Command line: [exonerate -m p2g --showtargetgff -q SEPSECS.fa -t SEPSECS.subseq] Hostname: [ws101098U] C4 Alignment: ------------ Query: SPP00002945_2.0 # Protein # Sep (O-phosphoserine) tRNA:Sec tRNA synthase (SEPSECS) # Human Target: JSZB01003377.1:subseq(0,75891) Manis javanica isolate MP_PG03-UM SCAFFOLD3793, whole genome shotgun sequence Model: protein2genome:local Raw score: 2349 Query range: 0 -> 501 Target range: 34854 -> 66215 1 : MetAsnArgGluSerPheAlaAlaGlyGluArgLeuValSerProAlaTyrValArgGln : 20 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MetAsnArgGluSerPheAlaAlaGlyGluArgLeuValSerProAlaTyrValArgGln 34855 : ATGAACCGCGAGAGCTTTGCGGCAGGCGAGCGGCTGGTGTCGCCGGCTTACGTGCGGCAG : 34912 21 : GlyCysGluAlaArgArgSerHisGluHisLeuIleArgLeuLeuLeuGluLys >>>> : 39 |||||||||||||||||||||||||||||||||||||||||||||||||||||| GlyCysGluAlaArgArgSerHisGluHisLeuIleArgLeuLeuLeuGluLys++ 34913 : GGCTGTGAGGCCCGCCGCTCGCATGAGCACCTCATACGGCTGCTTCTGGAGAAGgt.... : 34971 40 : Target Intron 1 >>>> GlyLysCysProGluAsnGlyTrpAspGluSerThrL : 51 796 bp |||||||||||||||:!!||||||||||||||||||| ++GlyLysCysProGluAspGlyTrpAspGluSerThrL 34972 : .....................agggcaagTGTCCTGAGGATGGCTGGGATGAAAGTACAC : 35801 52 : euGluLeuPheLeuHisGluLeuAlaIleMetAspSerAsnAsnPheLeuGlyAsnCysG : 71 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| euGluLeuPheLeuHisGluLeuAlaIleMetAspSerAsnAsnPheLeuGlyAsnCysG 35802 : TTGAACTCTTTCTACATGAACTTGCAATTATGGATAGCAACAATTTCCTGGGCAATTGtg : 35861 72 : lyValGlyGluArgGluGlyArgValAlaSerAlaLeuValAlaArgArgHisTyr{Ar} : 90 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||{||} lyValGlyGluArgGluGlyArgValAlaSerAlaLeuValAlaArgArgHisTyr{Ar} 35862 : gtgtgggagaaagggaaggaagagtgGCATCTGCTTTAGTTGCTCGGCGTCATtac{ag} : 35918 91 : >>>> Target Intron 2 >>>> {g}PheIleHisGlyIleGlyArgSerGlyA : 100 2044 bp {|}|||||||||||||||||||||||||||| ++ ++{g}PheIleHisGlyIleGlyArgSerGlyA 35919 : gt.........................ag{g}tTCATTCATGGAATTGGACGATCTGGTG : 37992 101 : spIleSerAlaValGlnProLysAlaAlaGlySerSerLeuLeuAsnLysIleThrAsnS : 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| spIleSerAlaValGlnProLysAlaAlaGlySerSerLeuLeuAsnLysIleThrAsnS 37993 : ATATTTCTGCTGTGCAACCAAAAGCTGCAGGTTCTAGTCTTTTGAACAAAATTACCAATT : 38052 121 : erLeuValLeuAspIleIleLysLeuAla{G} >>>> Target Intron 3 >>>> : 130 |||||||||||||||||||||||||||||{|} 357 bp erLeuValLeuAspIleIleLysLeuAla{G}++ + 38053 : CTTTGGTCCTGGACATCATAAAGTTGGCT{G}gt.........................a : 38438 131 : {ly}ValHisThrValAlaAsnCysPheValValProMetAlaThrGlyMetSerLeuT : 149 {||}||||||||||||.!!|||||||||||||||||||||||||||||||||||||||| +{ly}ValHisThrValThrAsnCysPheValValProMetAlaThrGlyMetSerLeuT 38439 : g{GT}GTCCATACAGTGACCAACTGCTTTGTAGTTCCAATGGCAACTGGTATGAGTCTAA : 38496 150 : hrLeuCysPheLeuThrLeuArgHisLysArgProLysAlaLysTyrIleIleTrpProA : 169 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| hrLeuCysPheLeuThrLeuArgHisLysArgProLysAlaLysTyrIleIleTrpProA 38497 : CCCTGTGTTTCTTAACATTACGACACAAAAGACCAAAGGCAAAATATATTATATGGCCAC : 38556 170 : rgIleAspGlnLysSerCysPheLysSerMetIleThrAla{G} >>>> Target In : 183 |||||||||||||||||||||||||||||||||||||||||{|} 2466 rgIleAspGlnLysSerCysPheLysSerMetIleThrAla{G}++ 38557 : GAATAGACCAGAAGTCCTGCTTTAAATCCATGATCACTGCA{G}gt.............. : 38601 184 : tron 4 >>>> {ly}PheGluProValValIleGluAsnValLeuGluGlyAspGluL : 198 bp {||}||||||||||||||||||||||||||||||||||||||||||| ++{ly}PheGluProValValIleGluAsnValLeuGluGlyAspGluL 38602 : ...........ag{GT}TTTGAGCCTGTGGTGATAGAGAACGTTTTAGAAGGTGATGAGC : 41109 199 : euArgThrAspLeuLysAlaValGluAlaLysValGlnGluLeuGlyProAspCysIleL : 218 |||||||||||||||||||||||||||||||||||||||||||||||||||||! !:!!| euArgThrAspLeuLysAlaValGluAlaLysValGlnGluLeuGlyProAspTyrValL 41110 : TGCGCACAGACCTGAAAGCGGTGGAGGCTAAAGTCCAGGAACTTGGGCCTGATTATGTTC : 41169 219 : euCysIleHisSerThrThrSerCysPheAlaProArgValProAsp{Ar} >>>> Ta : 234 |||||:!!