Command line: [exonerate -m p2g --showtargetgff -q lrp8_hs.aa.fa.txt -t genomelrp8_652.fa] Hostname: [ws101099u] C4 Alignment: ------------ Query: SPP00002936_2.0 # Protein # low density lipoprotein receptor-related protein 8 (LRP8) # Human Target: JXSJ01000652.1:subseq(10670,5330) Miichthys miiuy scaffold652, whole genome shotgun sequence Model: protein2genome:local Raw score: 1373 Query range: 83 -> 582 Target range: 410 -> 4398 84 : LysThrCysAlaAspSerAspPheThrCysAspAsnGlyHisCysIleHisGluArgTrpLy : 104 ||| !|||.!! !!!!!!:||| !|||..!!:!|||!!.|||:!: ... !!:: LysGlnCysThrThrThrGluPheArgCysSerSerGlyGlnCysValSerSerSerPheVa 411 : AAGCAGTGCACAACCACAGAGTTTCGCTGCAGCAGCGGCCAGTGCGTGTCGTCCTCCTTCGT : 471 105 : sCysAspGlyGluGluGluCysProAspGlySerAspGluSerGluAlaThrCysThrLysG : 125 !||||||! !|||! !!!:||| !|||||||||||| ||||||:!!||| !! lCysAspAspGluAlaAspCysAspAspGlySerAsp------GluAlaSerCysProProV 472 : GTGCGACGACGAGGCGGACTGTGACGACGGCAGCGAC------GAGGCCTCCTGCCCGCCTG : 528 126 : lnValCysProAlaGluLysLeuSerCysGlyProThrSerHisLysCysValProAlaSer : 145 ..!||| !!:!! !...!!!..!|||..! !||| ||||||||| ! ! alThrCysThrSerThrSerPheGlnCysAsnAsnThr------ValCysValProArgLeu 529 : TCACTTGCACCTCCACGTCCTTCCAGTGCAACAACACC------GTTTGCGTTCCGCGCCTG : 582 146 : TrpArgCysAspGlyGluLysAspCysGluGlyGlyAlaAspGluAlaGlyCysAlaThr{T : 166 ||| !||||||||||||!..|||||| ! !|||:!!|||||| ! ! ! !{ TrpValCysAspGlyGluSerAspCysThrAspGlySerAspGluTrpProGlnAsnCys{G 583 : TGGGTTTGCGACGGCGAAAGCGACTGCACCGACGGCTCGGATGAGTGGCCCCAGAACTGC{G : 645 167 : } >>>> Target Intron 1 >>>> {rp}LeuAsnGluCysLeuHisAsnAsnGlyG : 176 } 687 bp {! }! !||||||||||||:!!!:!||||||| }++ ++{ly}SerAsnGluCysLeuTyrSerAsnGlyG 646 : }gt.........................ag{GC}TCCAATGAATGCCTGTACAGCAACGGTG : 1362 177 : lyCysSerHisIleCysThrAspLeuLysIleGlyPheGluCysThrCysProAlaGlyPhe : 196 |||||||||||||||||!.!|||||||||||||||!:!|||||| !||||||.!!|||!:! lyCysSerHisIleCysAsnAspLeuLysIleGlyTyrGluCysLeuCysProThrGlyTyr 1363 : GTTGCTCTCACATTTGCAATGACCTGAAGATCGGCTATGAGTGCCTATGCCCCACTGGATAT : 1422 197 : GlnLeuLeuAspGlnLysThrCysGly{A} >>>> Target Intron 2 >>>> {sp : 206 !::|||:!!|||:!!||| !|||! !{|} 229 bp {|| ArgLeuValAspLysLysArgCysGlu{A}++ ++{sp 1423 : CGCCTGGTTGACAAAAAACGCTGTGAA{G}gt.........................ag{AT : 1682 207 : }IleAspGluCysLysAspProAspAlaCysSerGlnIleCysValAsnTyrLysGlyTyrP : 227 }|||||||||||| |||||||||.!!|||||||||||||||:!!||| ! ! ||| !! }IleAspGluCysAlaAspProAspThrCysSerGlnIleCysIleAsnGlnIleGlySerT 1683 : }ATCGATGAGTGTGCTGACCCGGACACCTGCAGCCAAATCTGCATCAACCAGATCGGCAGCT : 1744 228 : heLysCysGluCysTyrProGlyTyrGluMetAspLeuLeuThrLysAsnCysLysAlaAla : 247 :!||||||:!!||| ! !||||||:!!:!:|||! ! !|||||| !|||||| ||| yrLysCysGlnCysGluGluGlyTyrGlnValAspProAlaThrLysAlaCysLys---Ala 1745 : ACAAATGCCAGTGCGAGGAGGGTTACCAAGTTGACCCAGCAACCAAAGCCTGCAAG---GCC : 1801 248 : Ala{G} >>>> Target Intron 3 >>>> {ly}LysSerProSerLeuIlePheTh : 257 !{|} 717 bp {||}! ! ! !!! !|||.!!||||| Ile{G}++ ++{ly}ThrValAlaTyrLeuPhePheTh 1802 : ATC{G}gt.........................ag{GT}ACAGTAGCCTACCTTTTCTTCAC : 2548 258 : rAsnArgHisGluValArgArgIleAspLeuValLysArgAsnTyrSerArgLeuIleProM : 278 |||||||||||||||||||!:!!!: !|||! !|||!!!.!.|||:!!|||:!!|||||| rAsnArgHisGluValArgLysMetThrLeuAspLysSerGluTyrAlaArgValIleProA 2549 : CAATCGTCATGAAGTAAGAAAGATGACTTTGGACAAAAGCGAGTACGCCAGAGTGATCCCCC : 2611 279 : etLeuLysAsnValValAlaLeuAspValGluValAlaThrAsnArgIleTyrTrpCysAsp : 298 |||||||||||||||:!!