ||||||:!!! !:!: ArgAlaPheAspGln++ ++GlnMetAlaLeuLeu 59673 : CGGGCCTTCGACCAGgt..........................agCAAATGGCTTTGCTT : 60808 264 : ValIleGluHisMetAlaSerHisGlyThrArgPheLeuArgGlyCysAlaProSerArg : 283 |||! !||||||||||||.!!|||||||||||| !!||||||||||||||||||..!||| ValThrGluHisMetAlaGlyHisGlyThrArgValLeuArgGlyCysAlaProGluArg 60809 : GTCACCGAGCACATGGCTGGCCACGGCACCCGGGTCCTGCGGGGCTGCGCCCCCGAGAGG : 60868 284 : ValArgArgLeuProAspGlyGlnLeuGlnValThrTrpGluAspSerThrThrGlyLys : 303 |||..!!:!||||||! ! !||||||!::|||||||||! !||| !.!!:!!! !::! ValGluLysLeuProGlyGlnGlnLeuArgValThrTrpValAspLeuAlaSerAspArg 60869 : GTGGAGAAGCTCCCAGGCCAGCAGCTCCGCGTCACCTGGGTGGACCTTGCCTCGGACCGG : 60928 304 : GluAspThrGlyThrPheAspThrValLeuTrpAlaIle{G} >>>> Target Intr : 317 :!!|||.!!||||||||||||||||||||||||||||||{|} 5963 b LysAspAlaGlyThrPheAspThrValLeuTrpAlaIle{G}++ 60929 : AAGGATGCGGGCACCTTTGACACCGTGCTCTGGGCCATA{G}gt................ : 60973 318 : on 14 >>>> {ly}ArgValProAspThrArgSerLeuAsnLeuGluLysAlaGlyVa : 332 p {||}|||||||||!!:||| |||||||||||||||||||||||||| ++{ly}ArgValProGluThrAlaSerLeuAsnLeuGluLysAlaGlyVa 60974 : ..........ag{GC}CGAGTTCCAGAAACCGcgagtctgaatttggaaaaggCTGGTGT : 66978 333 : lAspThrSerProAspThrGlnLysIleLeuValAspSerArgGluAlaThrSerValPr : 352 | !|||!:!|||! !||| !||||||!!!||||||:!!!:!||||||||||||:!!|| lArgThrAsnProValThrGlyLysIlePheValAspAlaGlnGluAlaThrSerIlePr 66979 : GCGTACGAACCCCGTCACTGGGAAGATCTTCGTTGATGCCCAGGAAGCCACCTCCATCCC : 67038 353 : oHisIleTyrAlaIleGlyAspValValGlu >>>> Target Intron 15 >>>> : 363 |||||||||||||||||||||||||!.!||| 1025 bp oHisIleTyrAlaIleGlyAspValAlaGlu++ + 67039 : CCACATCTACGCCATCGGCGACGTGGCAGAGgt..........................a : 68094 364 : GlyArgProGluLeuThrProIleAlaIleMetAlaGlyArgLeuLeuValGlnArgLe : 382 |||||||||||||||||||||! !||||||||||||||||||||||||!.!|||||||| +GlyArgProGluLeuThrProThrAlaIleMetAlaGlyArgLeuLeuAlaGlnArgLe 68095 : gGGGCGGCCGGAGCTGACACCCACAGCCATCATGGCCGGGCGGCTCCTGGCCCAGCGGCT : 68153 383 : uPheGlyGlySerSerAspLeuMetAspTyrAspAsn >>>> Target Intron 16 : 395 | !||| !!!!!||||||||||||||||||..!!:! 379 bp uSerGlyArgThrSerAspLeuMetAspTyrSerSer++ 68154 : GAGCGGCCGGACCTCAGACCTGATGGACTACAGCAGCgt..................... : 68194 396 : >>>> ValProThrThrValPheThrProLeuGluTyrGlyCysValGlyLeuSerGl : 412 ||||||||||||||||||||||||||||||||||||||||||||||||||||| ++ValProThrThrValPheThrProLeuGluTyrGlyCysValGlyLeuSerGl 68195 : .....agGTCCCCACGACTGTCTTCACTCCCCTGGAGTATGGCTGCGTGGGGCTGTCAGA : 68622 413 : uGluGluAlaValAlaArgHisGlyGlnGluHisValGlu >>>> Target Intron : 426 ||||! !||||||||||||||||||:!!|||||||||||| 1213 bp uGluAlaAlaValAlaArgHisGlyGluGluHisValGlu++ 68623 : GGAGGCAGCCGTGGCTCGCCATGGAGAAGAGCACGTGGAGgt.................. : 68666 427 : 17 >>>> ValTyrHisAlaHisTyrLysProLeuGluPheThrValAlaGlyArgAs : 442 |||||||||||| !|||||||||||||||||||||||| !! !||||| ++ValTyrHisAlaPheTyrLysProLeuGluPheThrValProGlnArgAs 68667 : ........agGTTTACCATGCGTTCTATAAACCGCTGGAGTTCACTGTCCCCCAGCGGGA : 69925 443 : pAlaSerGlnCysTyrValLys >>>> Target Intron 18 >>>> MetValCy : 452 |||||||||||||||||||||| 69 bp |||||||| pAlaSerGlnCysTyrValLys++ ++MetValCy 69926 : TGCATCTCAGTGCTACGTAAAGgt..........................agATGGTGTG : 70024 453 : sLeuArgGluProProGlnLeuValLeuGlyLeuHisPheLeuGlyProAsnAlaGlyGl : 472 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sLeuArgGluProProGlnLeuValLeuGlyLeuHisPheLeuGlyProAsnAlaGlyGl 70025 : TCTGCGGGAGCCCCCACAGCTGGTGCTGGGCCTGCACTTCCTCGGCCCCAACGCAGGCGA : 70084 473 : uValThrGlnGlyPheAlaLeuGlyIle{Ly} >>>> Target Intron 19 >>>> : 482 ||||||||||||||||||||||||||||{||} 641 bp uValThrGlnGlyPheAlaLeuGlyIle{Ly}++ 70085 : AGTTACTCAGGGGTTTGCCCTGGGGATC{AA}gt.......................... : 70118 483 : {s}CysGlyAlaSerTyrAlaGlnValMetArgThrValGlyIleHisProThrCysS : 501 {|}||||||||||||!:! !||||||!!:|||||||||||||||||||||||||||: ++{s}CysGlyAlaSerPheGlnGlnValIleArgThrValGlyIleHisProThrCysA 70119 : ag{G}TGTGGGGCCTCCTTCCAGCAGGTGATACGCACGGTGGGCATCCACCCCACCTGTG : 70812 502 : erGluGluValValLysLeuArgIleSerLysArgSerGlyLeuAspProThrValThrG : 521 !!|||||||||!.!