Command line: [exonerate -m p2g --showtargetgff -q SPP00000019_1.0.fa -t SPP00000019_1.0.GL397546.1/GL397546.1.subseq] Hostname: [upf-OptiPlex-755] C4 Alignment: ------------ Query: SPP00000019_1.0 # Protein # Selenoprotein O (SelO) # Homo sapiens # Complete Target: GL397546.1:subseq(159884,116409) dna:supercontig supercontig:Nleu1.0:GL397546.1:1:827548:1 REF Model: protein2genome:local Raw score: 2624 Query range: 139 -> 669 Target range: 49999 -> 66409 140 : TyrCysGlyHisGlnPheGlyGlnPheAlaGlyGlnLeuGlyAspGlyAlaAlaMetTyr : 159 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| TyrCysGlyHisGlnPheGlyGlnPheAlaGlyGlnLeuGlyAspGlyAlaAlaMetTyr 50000 : TACTGCGGCCACCAGTTCGGCCAGTTCGCCGGGCAGCTGGGCGACGGCGCCGCCATGTAC : 50057 160 : LeuGlyGluValCysThrAlaThrGlyGluArgTrpGluLeuGlnLeuLysGlyAlaGly : 179 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| LeuGlyGluValCysThrAlaThrGlyGluArgTrpGluLeuGlnLeuLysGlyAlaGly 50058 : CTGGGCGAGGTGTGCACGGCGACTGGCGAGCGCTGGGAGCTGCAGCTCAAGGGCGCCGGG : 50117 180 : ProThrProPheSer{Ar} >>>> Target Intron 1 >>>> {g}GlnAlaAsp : 188 |||||||||||||||{||} 5039 bp {|}||||||||| ProThrProPheSer{Ar}++ ++{g}GlnAlaAsp 50118 : CCCACGCCCTTCTCC{AG}gt.........................ag{A}CAGGCCGAC : 55183 189 : GlyArgLysValLeuArgSerSerIleArgGluPheLeuCysSerGluAlaMetPheHis : 208 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GlyArgLysValLeuArgSerSerIleArgGluPheLeuCysSerGluAlaMetPheHis 55184 : GGTCGCAAGGTCCTACGGTCCAGCATCCGGGAGTTCCTGTGCAGCGAAGCCATGTTCCAC : 55243 209 : LeuGlyValProThrThrArgAlaGlyAlaCysValThrSerGluSerThrValValArg : 228 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| LeuGlyValProThrThrArgAlaGlyAlaCysValThrSerGluSerThrValValArg 55244 : CTGGGAGTCCCCACCACGCGGGCCGGCGCCTGCGTGACGTCCGAGTCCACGGTGGTGCGC : 55303 229 : AspValPheTyrAspGlyAsnProLysTyrGluGlnCysThrValValLeuArgValAla : 248 ||||||||||||||||||||||||||||||||||||||||||||||||||||||:!!||| AspValPheTyrAspGlyAsnProLysTyrGluGlnCysThrValValLeuArgIleAla 55304 : GACGTGTTCTATGATGGTAATCCCAAATATGAACAATGCACGGTTGTGTTGCGTATAGCT : 55363 249 : SerThrPheIle{Ar} >>>> Target Intron 2 >>>> {g}PheGlySerPhe : 257 ||||||||||||{||} 2031 bp {|}|||||||||||| SerThrPheIle{Ar}++ ++{g}PheGlySerPhe 55364 : TCCACTTTCATA{AG}gt.........................ag{G}TTTGGATCCTTT : 57421 258 : GluIlePheLysSerAlaAspGluHisThrGlyArgAlaGlyProSerValGlyArgAsn : 277 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GluIlePheLysSerAlaAspGluHisThrGlyArgAlaGlyProSerValGlyArgAsn 57422 : GAGATTTTTAAGTCTGCAGATGAGCACACAGGGCGTGCAGGCCCCAGCGTGGGGAGGAAC : 57481 278 : AspIleArgValGlnLeuLeuAspTyrValIleSerSerPheTyrProGluIleGlnAla : 297 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| AspIleArgValGlnLeuLeuAspTyrValIleSerSerPheTyrProGluIleGlnAla 57482 : GACATTCGAGTGCAGCTGCTCGACTATGTCATCAGCTCCTTTTACCCCGAGATCCAGGCT : 57541 298 : AlaHisAlaSerAspSerValGlnArgAsnAlaAlaPhePheArgGlu >>>> Targe : 314 |||||||||||||||||||||||||||||||||||||||||||||||| 1 AlaHisAlaSerAspSerValGlnArgAsnAlaAlaPhePheArgGlu++ 57542 : GCTCATGCCAGCGACAGCGTGCAGAGAAACGCCGCCTTCTTCCGGGAGgt.......... : 57594 315 : t Intron 3 >>>> ValThrArgArgThrAlaArgMetValAlaGluTrpGlnCysV : 328 472 bp ||||||||||||||||||||||||||||||||||||||||||| ++ValThrArgArgThrAlaArgMetValAlaGluTrpGlnCysV 57595 : ...............agGTGACGCGGCGCACGGCGCGGATGGTGGCCGAGTGGCAGTGCG : 59106 329 : alGlyPheCysHisGlyValLeuAsnThrAspAsnMetSerIleLeuGlyLeuThrIleA : 348 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| alGlyPheCysHisGlyValLeuAsnThrAspAsnMetSerIleLeuGlyLeuThrIleA 59107 : TGGGCTTCTGCCACGGCGTGCTCAACACTGACAACATGAGCATCCTGGGGCTCACCATCG : 59166 349 : spTyrGlyProPheGlyPheLeuAsp{Ar} >>>> Target Intron 4 >>>> { : 357 ||||||||||||||||||||||||||{||} 319 bp { spTyrGlyProPheGlyPheLeuAsp{Ar}++ ++{ 59167 : ACTACGGGCCCTTTGGCTTCCTGGAC{AG}gt.........................ag{ : 59514 358 : g}TyrAspProAspHisValCysAsnAlaSerAspAsnThrGlyArgTyrAlaTyrSerL : 377 |}|||||||||||||||||||||||||||||||||||||||||||||||||||||||||| g}TyrAspProAspHisValCysAsnAlaSerAspAsnThrGlyArgTyrAlaTyrSerL 59515 : G}TACGACCCCGACCACGTGTGCAATGCCTCCGACAACACCGGCCGCTATGCATACAGCA : 59572 378 : ysGlnProGluValCysArgTrpAsnLeuArgLysLeuAlaGluAlaLeuGlnProGluL : 397 |||||||||||||||||!:!||||||||| !!|||||||||||||||||||||||||||| ysGlnProGluValCysLysTrpAsnLeuGlyLysLeuAlaGluAlaLeuGlnProGluL 59573 : AGCAGCCTGAGGTGTGCAAGTGGAACCTGGGGAAGCTGGCCGAGGCCCTGCAGCCAGAGC : 59632 398 : euProLeuGluLeuGlyGluAlaIleLeuAlaGluGluPheAspAlaGluPheGlnArgH : 417 |||||||||||||||||||||||||||||!.!|||||||||||||||||||||||||||| euProLeuGluLeuGlyGluAlaIleLeuValGluGluPheAspAlaGluPheGlnArgH 59633 : TGCCCCTGGAGCTGGGTGAGGCCATCCTGGTCGAGGAGTTTGATGCCGAGTTCCAAAGGC : 59692 418 : isTyrLeuGlnLysMetArgArgLysLeuGlyLeuValGlnValGluLeuGluGluAspG : 437 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| isTyrLeuGlnLysMetArgArgLysLeuGlyLeuValGlnValGluLeuGluGluAspA 59693 : ACTACCTGCAGAAGATGCGCAGGAAGCTGGGCCTCGTGCAGGTGGAGCTGGAGGAAGACA : 59752 438 : lyAlaLeuValSerLysLeuLeuGluThrMetHisLeuThr{G} >>>> Target In : 451 !!|||||||||||||||||||||||||||||||||||||||{|} 4982 rgAlaLeuValSerLysLeuLeuGluThrMetHisLeuThr{G}++ 59753 : GGGCGCTGGTGTCCAAGCTCCTGGAGACCATGCACCTGACC{G}gt.............. : 59797 452 : tron 5 >>>> {ly}AlaAspPheThrAsnThrPheTyrLeuLeuSerSerPheProV : 466 bp {||}||||||||||||||||||||||||||||||||||||||||||| ++{ly}AlaAspPheThrAsnThrPheTyrLeuLeuSerSerPheProV 59798 : ...........ag{GT}GCCGACTTCACAAACACCTTCTACTTGCTGAGCTCCTTTCCAG : 64821 467 : alGluLeuGluSerProGlyLeuAlaGluPheLeuAlaArgLeuMetGluGlnCysAlaS : 486 |||||! !