||||||:!!.!.:!!|||||||||..!|||||||||! ||| rgLeuLysAsnValValSerLeuAspMetAsnMetAlaThrAsnGluIleTyrTrpSerAsp 2612 : GTCTAAAGAACGTTGTGTCTCTCGACATGAACATGGCCACCAACGAGATCTATTGGTCGGAC : 2671 299 : LeuSerTyrArgLysIleTyr{Se} >>>> Target Intron 4 >>>> {r}AlaTy : 308 :!!||| ! !:!|||||||||{!!} 92 bp {!}||| ! IleSerGlnLysLysIleTyr{Ar}++ ++{g}AlaGl 2672 : ATCTCCCAAAAGAAGATTTAC{AG}gt.........................ag{A}GCTCA : 2793 309 : rMetAspLysAlaSerAspProLysGluGlnGluValLeuIleAspGluGlnLeuHisSerP : 329 ||||||..!|||..!||| !!! :!!!!......!:!!!!:|||....!.:!! !!:!!| nMetAspSerAlaGluAspSerThrGlnHisSerThrValMetAspSerAspIleAspAlaP 2794 : GATGGACTCGGCCGAAGACTCCACTCAGCACAGCACTGTCATGGATAGCGACATTGACGCCC : 2856 330 : roGluGlyLeuAlaValAspTrpValHisLysHisIleTyrTrpThrAspSerGlyAsnLys : 349 ||||||||:!!||| !!||||||:!!||| :!!:!:||||||||||||||| !..!!.. roGluGlyIleAlaPheAspTrpIleHisGlyAsnLeuTyrTrpThrAspSerIleArgSer 2857 : CTGAAGGCATTGCATTTGACTGGATCCATGGCAACTTGTATTGGACTGACAGCATTCGCAGC : 2916 350 : ThrIleSerValAlaThrValAspGlyGlyArgArgArgThrLeuPheSerArgAsnLeuSe : 370 ||||||||||||!.!|||!.!|||||| !||||||!:!||||||||| !|||:!!|||!! ThrIleSerValValThrAlaAspGlyGlnArgArgLysThrLeuPheHisArgAspLeuTh 2917 : ACCATCTCTGTGGTAACCGCTGATGGTCAGCGTCGCAAGACTCTCTTCCACCGAGACTTAAC : 2979 371 : rGluProArgAlaIleAlaValAspProLeuArg{Gl} >>>> Target Intron 5 > : 382 !:!!||||||||||||!.!|||||||||! !!!!{..} 99 bp rLysProArgAlaIleValValAspProHisSer{As}++ 2980 : GAAACCCCGTGCTATCGTGGTCGACCCCCACAGC{AA}gt...................... : 3019 383 : >>> {y}PheMetTyrTrpSerAspTrpGlyAspGlnAlaLysIleGluLysSerGlyLeu : 400 {!}|||!!:||||||!!!|||||||||:!!! !|||||||||||||||:!!|||||| ++{n}PheIleTyrTrpThrAspTrpGlyAsnProAlaLysIleGluLysAlaGlyLeu 3020 : ...ag{C}TTCATTTACTGGACAGACTGGGGGAATCCAGCTAAGATCGAGAAGGCAGGTCTC : 3168 401 : AsnGlyValAspArgGlnThrLeuValSerAspAsnIleGluTrpProAsnGlyIleThrLe : 421 ||||||! !|||||| .!!||||||!!!|||||||||! !|||||||||||||||||||| AsnGlyGlyAspArgThrAlaLeuValThrAspAsnIleValTrpProAsnGlyIleThrLe 3169 : AACGGAGGGGATCGCACTGCTCTGGTCACGGACAACATTGTGTGGCCTAACGGGATTACACT : 3231 422 : u{A} >>>> Target Intron 6 >>>> {sp}LeuLeuSerGlnArgLeuTyrTrpV : 431 |{|} 98 bp {||}! !|||!:!|||||||||||||||| u{A}++ ++{sp}GlnLeuAsnGlnArgLeuTyrTrpV 3232 : T{G}gt.........................ag{AC}CAGCTGAACCAGCGGCTCTACTGGG : 3359 432 : alAspSerLysLeuHisGlnLeuSerSerIleAspPheSerGlyGlyAsnArgLysThrLeu : 451 ||||||||||||||||| ||||||||||||||| ! ..!||||||..!|||:::|||||| alAspSerLysLeuHisThrLeuSerSerIleAspValGlnGlyGlyGlyArgArgThrLeu 3360 : TGGACTCTAAGCTGCACACCCTCTCCAGTATCGATGTGCAGGGCGGTGGTCGACGCACCCTC : 3419 452 : IleSerSerThrAspPheLeuSerHisProPheGlyIleAlaValPheGlu >>>> Targ : 469 |||! !..! !||| |||:!!||||||.!.|||:!!.!!||||||||| IleIleAspGluAspLysLeuAlaHisProLeuGlyLeuThrValPheGlu++ 3420 : ATCATTGATGAAGACAAGCTGGCTCACCCACTGGGACTCACTGTGTTTGAGgt......... : 3475 470 : et Intron 7 >>>> AspLysValPheTrpThrAspLeuGluAsnGluAlaIlePheSe : 483 174 bp !!:!:!|||||||||||||||:!!...|||.!.||||||.!!|| ++GluArgValPheTrpThrAspValSerAsnAsnAlaIleLeuSe 3476 : ................agGAAAGAGTTTTCTGGACGGACGTCAGTAATAACGCCATCCTCAG : 3689 484 : rAlaAsnArgLeuAsnGlyLeuGluIleSerIleLeuAlaGluAsnLeuAsnAsnProHisA : 504 |||||||||||||!..||| !!!:|||!!! !|||||||||:!!||| ::!|||.!.