|||||||||||||||||||||||||||||||||||||||||||||| laGluGluValAlaLysLeuArgIleSerLysArgSerGlyLeuAspProThrValThrG 70813 : CGGAGGAGGTGGCCAAGCTCCGCATCTCCAAGCGCTCCGGCCTGGACCCCACGGTGACCG : 70872 522 : lyCysUnkGly : 524 ||||| ||| lyCys***Gly 70873 : GCTGCTGAGGC : 70883 vulgar: SPP00000035_1.0 2 524 . NIVO01019577.1:subseq(189524,120883) 1188 70883 + 2116 M 11 33 S 0 1 5 0 2 I 0 2353 3 0 2 S 1 2 M 11 33 S 0 2 5 0 2 I 0 8149 3 0 2 S 1 1 M 8 24 5 0 2 I 0 12578 3 0 2 M 1 3 S 0 1 5 0 2 I 0 22299 3 0 2 S 1 2 M 21 63 S 0 1 5 0 2 I 0 3247 3 0 2 S 1 2 M 18 54 S 0 1 5 0 2 I 0 114 3 0 2 S 1 2 M 42 126 G 1 0 M 4 12 S 0 2 5 0 2 I 0 344 3 0 2 S 1 1 M 24 72 S 0 2 5 0 2 I 0 613 3 0 2 S 1 1 M 26 78 5 0 2 I 0 410 3 0 2 M 21 63 5 0 2 I 0 861 3 0 2 M 23 69 S 0 2 5 0 2 I 0 6121 3 0 2 S 1 1 M 6 18 S 0 1 5 0 2 I 0 599 3 0 2 S 1 2 M 30 90 5 0 2 I 0 1102 3 0 2 M 58 174 S 0 1 5 0 2 I 0 5959 3 0 2 S 1 2 M 45 135 5 0 2 I 0 1021 3 0 2 M 32 96 5 0 2 I 0 375 3 0 2 M 31 93 5 0 2 I 0 1209 3 0 2 M 24 72 5 0 2 I 0 65 3 0 2 M 32 96 S 0 2 5 0 2 I 0 637 3 0 2 S 1 1 M 42 126 # --- 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 # NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local gene 1189 70883 2116 + . gene_id 1 ; sequence SPP00000035_1.0 ; gene_orientation + NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 1189 1222 . + . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 1189 1222 . + . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 1223 1224 . + . intron_id 1 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 1223 3579 . + . intron_id 1 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 3578 3579 . + . intron_id 0 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 3580 3616 . + . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 3580 3616 . + . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 3617 3618 . + . intron_id 2 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 3617 11769 . + . intron_id 2 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 11768 11769 . + . intron_id 1 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 11770 11794 . + . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 11770 11794 . + . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 11795 11796 . + . intron_id 3 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 11795 24376 . + . intron_id 3 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 24375 24376 . + . intron_id 2 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 24377 24380 . + . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 24377 24380 . + . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 24381 24382 . + . intron_id 4 ; splice_site "CT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 24381 46683 . + . intron_id 4 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 46682 46683 . + . intron_id 3 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 46684 46749 . + . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 46684 46749 . + . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 46750 46751 . + . intron_id 5 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 46750 50000 . + . intron_id 5 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 49999 50000 . + . intron_id 4 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 50001 50057 . + . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 50001 50057 . + . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 50058 50059 . + . intron_id 6 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 50058 50175 . + . intron_id 6 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 50174 50175 . + . intron_id 5 ; splice_site "ag" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 50176 50317 . + . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 50176 50317 . + . insertions 0 ; deletions 1 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 50318 50319 . + . intron_id 7 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 50318 50665 . + . intron_id 7 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 50664 50665 . + . intron_id 6 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 50666 50740 . + . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 50666 50740 . + . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 50741 50742 . + . intron_id 8 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 50741 51357 . + . intron_id 8 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 51356 51357 . + . intron_id 7 ; splice_site "ag" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 51358 51436 . + . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 51358 51436 . + . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 51437 51438 . + . intron_id 9 ; splice_site "gt" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 51437 51850 . + . intron_id 9 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 51849 51850 . + . intron_id 8 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 51851 51913 . + . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 51851 51913 . + . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 51914 51915 . + . intron_id 10 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 51914 52778 . + . intron_id 10 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 52777 52778 . + . intron_id 9 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 52779 52849 . + . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 52779 52849 . + . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 52850 52851 . + . intron_id 11 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 52850 58974 . + . intron_id 11 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 58973 58974 . + . intron_id 10 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 58975 58994 . + . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 58975 58994 . + . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 58995 58996 . + . intron_id 12 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 58995 59597 . + . intron_id 12 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 59596 59597 . + . intron_id 11 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 59598 59689 . + . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 59598 59689 . + . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 59690 59691 . + . intron_id 13 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 59690 60795 . + . intron_id 13 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 60794 60795 . + . intron_id 12 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 60796 60970 . + . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 60796 60970 . + . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 60971 60972 . + . intron_id 14 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 60971 66933 . + . intron_id 14 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 66932 66933 . + . intron_id 13 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 66934 67070 . + . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 66934 67070 . + . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 67071 67072 . + . intron_id 15 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 67071 68095 . + . intron_id 15 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 68094 68095 . + . intron_id 14 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 68096 68191 . + . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 68096 68191 . + . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 68192 68193 . + . intron_id 16 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 68192 68570 . + . intron_id 16 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 68569 68570 . + . intron_id 15 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 68571 68663 . + . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 68571 68663 . + . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 68664 68665 . + . intron_id 17 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 68664 69876 . + . intron_id 17 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 69875 69876 . + . intron_id 16 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 69877 69948 . + . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 69877 69948 . + . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 69949 69950 . + . intron_id 18 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 69949 70017 . + . intron_id 18 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 70016 70017 . + . intron_id 17 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 70018 70115 . + . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 70018 70115 . + . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 70116 70117 . + . intron_id 19 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 70116 70756 . + . intron_id 19 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 70755 70756 . + . intron_id 18 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 70757 70883 . + . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 70757 70883 . + . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local similarity 1189 70883 2116 + . alignment_id 1 ; Query SPP00000035_1.0 ; Align 1189 3 33 ; Align 3582 15 33 ; Align 11771 27 24 ; Align 24377 35 3 ; Align 46686 37 63 ; Align 50003 59 54 ; Align 50178 78 126 ; Align 50304 121 12 ; Align 50667 126 72 ; Align 51359 151 78 ; Align 51851 177 63 ; Align 52779 198 69 ; Align 58976 222 18 ; Align 59600 229 90 ; Align 60796 259 174 ; Align 66936 318 135 ; Align 68096 363 96 ; Align 68571 395 93 ; Align 69877 426 72 ; Align 70018 450 96 ; Align 70758 483 126 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000035_1.0 # Protein # Thioredoxin reductase 2 (TR2) # Homo sapiens # Complete Target: NIVO01019577.1:subseq(189524,120883) Ammotragus lervia isolate NAZ scaffold5500_len738321_cov71, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 101 Query range: 0 -> 146 Target range: 87354 -> 8967 1 : MetAlaAlaMetAlaValAlaLeuArgGlyLeu{Gl} >>>> Target Intron 1 : 12 ...||||||.!.!.!:!!||||||||||||! !{.!} 12304 bp GlnAlaAlaPheValIleAlaLeuArgGlyGln{Se}++ 87354 : CAAGCGGCTTTTGTGATTGCACTCCGTGGGCAA{AG}gt..................... : 87317 13 : >>>> {y}Gly{Ar} >>>> Target Intron 2 >>>> {g}PheArgTrpArg : 18 {!}|||{||} 1212 bp {|} !||| ! ||| +-{r}Gly{Ar}++ ++{g}AlaArgGlyArg 87316 : ....ac{t}ggc{ag}gt.........................ag{G}GCCCGGGGCCGC : 73787 19 : ThrGlnAlaValAlaGlyGlyValArg{G} >>>> Target Intron 3 >>>> { : 28 ! !|||:!!::! !!.!:!!!!!{|} 2829 bp { LeuAlaAlaLeuSerGlnAlaMetSer{G}++ ++{ 73786 : CTGGCAGCTCTGAGTCAGGCGATGAGC{G}gt.........................ag{ : 70927 29 : ly}AlaAlaArgGlyAlaAlaAlaGlyGlnArgAspTyrAspLeuLeuValValGlyGly : 47 ||}|||||| !||| !||| !! !! !||| ! !||| ! !!.!!.!||| ly}AlaAlaAlaGlyArgAlaProTrpAlaAlaAspGlyCysLeuAlaSerAlaAlaGly 70926 : GG}GCGGCAGCGGGCCGAGCGCCCTGGGCTGCGGATGGCTGCCTAGCCTCAGCAGCCGGT : 70871 48 : GlySerGlyGlyLeuAlaCysAlaLysGluAlaAlaGlnLeuGlyArgLysValAlaVal : 67 ! !!|||! !! !||| ! ||| ! !! !|||:!!||||||!.! :!! !..! HisArgGlyValGlnAlaGlyAlaLeuGlyAspAlaGluLeuGlyHisLeuLeuArgThr 70870 : CACCGTGGGGTCCAGGCCGGAGCGCTTGGAGATGCGGAGCTTGGCCACCTCCTCCGCACA : 70811 68 : {V} >>>> Target Intron 4 >>>> {al}AspTyrValGluProSerProGln : 76 {!} 14958 bp {.!}! :!!..!! ! ! !! !!!:: {A}++ ++{la}AlaHisThrAlaGlyProAlaArg 70810 : {G}gt.........................ag{CC}GCGCACACCGCGGGCCCAGCACGT : 55826 77 : GlyThrArgTrpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLys > : 96 ||| !!:! ! |||! !!.!||| !!|||!.!...!.!..!||| !||| :!! GlyGlnGlnGlyGlyHisAlaGlyProCysAlaArgAlaSerCysAlaProAlaGln+- 55825 : GGTCAGCAGGGCGGCCACGCGGGGCCCTGCGCCCGAGCTTCCTGTGCCCCGGCCCAGgc. : 55764 97 : >>> Target Intron 5 >>>> LeuMetHisGlnAlaAlaLeuLeu{G} >>>> : 104 11882 bp ! !:!:|||:!!|||:!!! !|||{|} ++SerLeuHisGluAlaSerTrpLeu{G}++ 55763 : ........................agTCTTTACATGAGGCCTCGTGGCTG{G}gt..... : 43857 105 : Target Intron 6 >>>> {ly}GlyLeuIleGlnAspAlaProAsnTyrGly{T} : 115 19285 bp {||}||| ! !::!||||||||| ! !.!{ } ++{ly}GlyThrGlyArgAspAlaProProArgAla{G}+ 43856 : ....................ag{GA}GGGACAGGTAGAGACGCACCACCTCGGGCT{G}g : 24541 116 : >>>> Target Intron 7 >>>> {rp}GluValAlaGlnProValProHisAspT : 125 8234 bp {! }...:!!::! |||! ! !||| !! + ++{ly}SerLeuSerThrProGlyValHisHisG 24540 : t.........................ag{GC}TCCCTCAGCACCCCTGGCGTCCACCACG : 16278 126 : rpArgLysMetAla{Gl} >>>> Target Intron 8 >>>> {u}AlaValGlnA : 134 !!..! ! !::!{..} 7245 bp {!}|||! !|||! lyGluGlyArgSer{Ar}++ ++{g}AlaGlyGlnT 16277 : GGGAAGGTAGGAGC{CG}gt.........................ag{G}GCTGGCCAAA : 9006 135 : snHisValLysSerLeuAsnTrpGlyHisArgValGln : 146 .!!..:!!:!!!.!! !|||!! ||| !!