|||||||||||||||||||||||||||||||||||||||||||||||||||| alGluProGluSerProGlyLeuAlaGluPheLeuAlaArgLeuMetGluGlnCysAlaS 64822 : TGGAGCCAGAGTCGCCAGGCCTGGCGGAATTCCTGGCCAGGCTGATGGAGCAGTGTGCCT : 64881 487 : erLeuGluGluLeuArgLeuAlaPheArgProGlnMetAspPro{Ar} >>>> Targe : 501 ||||||||||||||||||||||||||||||||||||||||||||{||} erLeuGluGluLeuArgLeuAlaPheArgProGlnMetAspPro{Ar}++ 64882 : CCCTGGAAGAGCTAAGGCTGGCATTCCGGCCCCAGATGGATCCC{CG}gt.......... : 64930 502 : t Intron 6 >>>> {g}GlnLeuSerMetMetLeuMetLeuAlaGlnSerAsnProG : 515 810 bp {|}|||||||||||||||||||||||||||||||||||||||| ++{g}GlnLeuSerMetMetLeuMetLeuAlaGlnSerAsnProG 64931 : ...............ag{G}CAGCTATCCATGATGTTGATGCTGGCACAGTCAAACCCAC : 65778 516 : lnLeuPheAlaLeuMetGlyThrArgAlaGlyIleAlaArgGluLeuGluArgValGluG : 535 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| lnLeuPheAlaLeuMetGlyThrArgAlaGlyIleAlaArgGluLeuGluArgValGluG 65779 : AGCTGTTCGCGCTCATGGGCACTCGGGCGGGCATCGCCAGGGAGCTGGAGCGTGTGGAGC : 65838 536 : lnGlnSerArgLeuGluGlnLeuSerAlaAlaGluLeuGlnSerArgAsnGlnGlyHisT : 555 ||||||||||||||||||||||||||!.!||||||||||||||||||||||||||||||| lnGlnSerArgLeuGluGlnLeuSerValAlaGluLeuGlnSerArgAsnGlnGlyHisT 65839 : AGCAGTCTCGGCTGGAGCAGCTGAGTGTGGCAGAGCTGCAGAGCAGGAACCAGGGCCACT : 65898 556 : rpAlaAspTrpLeuGlnAlaTyr{Ar} >>>> Target Intron 7 >>>> {g}A : 564 |||||||||||||||||||||||{||} 92 bp {|}| rpAlaAspTrpLeuGlnAlaTyr{Ar}++ ++{g}A 65899 : GGGCTGATTGGCTACAGGCGTAC{AG}gt.........................ag{A}G : 66017 565 : laArgLeuAspLysAspLeuGluGlyAlaGlyAspAlaAlaAlaTrpGlnAlaGluHisV : 584 ||||||||||||||||||||||||||.!!||||||||||||||||||!:!||||||!.!| laArgLeuAspLysAspLeuGluGlyThrGlyAspAlaAlaAlaTrpArgAlaGluArgV 66018 : CCCGGCTAGATAAGGACCTGGAAGGCACCGGGGATGCTGCCGCCTGGCGGGCTGAGCGTG : 66077 585 : alArgValMetHisAlaAsnAsnProLysTyrValLeuArgAsnTyrIleAlaGlnAsnA : 604 |||||:!!|||||||||||||||||||||||||||||||||||||||||||||||||||| alArgMetMetHisAlaAsnAsnProLysTyrValLeuArgAsnTyrIleAlaGlnAsnA 66078 : TGCGCATGATGCACGCCAACAACCCCAAGTACGTGCTGAGGAACTACATTGCGCAGAACG : 66137 605 : laIleGluAlaAlaGluArgGlyAspPheSerGlu >>>> Target Intron 8 >> : 616 ||||||||||||||||||||||||||||||||||| 75 bp laIleGluAlaAlaGluArgGlyAspPheSerGlu+- 66138 : CCATCGAGGCTGCCGAGCGTGGGGACTTCTCAGAGgc....................... : 66175 617 : >> ValArgArgValLeuLysLeuLeuGluThrProTyrHisCysGluAlaGlyAlaAl : 634 |||||||||||||||||||||||||||||||||||||||||||||||||||||||| ++ValArgArgValLeuLysLeuLeuGluThrProTyrHisCysGluAlaGlyAlaAl 66176 : ..agGTGCGGCGGGTGCTGAAGCTACTGGAGACCCCTTACCACTGCGAGGCGGGGGCCGC : 66302 635 : aThrAspAlaGluAlaThrGluAlaAspGlyAlaAspGlyArgGlnArgSerTyrSerSe : 654 ||||||| !!:!!||||||||||||||||||||||||||||||||||||||||||||||| aThrAspProGlnAlaThrGluAlaAspGlyAlaAspGlyArgGlnArgSerTyrSerSe 66303 : CACAGACCCCCAGGCCACGGAGGCCGACGGGGCGGACGGCAGGCAGCGCTCCTACAGCAG : 66362 655 : rLysProProLeuTrpAlaAlaGluLeuCysValThrUnkSerSer : 669 ||||||||||||||||||||||||||||||||||||| |||||| rLysProProLeuTrpAlaAlaGluLeuCysValThr***SerSer 66363 : TAAGCCCCCGCTCTGGGCAGCAGAACTGTGCGTGACATGATCTTCG : 66409 vulgar: SPP00000019_1.0 