| rAlaAsnArgLeuThrGlyGlyAspIleThrProLeuAlaGluHisLeuAlaSerProGluA 3690 : TGCAAACAGGCTGACGGGTGGTGACATTACACCATTGGCAGAGCACCTGGCATCCCCAGAAG : 3752 505 : spIleValIlePheHisGluLeuLysGlnProArg{A} >>>> Target Intron 8 > : 516 |||||:!!:!!!:!|||.!.|||||||||||| !{!} 425 bp spIleIleLeuTyrHisAsnLeuLysGlnProAla{G}++ 3753 : ACATTATTCTTTACCATAACCTCAAACAACCGGCT{G}gt...................... : 3791 517 : >>> {la}ProAspAlaCysGluLeuSerValGlnProAsnGlyGlyCysGluTyrLeuCy : 534 {.!} !||| !|||:!!:!!||| !.!||||||!:!:!!|| ++{ly}ArgAspTrpCysGlnValSer---------------AlaCysGluPheMetCy 3792 : ...ag{GC}AGAGATTGGTGTCAGGTATCC---------------GCCTGTGAATTCATGTG : 4252 535 : sLeuProAlaProGlnIleSerSerHisSerProLysTyrThrCysAlaCysProAspThrM : 555 |||| !|||||||||:!:.!!!!!||| !!|||||||||||||||!.!|||||||||!.!| sLeuGlyAlaProGlnValGlyArgHisProProLysTyrThrCysValCysProAspAsnM 4253 : TTTGGGAGCTCCTCAAGTGGGAAGACATCCGCCCAAATACACCTGTGTCTGTCCAGATAACA : 4315 556 : etTrpLeuGlyProAspMetLysArgCysTyrArgAlaProGlnSerThrSerThrThrThr : 575 || !|||!.! !||||||!:!! !||| ! !!.! ! !!! !|||!.! ||| etMetLeuAlaArgAspMetArgThrCysValProGlyMet***IleThrLysGlu***Thr 4316 : TGATGCTAGCCAGGGATATGAGGACATGTGTACCTGGTATGTAAATCACCAAAGAgtaaaca : 4375 576 : LeuAlaSerThrMetThrArg : 582 ...|||..!!!: !||| TyrCysSerValIleGlnArg 4376 : tactgtagtgtAATACAGAGG : 4398 vulgar: SPP00002936_2.0 83 582 . JXSJ01000652.1:subseq(10670,5330) 410 4398 + 1373 M 33 99 G 2 0 M 19 57 G 2 0 M 26 78 S 0 1 5 0 2 I 0 683 3 0 2 S 1 2 M 39 117 S 0 1 5 0 2 I 0 225 3 0 2 S 1 2 M 39 117 G 1 0 M 2 6 S 0 1 5 0 2 I 0 713 3 0 2 S 1 2 M 56 168 S 0 2 5 0 2 I 0 88 3 0 2 S 1 1 M 75 225 S 0 2 5 0 2 I 0 95 3 0 2 S 1 1 M 39 117 S 0 1 5 0 2 I 0 94 3 0 2 S 1 2 M 46 138 5 0 2 I 0 170 3 0 2 M 47 141 S 0 1 5 0 2 I 0 421 3 0 2 S 1 2 M 7 21 G 5 0 M 54 162 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-12-02 ##type DNA # # # seqname source feature start end score strand frame attributes # JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local gene 411 4398 1373 + . gene_id 1 ; sequence SPP00002936_2.0 ; gene_orientation + JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local cds 411 645 . + . JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local exon 411 645 . + . insertions 0 ; deletions 4 JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local splice5 646 647 . + . intron_id 1 ; splice_site "GT" JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local intron 646 1332 . + . intron_id 1 JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local splice3 1331 1332 . + . intron_id 0 ; splice_site "AG" JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local cds 1333 1452 . + . JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local exon 1333 1452 . + . insertions 0 ; deletions 0 JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local splice5 1453 1454 . + . intron_id 2 ; splice_site "GT" JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local intron 1453 1681 . + . intron_id 2 JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local splice3 1680 1681 . + . intron_id 1 ; splice_site "AG" JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local cds 1682 1807 . + . JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local exon 1682 1807 . + . insertions 0 ; deletions 1 JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local splice5 1808 1809 . + . intron_id 3 ; splice_site "GT" JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local intron 