Command line: [exonerate -m p2g --showtargetgff -q SELENON.fa -t genomic.fa] Hostname: [ws101074U] C4 Alignment: ------------ Query: SPP00000639_2.0 # Protein # Selenoprotein N (SELENON) # Zebrafish Target: CM004422.1:subseq(27130000,150000) Ictalurus punctatus breed USDA103 chromosome 9, whole genome shotgun sequence Model: protein2genome:local Raw score: 2089 Query range: 58 -> 557 Target range: 7327 -> 14662 59 : PheValLysArgHisGluAlaGlyLeuLysAlaLeuGlyAlaAspGlyLeuPhePhePhe : 78 |||:!! !!!.||||||!.!||||||.!!|||||||||!!:|||||||||.!!||| PheLeuPhePheGlnGluAlaAlaLeuLysThrLeuGlyAlaGluGlyLeuPheLeuPhe 7328 : TTCCTGTTTTTCCAGGAAGCGGCGCTGAAGACCCTAGGAGCAGAAGGACTTTTCCTCTTC : 7385 79 : SerSerLeuAspThrAspHisAspLeuTyrLeuSerProGluGluPheLysProIleAla : 98 ||||||||||||..!|||||||||||||||||||||||||||||||||||||||:!!||| SerSerLeuAspValAspHisAspLeuTyrLeuSerProGluGluPheLysProValAla 7386 : TCGTCTCTGGATGTAGATCACGACCTCTACCTCAGTCCCGAGGAGTTTAAACCCGTCGCC : 7445 99 : GluLysLeuThr{G} >>>> Target Intron 1 >>>> {ly}ValAlaProPro : 107 ||||||||||||{|} 122 bp {||}|||||||||||| GluLysLeuThr{G}++ ++{ly}ValAlaProPro 7446 : GAAAAGCTCACA{G}gt.........................ag{GC}GTCGCTCCTCCT : 7594 108 : ProGluTyrGluGluGluIleProHisAspProAsnGlyGluThrLeuThrLeuHisAla : 127 !!|||!:!|||||||||.!! ! !|||||||||||||||! !||||||||||||||| AlaGluPheGluGluGluPheValSerAspProAsnGlyGluLysLeuThrLeuHisAla 7595 : GCGGAGTTCGAAGAGGAGTTCGTCTCTGACCCGAACGGAGAGAAGCTCACGCTTCACGCG : 7654 128 : LysMetGlnProLeuLeuLeuGluSerMetThrLysSerLysAspGlyPheLeuGly > : 147 |||||||||||||||||||||!!!|||||||||||||||||||||||||||||| AlaMetGlnProLeuLeuLeuGluThrMetThrLysSerLysAspGlyPheLeuGly++ 7655 : GCCATGCAACCGCTCCTGCTCGAGACCATGACCAAGAGCAAGGACGGCTTTCTCGGGgt. : 7716 148 : >>> Target Intron 2 >>>> ValSerHisSerSerLeuSerGlyLeuArgSerT : 158 293 bp |||||||||.!!:!!||||||||||||||||||| ++ValSerHisGlyAlaLeuSerGlyLeuArgSerT 7717 : ........................agGTTTCCCATGGTGCTCTGAGTGGGCTGCGTTCAT : 8040 159 : rpLysArgProAlaIleSerSerSerThrPheTyrAlaSerGlnPheLysValPheLeuP : 178 ||||||||||||||:!! !!||||||!:!|||! |||!!!||||||::!:!!||||||| rpLysArgProAlaValProSerSerSerPheSerAlaThrGlnPheArgIlePheLeuP 8041 : GGAAGCGTCCCGCTGTTCCGTCCTCCAGCTTCTCGGCTACTCAGTTCCGGATCTTTCTGC : 8100 179 : roProSerGlyLysSerAlaValGlyAspThrTrpTrpIleIleProSerGluLeuAsnI : 198 |||||!.!||||||.!!! ! !||||||||||||||||||||||||||||||||||||| roProLysGlyLysGlyGluProGlyAspThrTrpTrpIleIleProSerGluLeuAsnI 8101 : CCCCGAAGGGTAAAGGGGAGCCGGGGGACACGTGGTGGATCATACCGAGTGAGCTCAACA : 8160 199 : lePheThrGlyTyrLeuProAsnAsnArgPheHisProProThrProArgGlyLysGlu : 218 |||||||||||||||||||||||!.!|||!:!||||||||||||||||||||||||||| lePheThrGlyTyrLeuProAsnThrArgTyrHisProProThrProArgGlyLysGlu+ 8161 : TCTTCACTGGATATCTGCCCAACACTCGGTACCACCCGCCCACCCCTCGGGGCAAAGAGg : 8220 219 : >>>> Target Intron 3 >>>> ValLeuIleHisSerLeuLeuSerMetPheHi : 228 1659 bp ||||||||||||!!!||||||||||||||||| + ++ValLeuIleHisThrLeuLeuSerMetPheHi 8221 : t.........................agGTTCTGATCCACACCCTGCTCAGCATGTTTCA : 9909 229 : sProArgProPheValLysSerArgPheAlaProGlnGlyAlaValAlaCysIleArgAl : 248 |||||||||||||:!!|||||||||||||||||||||||||||||||||||||||||||| sProArgProPheIleLysSerArgPheAlaProGlnGlyAlaValAlaCysIleArgAl 9910 : TCCTCGCCCGTTCATCAAATCCCGCTTCGCTCCTCAGGGAGCCGTGGCCTGTATCCGAGC : 9969 249 : aThrSerAspPheTyrTyrAspIleValPhe{Ar} >>>> Target Intron 4 >> : 259 |..!.!!|||||||||||||||:!!||||||{||} 690 bp aValGlyAspPheTyrTyrAspValValPhe{Ar}++ 9970 : CGTCGGCGACTTCTACTATGACGTCGTGTTC{AG}gt....................... : 10006 260 : >> {g}IleHisAlaGluPheGlnLeuAsnAspValProAspPheProPheTrpPheTh : 277 {|}||||||||||||||||||||||||||||||||||||||||||||||||||||| ++{g}IleHisAlaGluPheGlnLeuAsnAspValProAspPheProPheTrpPheTh 10007 : ..ag{G}ATACACGCAGAGTTCCAGCTGAACGACGTTCCCGATTTCCCGTTCTGGTTCAC : 10746 278 : rProGlyGlnPheAlaGlyHisIleIleLeuSerLysAspAlaSerHisValArgAspPh : 297 ||||||||||||||||||||||:!!:!:||||||!:!