|||||||||||||||||||||||||||||||||||||||{||} euCysValHisSerThrThrSerCysPheAlaProArgValProAsp{Ar}++ 41170 : TGTGTGTTCATTCTACTACGTCCTGTTTTGCTCCAAGGGTGCCTGAC{AG}gt....... : 41221 235 : rget Intron 5 >>>> {g}LeuGluGluLeuAlaValIleCysAlaAsnTyrAspI : 247 2975 bp {|}||||||||||||||||||||||||||||||||||||| ++{g}LeuGluGluLeuAlaValIleCysAlaAsnTyrAspI 41222 : ..................ag{A}TTAGAAGAACTGGCTGTGATTTGTGCTAATTATGATA : 44231 248 : leProHisIleValAsnAsnAlaTyrGlyValGlnSerSerLysCysMetHisLeuIleG : 267 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| leProHisIleValAsnAsnAlaTyrGlyValGlnSerSerLysCysMetHisLeuIleG 44232 : TCCCACATATAGTCAACAATGCTTATGGAGTGCAGTCTTCAAAGTGTATGCACCTCATTC : 44291 268 : lnGln >>>> Target Intron 6 >>>> GlyAlaArgValGlyArgIleAspAl : 277 ||||| 9086 bp |||||||||||||||||||||||||| lnGln++ ++GlyAlaArgValGlyArgIleAspAl 44292 : AGCAGgt.........................agGGGGCACGGGTTGGAAGAATAGATGC : 53407 278 : aPheValGlnSerLeuAspLysAsnPheMetValProValGlyGlyAlaIleIleAlaGl : 297 ||||:!!||||||||||||||||||||||||||||||||||||||||||||||||||||| aPheIleGlnSerLeuAspLysAsnPheMetValProValGlyGlyAlaIleIleAlaGl 53408 : TTTCATTCAGAGCTTGGACAAAAATTTTATGGTTCCAGTAGGTGGTGCTATAATTGCTGG : 53467 298 : yPheAsnAspSerPheIleGlnGluIleSerLysMetTyrPro{G} >>>> Target : 312 |||||||||||||||||||||||||||||||||||||||||||{|} 13 yPheAsnAspSerPheIleGlnGluIleSerLysMetTyrPro{G}++ 53468 : CTTTAATGATTCCTTCATTCAAGAAATCAGCAAGATGTATCCA{G}gt............ : 53515 313 : Intron 7 >>>> {ly}ArgAlaSerAlaSerProSerLeuAspValLeuIleThrLe : 326 2 bp {||}||||||||||||||||||||||||||||||||||||||||| ++{ly}ArgAlaSerAlaSerProSerLeuAspValLeuIleThrLe 53516 : .............ag{GA}AGAGCTTCAGCTTCCCCTTCTTTAGATGTTCTTATTACTTT : 53686 327 : uLeuSerLeuGlySerAsnGlyTyrLysLysLeuLeuLysGluArgLys >>>> Targ : 343 ||||||||||||||||||||||||||||||||||||||||||||||||| uLeuSerLeuGlySerAsnGlyTyrLysLysLeuLeuLysGluArgLys++ 53687 : ATTATCACTTGGATCAAATGGCTATAAGAagctattaaaagaaagaaaggt......... : 53739 344 : et Intron 8 >>>> GluMetPheSerTyrLeuSerAsnGlnIleLysLysLeuSer : 356 8946 bp |||||||||||||||||||||||||||:!!|||||||||||| ++GluMetPheSerTyrLeuSerAsnGlnLeuLysLysLeuSer 53740 : ................agGAAATGTTTTCGTATTTGTCCAACCAGCTAAAGAAGCTGTCA : 62722 357 : GluAlaTyrAsnGluArgLeuLeuHisThrProHisAsnProIleSerLeu{A} >>>> : 374 |||.!!|||!:!|||||||||||||||||||||||||||||||||||||||{|} GluThrTyrSerGluArgLeuLeuHisThrProHisAsnProIleSerLeu{A}++ 62723 : GAAACCTACAGTGAAAGACTGTTGCATACACCTCACAATCCTATATcttta{g}gt.... : 62779 375 : Target Intron 9 >>>> {la}MetThrLeuLysThrLeuAspGluHisArgAsp : 385 1673 bp {||}:!!||||||! !||||||||||||!!. !!||| ++{la}ValThrLeuThrThrLeuAspGluGlnCysAsp 62780 : .....................ag{ct}GTGACACTTACGACACTAGATGAACAGTGTGAC : 64482 386 : LysAlaValThrGlnLeuGlySerMetLeuPheThrArgGlnValSerGlyAla{Ar} : 404 ||||||||||||||||||||||||||||||||||||||||||||||||||||||{||} LysAlaValThrGlnLeuGlySerMetLeuPheThrArgGlnValSerGlyAla{Ar}++ 64483 : AAAGCTGTCACTCAGCTTGGCTCAATGCTTTTTACCAGACAGGTTTCTGGAGCC{AG}gt : 64541 405 : >>>> Target Intron 10 >>>> {g}ValValProLeuGlySerMetGlnThrVa : 414 1371 bp {|}||||||||||||||||||:!!|||||||| ++{g}ValValProLeuGlySerValGlnThrVa 64542 : ..........................ag{G}GTTGTGCCACTTGGGTCTGTGCAAACCGT : 65940 415 : lSerGlyTyrThrPheArgGlyPheMetSerHisThrAsnAsnTyrProCysAlaTyrLe : 434 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| lSerGlyTyrThrPheArgGlyPheMetSerHisThrAsnAsnTyrProCysAlaTyrLe 65941 : GAGTGGCTACACTTTCAGAGGCTTTATGTCACATACAAATAATTACCCTTGTGCTTACCT : 66000 435 : uAsnAlaAlaSerAlaIleGlyMetLysMetGlnAspValAspLeuPheIleLysArgLe : 454 ||||||||||||||||||||||||||||!!:||||||||||||||||||||||||||||| uAsnAlaAlaSerAlaIleGlyMetLysIleGlnAspValAspLeuPheIleLysArgLe 66001 : CAATGCTGCCTCAGCCATTGGAATGAAGATCCAGGATGTGGACTTGTTCATAAAGAGACT : 66060 455 : uAspArgCysLeuLysAlaValArgLysGluArgSerLysGluSerAsp<-><-><-><- : 471 ||||!:!