1808 2524 . + . intron_id 3 JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local splice3 2523 2524 . + . intron_id 2 ; splice_site "AG" JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local cds 2525 2696 . + . JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local exon 2525 2696 . + . insertions 0 ; deletions 0 JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local splice5 2697 2698 . + . intron_id 4 ; splice_site "GT" JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local intron 2697 2788 . + . intron_id 4 JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local splice3 2787 2788 . + . intron_id 3 ; splice_site "AG" JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local cds 2789 3016 . + . JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local exon 2789 3016 . + . insertions 0 ; deletions 0 JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local splice5 3017 3018 . + . intron_id 5 ; splice_site "GT" JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local intron 3017 3115 . + . intron_id 5 JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local splice3 3114 3115 . + . intron_id 4 ; splice_site "AG" JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local cds 3116 3234 . + . JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local exon 3116 3234 . + . insertions 0 ; deletions 0 JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local splice5 3235 3236 . + . intron_id 6 ; splice_site "GT" JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local intron 3235 3332 . + . intron_id 6 JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local splice3 3331 3332 . + . intron_id 5 ; splice_site "AG" JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local cds 3333 3472 . + . JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local exon 3333 3472 . + . insertions 0 ; deletions 0 JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local splice5 3473 3474 . + . intron_id 7 ; splice_site "GT" JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local intron 3473 3646 . + . intron_id 7 JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local splice3 3645 3646 . + . intron_id 6 ; splice_site "aG" JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local cds 3647 3788 . + . JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local exon 3647 3788 . + . insertions 0 ; deletions 0 JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local splice5 3789 3790 . + . intron_id 8 ; splice_site "GT" JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local intron 3789 4213 . + . intron_id 8 JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local splice3 4212 4213 . + . intron_id 7 ; splice_site "AG" JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local cds 4214 4398 . + . JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local exon 4214 4398 . + . insertions 0 ; deletions 5 JXSJ01000652.1:subseq(10670,5330) exonerate:protein2genome:local similarity 411 4398 1373 + . alignment_id 1 ; Query SPP00002936_2.0 ; Align 411 84 99 ; Align 510 119 57 ; Align 567 140 78 ; Align 1335 167 117 ; Align 1684 207 117 ; Align 1801 247 6 ; Align 2527 250 168 ; Align 2790 307 225 ; Align 3117 383 117 ; Align 3335 423 138 ; Align 3647 469 141 ; Align 4216 517 21 ; Align 4237 529 162 # --- END OF GFF DUMP ---