||||||||||||||||||||||| rProGlyGlnPheAlaGlyHisValValLeuSerArgAspAlaSerHisValArgAspPh 10747 : ACCCGGTCAGTTCGCCGGCCACGTCGTGCTCTCCAGAGATGCATCTCATGTCCGAGACTT : 10806 298 : eHisIleTyrValProAsnAsp{Ly} >>>> Target Intron 5 >>>> {s}Th : 306 ||||:!:|||||||||||||||{||} 203 bp {|}:! eHisLeuTyrValProAsnAsp{Ly}++ ++{s}Se 10807 : CCATCTGTATGTCCCTAATGAC{AA}gt.........................ag{G}TC : 11036 307 : rLeuAsnValAspMetGluTrpLeuTyrGlyAlaSerGluThrSerAsnMetGluValAs : 326 !|||||||||||||||||||||||||||||||||||||||!:!|||!:!||||||||||| rLeuAsnValAspMetGluTrpLeuTyrGlyAlaSerGluSerSerSerMetGluValAs 11037 : TCTGAATGTTGATATGGAGTGGCTGTACGGTGCCAGCGAGAGCAGCAGCATGGAAGTTGA : 11096 327 : pIleGlyTyrLeuProGln >>>> Target Intron 6 >>>> MetGluLeuGly : 336 ||||||||||||||||||| 340 bp ||||||||| !! pIleGlyTyrLeuProGln++ ++MetGluLeuArg 11097 : CATCGGCTACCTGCCACAGgt.........................agATGGAGTTGCGA : 11466 337 : AlaGluGlyProSerThrProSerValIleTyrAspGluGlnGlyAsnMetIleAspSer : 356 |||! |||||||||||||||||||||||||||||||||||||||!!. !||||||!!! AlaAlaGlyProSerThrProSerValIleTyrAspGluGlnGlyLysAlaIleAspThr 11467 : GCGGCCGGTCCGTCCACGCCCTCCGTGATCTACGACGAGCAGGGGAAGGCGATCGACACC : 11526 357 : ArgGlyGluGlyGlyGluProIleGlnPheValPheGluGluIleValTrpSerGluGlu : 376 |||!.!||||||||||||||||||!!.|||||||||||||||||| !||||||...||| ArgAlaGluGlyGlyGluProIleHisPheValPheGluGluIleArgTrpSerSerGlu 11527 : CGGGCGGAGGGAGGAGAACCCATCCACTTTGTGTTCGAGGAGATCCGCTGGAGCTCCGAG : 11586 377 : LeuLysArgGluGluAlaSerArgArgLeuGluValThrMetTyrProPheLysLys > : 396 :!!!..|||!!:||||||:!! !!|||||||||||||||.!.||||||||||||||| IleSerArgAspGluAlaAlaGlyArgLeuGluValThrPheTyrProPheLysLys++ 11587 : ATCAGCCGGGACGAGGCAGCCGGTCGTCTCGAGGTCACCTTTTATCCTTTCAAAAAGgt. : 11648 397 : >>> Target Intron 7 >>>> ValProTyrLeuProPheSerGluAlaPheSerA : 407 78 bp ||| !!|||||||||||| !!||||||||||||| ++ValAlaTyrLeuProPheProGluAlaPheSerA 11649 : ........................agGTGGCATACCTGCCTTTCCCGGAAGCCTTCAGCA : 11757 408 : rgAlaSerAlaGluLysLysLeuValHisSerIleLeuLeuTrpGlyAlaLeuAspAspG : 427 |||||..!|||||| !|||||||||||||||:!!||||||||||||||||||||||||| rgAlaGluAlaGluGlyLysLeuValHisSerValLeuLeuTrpGlyAlaLeuAspAspG 11758 : GGGCAGAAGCAGAGGGGAAACTGGTCCACTCCGTCCTGCTCTGGGGAGCGCTGGACGATC : 11817 428 : lnSerCysUnk{G} >>>> Target Intron 8 >>>> {ly}SerGlyArgThrL : 436 |||||||| {|} 675 bp {||}||||||||||||| lnSerCys***{G}++ ++{ly}SerGlyArgThrL 11818 : AGTCCTGCTGA{G}gt.........................ag{gt}tcgGGGCGAACTC : 12519 437 : euArgGluThrValLeuGluSerSerProValLeuAlaLeuLeuAsnGlnSerPheIleS : 456 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| euArgGluThrValLeuGluSerSerProValLeuAlaLeuLeuAsnGlnSerPheIleS 12520 : TCCGGGAGACCGTCCTGGAAAGTTCGCCCGTCCTGGCCTTGCTCAACCAGAGCTTCATCA : 12579 457 : erSerTrpSerLeuValLysGluLeuGluAspLeuGln >>>> Target Intron 9 : 469 |||||||||||||||||||||||||||||||||||||| 913 bp erSerTrpSerLeuValLysGluLeuGluAspLeuGln++ 12580 : GCAGCTGGTCTCTCGTCAAAGAGCTGGAGGACCTGCAGgt.................... : 12620 470 : >>>> GlyAspValLysAsnLeuGluLeuSerGluLysAlaArgLeuHisLeuGluLy : 486 ! !|||! !:!!||||||!!:||||||:!!|||||||||||||||||||||:: ++ValAspGluGluAsnLeuAspLeuSerGlnLysAlaArgLeuHisLeuGluAr 12621 : .....agGTCGACGAGGAGAATCTGGACTTGAGTCAGAAGGCGCGTTTACACCTGGAGCG : 13582 487 : sTyrThrPheProValGlnMetMetValValLeuProAsnGlyThrVal >>>> Targ : 503 !|||!:!|||||||||:!!|||||||||!.!