139 669 . GL397546.1:subseq(159884,116409) 49999 66409 + 2624 M 45 135 S 0 2 5 0 2 I 0 5035 3 0 2 S 1 1 M 67 201 S 0 2 5 0 2 I 0 2027 3 0 2 S 1 1 M 60 180 5 0 2 I 0 1468 3 0 2 M 43 129 S 0 2 5 0 2 I 0 315 3 0 2 S 1 1 M 93 279 S 0 1 5 0 2 I 0 4978 3 0 2 S 1 2 M 49 147 S 0 2 5 0 2 I 0 806 3 0 2 S 1 1 M 61 183 S 0 2 5 0 2 I 0 88 3 0 2 S 1 1 M 52 156 5 0 2 I 0 71 3 0 2 M 54 162 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2012-11-29 ##type DNA # # # seqname source feature start end score strand frame attributes # GL397546.1:subseq(159884,116409) exonerate:protein2genome:local gene 50000 66409 2624 + . gene_id 1 ; sequence SPP00000019_1.0 ; gene_orientation + GL397546.1:subseq(159884,116409) exonerate:protein2genome:local cds 50000 50136 . + . GL397546.1:subseq(159884,116409) exonerate:protein2genome:local exon 50000 50136 . + . insertions 0 ; deletions 0 GL397546.1:subseq(159884,116409) exonerate:protein2genome:local splice5 50137 50138 . + . intron_id 1 ; splice_site "GT" GL397546.1:subseq(159884,116409) exonerate:protein2genome:local intron 50137 55175 . + . intron_id 1 GL397546.1:subseq(159884,116409) exonerate:protein2genome:local splice3 55174 55175 . + . intron_id 0 ; splice_site "AG" GL397546.1:subseq(159884,116409) exonerate:protein2genome:local cds 55176 55379 . + . GL397546.1:subseq(159884,116409) exonerate:protein2genome:local exon 55176 55379 . + . insertions 0 ; deletions 0 GL397546.1:subseq(159884,116409) exonerate:protein2genome:local splice5 55380 55381 . + . intron_id 2 ; splice_site "GT" GL397546.1:subseq(159884,116409) exonerate:protein2genome:local intron 55380 57410 . + . intron_id 2 GL397546.1:subseq(159884,116409) exonerate:protein2genome:local splice3 57409 57410 . + . intron_id 1 ; splice_site "AG" GL397546.1:subseq(159884,116409) exonerate:protein2genome:local cds 57411 57591 . + . GL397546.1:subseq(159884,116409) exonerate:protein2genome:local exon 57411 57591 . + . insertions 0 ; deletions 0 GL397546.1:subseq(159884,116409) exonerate:protein2genome:local splice5 57592 57593 . + . intron_id 3 ; splice_site "GT" GL397546.1:subseq(159884,116409) exonerate:protein2genome:local intron 57592 59063 . + . intron_id 3 GL397546.1:subseq(159884,116409) exonerate:protein2genome:local splice3 59062 59063 . + . intron_id 2 ; splice_site "AG" GL397546.1:subseq(159884,116409) exonerate:protein2genome:local cds 59064 59194 . + . GL397546.1:subseq(159884,116409) exonerate:protein2genome:local exon 59064 59194 . + . insertions 0 ; deletions 0 GL397546.1:subseq(159884,116409) exonerate:protein2genome:local splice5 59195 59196 . + . intron_id 4 ; splice_site "GT" GL397546.1:subseq(159884,116409) exonerate:protein2genome:local intron 59195 59513 . + . intron_id 4 GL397546.1:subseq(159884,116409) exonerate:protein2genome:local splice3 59512 