||||||||| hrArgLeuGlnLysSerAsnCysGlyAspArgValGln 9005 : CCCGGCTCCAGAAATCAAACTGTGGGGACAGAGTCCAG : 8968 vulgar: SPP00000035_1.0 0 146 . NIVO01019577.1:subseq(189524,120883) 87354 8967 - 101 M 11 33 S 0 2 5 0 2 I 0 12300 3 0 2 S 1 1 M 1 3 S 0 2 5 0 2 I 0 1208 3 0 2 S 1 1 M 13 39 S 0 1 5 0 2 I 0 2825 3 0 2 S 1 2 M 39 117 S 0 1 5 0 2 I 0 14954 3 0 2 S 1 2 M 27 81 5 0 2 I 0 11878 3 0 2 M 8 24 S 0 1 5 0 2 I 0 19281 3 0 2 S 1 2 M 10 30 S 0 1 5 0 2 I 0 8230 3 0 2 S 1 2 M 14 42 S 0 2 5 0 2 I 0 7241 3 0 2 S 1 1 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 # NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local gene 8968 87354 101 - . gene_id 1 ; sequence SPP00000035_1.0 ; gene_orientation + NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 87320 87354 . - . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 87320 87354 . - . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 87318 87319 . - . intron_id 1 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 75016 87319 . - . intron_id 1 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 75016 75017 . - . intron_id 0 ; splice_site "ac" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 75010 75015 . - . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 75010 75015 . - . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 75008 75009 . - . intron_id 2 ; splice_site "gt" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 73798 75009 . - . intron_id 2 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 73798 73799 . - . intron_id 1 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 73757 73797 . - . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 73757 73797 . - . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 73755 73756 . - . intron_id 3 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 70928 73756 . - . intron_id 3 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 70928 70929 . - . intron_id 2 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 70808 70927 . - . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 70808 70927 . - . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 70806 70807 . - . intron_id 4 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 55850 70807 . - . intron_id 4 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 55850 55851 . - . intron_id 3 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 55767 55849 . - . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 55767 55849 . - . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 55765 55766 . - . intron_id 5 ; splice_site "GC" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 43885 55766 . - . intron_id 5 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 43885 43886 . - . intron_id 4 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 43860 43884 . - . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 43860 43884 . - . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 43858 43859 . - . intron_id 6 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 24575 43859 . - . intron_id 6 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 24575 24576 . - . intron_id 5 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 24542 24574 . - . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 24542 24574 . - . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 24540 24541 . - . intron_id 7 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 16308 24541 . - . intron_id 7 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 16308 16309 . - . intron_id 6 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 16262 16307 . - . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 16262 16307 . - . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice5 16260 16261 . - . intron_id 8 ; splice_site "GT" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local intron 9017 16261 . - . intron_id 8 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local splice3 9017 9018 . - . intron_id 7 ; splice_site "AG" NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local cds 8968 9016 . - . NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local exon 8968 9016 . - . insertions 0 ; deletions 0 NIVO01019577.1:subseq(189524,120883) exonerate:protein2genome:local similarity 8968 87354 101 - . alignment_id 1 ; Query SPP00000035_1.0 ; Align 87355 1 33 ; Align 75015 13 3 ; Align 73797 15 39 ; Align 70926 29 117 ; Align 55848 69 81 ; Align 43885 96 24 ; Align 24573 105 30 ; Align 16306 116 42 ; Align 9016 131 48 # --- END OF GFF DUMP --- # -- completed exonerate analysis