|||||||||.!.||||||||||||::::::|||||||||||| uAspLysCysLeuLysThrValArgLysGluGlnAsnLysGluSerAspValSerGlyIl 66061 : TGACAAATGTTTAAAGACagtaagaaaagaacaaaataaagagagTGATGTGTCCGGAAT : 66120 472 : >AspAsnTyrAspLysThrGluAspValAspIleGluGluMetAlaLeuLysLeuAspAs : 490 ! !||||||||||||||||||||||||:!!||||||||||||||||||||||||||||| eGlyAsnTyrAspLysThrGluAspValAsnIleGluGluMetAlaLeuLysLeuAspAs 66121 : TGGCAATTACGACAAAACTGAAGATGTGAATATTGAAGAAATGGCTTTAAAACTAGATAA : 66180 491 : nValLeuLeuAspThrTyrGlnAspAlaSerSer : 501 |||||||||||||||| !!|||:!!:!!|||||| nValLeuLeuAspThrAsnGlnAsnSerSerSer 66181 : TGTGCTTCTTGACACAAACCAGAATTCTTCTTCA : 66215 vulgar: SPP00002945_2.0 0 501 . JSZB01003377.1:subseq(0,75891) 34854 66215 + 2349 M 38 114 5 0 2 I 0 792 3 0 2 M 51 153 S 0 2 5 0 2 I 0 2040 3 0 2 S 1 1 M 39 117 S 0 1 5 0 2 I 0 353 3 0 2 S 1 2 M 52 156 S 0 1 5 0 2 I 0 2462 3 0 2 S 1 2 M 50 150 S 0 2 5 0 2 I 0 2971 3 0 2 S 1 1 M 34 102 5 0 2 I 0 9082 3 0 2 M 43 129 S 0 1 5 0 2 I 0 128 3 0 2 S 1 2 M 30 90 5 0 2 I 0 8942 3 0 2 M 31 93 S 0 1 5 0 2 I 0 1669 3 0 2 S 1 2 M 29 87 S 0 2 5 0 2 I 0 1367 3 0 2 S 1 1 M 66 198 G 0 12 M 31 93 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-09 ##type DNA # # # seqname source feature start end score strand frame attributes # JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local gene 34855 66215 2349 + . gene_id 1 ; sequence SPP00002945_2.0 ; gene_orientation + JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local cds 34855 34968 . + . JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local exon 34855 34968 . + . insertions 0 ; deletions 0 JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local splice5 34969 34970 . + . intron_id 1 ; splice_site "GT" JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local intron 34969 35764 . + . intron_id 1 JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local splice3 35763 35764 . + . intron_id 0 ; splice_site "ag" JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local cds 35765 35919 . + . JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local exon 35765 35919 . + . insertions 0 ; deletions 0 JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local splice5 35920 35921 . + . intron_id 2 ; splice_site "gt" JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local intron 35920 37963 . + . intron_id 2 JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local splice3 37962 37963 . + . intron_id 1 ; splice_site "ag" JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local cds 37964 38082 . + . JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local exon 37964 38082 . + . insertions 0 ; deletions 0 JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local splice5 38083 38084 . + . intron_id 3 ; splice_site "GT" JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local intron 38083 38439 . + . intron_id 3 JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local splice3 38438 38439 . + . intron_id 2 ; splice_site "ag" JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local cds 38440 38598 . + . JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local exon 38440 38598 . + . insertions 0 ; deletions 0 JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local splice5 38599 38600 . + . intron_id 4 ; splice_site "GT" JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local intron 38599 41064 . + . intron_id 4 JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local splice3 41063 41064 . + . intron_id 3 ; splice_site "AG" JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local cds 41065 