59513 . + . intron_id 3 ; splice_site "AG" GL397546.1:subseq(159884,116409) exonerate:protein2genome:local cds 59514 59794 . + . GL397546.1:subseq(159884,116409) exonerate:protein2genome:local exon 59514 59794 . + . insertions 0 ; deletions 0 GL397546.1:subseq(159884,116409) exonerate:protein2genome:local splice5 59795 59796 . + . intron_id 5 ; splice_site "GT" GL397546.1:subseq(159884,116409) exonerate:protein2genome:local intron 59795 64776 . + . intron_id 5 GL397546.1:subseq(159884,116409) exonerate:protein2genome:local splice3 64775 64776 . + . intron_id 4 ; splice_site "AG" GL397546.1:subseq(159884,116409) exonerate:protein2genome:local cds 64777 64927 . + . GL397546.1:subseq(159884,116409) exonerate:protein2genome:local exon 64777 64927 . + . insertions 0 ; deletions 0 GL397546.1:subseq(159884,116409) exonerate:protein2genome:local splice5 64928 64929 . + . intron_id 6 ; splice_site "GT" GL397546.1:subseq(159884,116409) exonerate:protein2genome:local intron 64928 65737 . + . intron_id 6 GL397546.1:subseq(159884,116409) exonerate:protein2genome:local splice3 65736 65737 . + . intron_id 5 ; splice_site "AG" GL397546.1:subseq(159884,116409) exonerate:protein2genome:local cds 65738 65923 . + . GL397546.1:subseq(159884,116409) exonerate:protein2genome:local exon 65738 65923 . + . insertions 0 ; deletions 0 GL397546.1:subseq(159884,116409) exonerate:protein2genome:local splice5 65924 65925 . + . intron_id 7 ; splice_site "GT" GL397546.1:subseq(159884,116409) exonerate:protein2genome:local intron 65924 66015 . + . intron_id 7 GL397546.1:subseq(159884,116409) exonerate:protein2genome:local splice3 66014 66015 . + . intron_id 6 ; splice_site "AG" GL397546.1:subseq(159884,116409) exonerate:protein2genome:local cds 66016 66172 . + . GL397546.1:subseq(159884,116409) exonerate:protein2genome:local exon 66016 66172 . + . insertions 0 ; deletions 0 GL397546.1:subseq(159884,116409) exonerate:protein2genome:local splice5 66173 66174 . + . intron_id 8 ; splice_site "GC" GL397546.1:subseq(159884,116409) exonerate:protein2genome:local intron 66173 66247 . + . intron_id 8 GL397546.1:subseq(159884,116409) exonerate:protein2genome:local splice3 66246 66247 . + . intron_id 7 ; splice_site "AG" GL397546.1:subseq(159884,116409) exonerate:protein2genome:local cds 66248 66409 . + . GL397546.1:subseq(159884,116409) exonerate:protein2genome:local exon 66248 66409 . + . insertions 0 ; deletions 0 GL397546.1:subseq(159884,116409) exonerate:protein2genome:local similarity 50000 66409 2624 + . alignment_id 1 ; Query SPP00000019_1.0 ; Align 50000 140 135 ; Align 55177 186 201 ; Align 57412 254 180 ; Align 59064 314 129 ; Align 59515 358 279 ; Align 64779 452 147 ; Align 65739 502 183 ; Align 66017 564 156 ; Align 66248 616 162 # --- END OF GFF DUMP --- # -- completed exonerate analysis