|||||||||||||||||| gTyrSerPheProValGluMetMetValAlaLeuProAsnGlyThrVal++ 13583 : GTACAGCTTCCCTGTGGAGATGATGGTGGCGTTGCCTAACGGGACCGTGgt......... : 13635 504 : et Intron 10 >>>> ValHisHisIleAsnAlaAsnAsnPheLeuAspGlnThrSe : 516 865 bp ||||||||||||||||||||||||||||||||||||||||| ++ValHisHisIleAsnAlaAsnAsnPheLeuAspGlnThrSe 13636 : .................agGTTCACCACATCAACGCTAACAACTTCCTGGACCAGACGTC : 14537 517 : rMetLysProGluAspGluGlyProGlyLeuSerPheSerAlaGlyPheGluAspProSe : 536 |||||||||||||!!:!!:! ! !!|||!!!.!!||||||!.!||||||||||||||||| rMetLysProGluGluAspValSerGlyPheGlyPheSerGlyGlyPheGluAspProSe 14538 : CATGAAGCCGGAGGAGGACGTGTCGGGGTTCGGCTTCTCGGGCGGGTTCGAGGACCCGTC : 14597 537 : rThrSerThrTyrIleArgPheLeuGlnGluGlyLeuGluLysAlaLysProTyrLeuGl : 556 |||||||.!!|||:!!|||||||||||||||||||||!!:||||||||| !!||||||:! rThrSerAlaTyrValArgPheLeuGlnGluGlyLeuAspLysAlaLysAlaTyrLeuGl 14598 : TACCTCCGCGTACGTCCGCTTCCTGCAGGAGGGACTGGACAAGGCCAAGGCTTACCTCCA : 14657 557 : uSer : 557 !||| nSer 14658 : Gtcg : 14662 vulgar: SPP00000639_2.0 58 557 . CM004422.1:subseq(27130000,150000) 7327 14662 + 2089 M 44 132 S 0 1 5 0 2 I 0 118 3 0 2 S 1 2 M 43 129 5 0 2 I 0 289 3 0 2 M 71 213 5 0 2 I 0 1655 3 0 2 M 41 123 S 0 2 5 0 2 I 0 686 3 0 2 S 1 1 M 45 135 S 0 2 5 0 2 I 0 199 3 0 2 S 1 1 M 27 81 5 0 2 I 0 336 3 0 2 M 63 189 5 0 2 I 0 74 3 0 2 M 35 105 S 0 1 5 0 2 I 0 671 3 0 2 S 1 2 M 37 111 5 0 2 I 0 909 3 0 2 M 34 102 5 0 2 I 0 861 3 0 2 M 55 165 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-25 ##type DNA # # # seqname source feature start end score strand frame attributes # CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local gene 7328 14662 2089 + . gene_id 1 ; sequence SPP00000639_2.0 ; gene_orientation + CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local cds 7328 7460 . + . CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local exon 7328 7460 . + . insertions 0 ; deletions 0 CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local splice5 7461 7462 . + . intron_id 1 ; splice_site "GT" CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local intron 7461 7582 . + . intron_id 1 CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local splice3 7581 7582 . + . intron_id 0 ; splice_site "AG" CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local cds 7583 7713 . + . CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local exon 7583 7713 . + . insertions 0 ; deletions 0 CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local splice5 7714 7715 . + . intron_id 2 ; splice_site "GT" CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local intron 7714 8006 . + . intron_id 2 CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local splice3 8005 8006 . + . intron_id 1 ; splice_site "AG" CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local cds 8007 8219 . + . CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local exon 8007 8219 . + . insertions 0 ; deletions 0 CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local splice5 8220 8221 . + . intron_id 3 ; splice_site "GT" CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local intron 8220 9878 . + . intron_id 3 CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local splice3 9877 9878 . + . intron_id 2 ; splice_site "AG" CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local cds 9879 10003 . + . CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local exon 9879 10003 . + . insertions 0 ; deletions 0 CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local splice5 10004 10005 . + . intron_id 4 ; splice_site "GT" CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local intron 10004 10693 . + . intron_id 4 CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local splice3 10692 10693 . + . intron_id 3 ; splice_site "AG" CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local cds 10694 10831 . + . CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local exon 10694 10831 . + . insertions 0 ; deletions 0 CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local splice5 10832 10833 . + . intron_id 5 ; splice_site "GT" CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local intron 10832 11034 . + . intron_id 5 CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local splice3 11033 11034 . + . intron_id 4 ; splice_site "AG" CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local cds 11035 11116 . + . CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local exon 11035 11116 . + . insertions 0 ; deletions 0 CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local splice5 11117 11118 . + . intron_id 6 ; splice_site "GT" CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local intron 11117 11456 . + . intron_id 6 CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local splice3 11455 11456 . + . intron_id 5 ; splice_site "AG" CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local cds 11457 11645 . + . CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local exon 11457 11645 . + . insertions 0 ; deletions 0 CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local splice5 11646 11647 . + . intron_id 7 ; splice_site "GT" CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local intron 11646 11723 . + . intron_id 7 CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local splice3 11722 11723 . + . intron_id 6 ; splice_site "AG" CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local cds 11724 11829 . + . CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local exon 11724 11829 . + . insertions 0 ; deletions 0 CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local splice5 11830 11831 . + . intron_id 8 ; splice_site "GT" CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local intron 11830 12504 . + . intron_id 8 CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local splice3 12503 12504 . + . intron_id 7 ; splice_site "ag" CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local cds 12505 12617 . + . CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local exon 12505 12617 . + . insertions 0 ; deletions 0 CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local splice5 12618 12619 . + . intron_id 9 ; splice_site "GT" CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local intron 12618 13530 . + . intron_id 9 CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local splice3 13529 13530 . + . intron_id 8 ; splice_site "AG" CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local cds 13531 13632 . + . CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local exon 13531 13632 . + . insertions 0 ; deletions 0 CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local splice5 13633 13634 . + . intron_id 10 ; splice_site "GT" CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local intron 13633 14497 . + . intron_id 10 CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local splice3 14496 14497 . + . intron_id 9 ; splice_site "AG" CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local cds 14498 14662 . + . CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local exon 14498 14662 . + . insertions 0 ; deletions 0 CM004422.1:subseq(27130000,150000) exonerate:protein2genome:local similarity 7328 14662 2089 + . alignment_id 1 ; Query SPP00000639_2.0 ; Align 7328 59 132 ; Align 7585 104 129 ; Align 8007 147 213 ; Align 9879 218 123 ; Align 10695 260 135 ; Align 11036 306 81 ; Align 11457 333 189 ; Align 11724 396 105 ; Align 12507 432 111 ; Align 13531 469 102 ; Align 14498 503 165 # --- END OF GFF DUMP --- # -- completed exonerate analysis