41218 . + . JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local exon 41065 41218 . + . insertions 0 ; deletions 0 JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local splice5 41219 41220 . + . intron_id 5 ; splice_site "GT" JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local intron 41219 44193 . + . intron_id 5 JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local splice3 44192 44193 . + . intron_id 4 ; splice_site "AG" JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local cds 44194 44296 . + . JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local exon 44194 44296 . + . insertions 0 ; deletions 0 JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local splice5 44297 44298 . + . intron_id 6 ; splice_site "GT" JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local intron 44297 53382 . + . intron_id 6 JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local splice3 53381 53382 . + . intron_id 5 ; splice_site "AG" JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local cds 53383 53512 . + . JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local exon 53383 53512 . + . insertions 0 ; deletions 0 JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local splice5 53513 53514 . + . intron_id 7 ; splice_site "GT" JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local intron 53513 53644 . + . intron_id 7 JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local splice3 53643 53644 . + . intron_id 6 ; splice_site "AG" JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local cds 53645 53736 . + . JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local exon 53645 53736 . + . insertions 0 ; deletions 0 JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local splice5 53737 53738 . + . intron_id 8 ; splice_site "gt" JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local intron 53737 62682 . + . intron_id 8 JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local splice3 62681 62682 . + . intron_id 7 ; splice_site "AG" JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local cds 62683 62776 . + . JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local exon 62683 62776 . + . insertions 0 ; deletions 0 JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local splice5 62777 62778 . + . intron_id 9 ; splice_site "gt" JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local intron 62777 64449 . + . intron_id 9 JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local splice3 64448 64449 . + . intron_id 8 ; splice_site "ag" JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local cds 64450 64540 . + . JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local exon 64450 64540 . + . insertions 0 ; deletions 0 JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local splice5 64541 64542 . + . intron_id 10 ; splice_site "GT" JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local intron 64541 65911 . + . intron_id 10 JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local splice3 65910 65911 . + . intron_id 9 ; splice_site "AG" JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local cds 65912 66215 . + . JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local exon 65912 66215 . + . insertions 12 ; deletions 0 JSZB01003377.1:subseq(0,75891) exonerate:protein2genome:local similarity 34855 66215 2349 + . alignment_id 1 ; Query SPP00002945_2.0 ; Align 34855 1 114 ; Align 35765 39 153 ; Align 37965 91 117 ; Align 38442 131 156 ; Align 41067 184 150 ; Align 44195 235 102 ; Align 53383 269 129 ; Align 53647 313 90 ; Align 62683 343 93 ; Align 64452 375 87 ; Align 65913 405 198 ; Align 66123 471 93 # --- END OF GFF DUMP --- # -- completed exonerate analysis