Command line: [/mnt/NFS_UPF/soft/exonerate/exonerate-2.2.0-x86_64/bin/exonerate -m p2g --showtargetgff --exhaustive yes -q query21 -t q_subseq] Hostname: [am30751-101042u] C4 Alignment: ------------ Query: SPP00000115_1.0 # Protein # Selenoprotein S (SelS) # Mus musculus # Complete Target: PVKD010001728.1:subseq(36210,192112) Cricetomys gambianus isolate US082 CriGam_scaffold_3453, whole genome shotgun sequence Model: protein2genome:local Raw score: 838 Query range: 0 -> 188 Target range: 98068 -> 106269 1 : MetAspArgAspGluGluProLeuSerAlaArgProAlaLeuGluThrGluSerLeuA : 20 |||!!:! !..!||||||! !||||||||||||||||||||||||||||||.!!|||| MetGluProSerGluGluLeuLeuSerAlaArgProAlaLeuGluThrGluGlyLeuA 98069 : ATGGAGCCAAGCGAGGAACTGCTGTCCGCGCGGCCGGCGCTGGAGACCGAGGGCCTGC : 98126 21 : rgPheLeuHisValThr{V} >>>> Target Intron 1 >>>> {al}GlySe : 28 |||||||||||||||||{|} 551 bp {||}||||| rgPheLeuHisValThr{V}++ ++{al}GlySe 98127 : GCTTCCTGCACGTCACG{G}gt.........................ag{tg}ggCTC : 98701 29 : rLeuLeuAlaSerTyrGlyTrpTyrIleLeuPheSerCysIleLeuLeuTyrIleVal : 47 ||||||||||||||||||||||||||||||||||||||||||||||||||||:!!||| rLeuLeuAlaSerTyrGlyTrpTyrIleLeuPheSerCysIleLeuLeuTyrValVal 98702 : CCTGCTGGCCAGCTACGGCTGGTACATCCTTTTCAGCTGTATCCTCCTCTACGTTGTC : 98758 48 : IleGlnArgLeuSerLeuArgLeuArgAlaLeuArgGlnArgGlnLeuAspGlnAlaG : 67 ||||||!:!||||||:!!||||||||||||||||||||||||||| ||| !|||| IleGlnLysLeuSerValArgLeuArgAlaLeuArgGlnArgGlnGlnAspGlyAlaG 98759 : ATCCAGAAGCTCTCCGTCCGACTGCGGGCtttgaggcagagacagcaggacgGAGCTG : 98818 68 : luThrValLeu{G} >>>> Target Intron 2 >>>> {lu}ProAspValVa : 75 || !!||||||{|} 1179 bp {||}||||||!.!|| luProValLeu{G}++ ++{lu}ProAspAlaVa 98819 : AGCCTGTTCTG{G}gt.........................ag{AA}CCTGATGCTGT : 100021 76 : lValLysArgGlnGluAlaLeuAlaAlaAlaArgLeuArgMetGlnGluAspLeuAsn : 94 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| lValLysArgGlnGluAlaLeuAlaAlaAlaArgLeuArgMetGlnGluAspLeuAsn 100022 : GGTTAAACGACAAGAGGCTTTAGCGGCTGCTCGTTTGAGAATGCAAGAAGATCTAAAT : 100078 95 : AlaGlnValGluLysHisLysGluLysLeuArgGln >>>> Target Intron 3 : 107 |||||||||||||||||||||||||||||||||||| 3167 bp AlaGlnValGluLysHisLysGluLysLeuArgGln++ 100079 : GCCCAAGTTGAAAAGCATAAGGAAAAACTAAGACAGgt.................... : 100119 108 : >>>> LeuGluGluGluLysArgArgGlnLysIleGluMetTrpAspSerMetGln : 123 ||||||||||||||||||||||||||||||||||||||||||||||||:!! ++LeuGluGluGluLysArgArgGlnLysIleGluMetTrpAspSerMetLys 100120 : .....agcttgaagaagagaaaaggaggcagaagatTGAAATGTGGGACAGCATGAAA : 103332 124 : GluGlyArgSerTyrLysArgAsnSerGlyArgProGln >>>> Target Intro : 137 |||||||||||||||!:!|||:!!||||||||||||||| 152 bp GluGlyArgSerTyrArgArgAspSerGlyArgProGln++ 103333 : GAAGGCAGAAGTTACAGAAGAGACTCTGGCCGGCCGCAGgt................. : 103376 138 : n 4 >>>> GluGluAspGlyProGlyProSerThrSerSerValIleProLysGly : 152 ||||||||||||||||||||||||||||||||||||! !|||||| !! ++GluGluAspGlyProGlyProSerThrSerSerValThrProLysArg 103377 : ........agGAAGAAGATGGTCCTGGACCTTCCACTTCATCTGTCACCCCCAAAAGA : 103571 153 : LysSerAspLysLysProLeuArgGlyGly{G} >>>> Target Intron 5 >> : 163 ||| !!||||||||||||||||||||||||{|} 2588 bp LysProAspLysLysProLeuArgGlyGly{G}++ 103572 : AAACCTGACAAAAAGCCTTTGCGCGGAGGT{G}gt....................... : 103607 164 : >> {ly}TyrAsnProLeuThrGlyGluGlyGlyGlyThrCysSerTrpArgProGl : 180 {||}!:!||||||||||||||||||||||||||||||||||||||||||||||| ++{ly}PheAsnProLeuThrGlyGluGlyGlyGlyThrCysSerTrpArgProGl 103608 : ..ag{GT}TTCAACCCTCTGACTGGTGAAGGCGGTGGTACCTGCTCCTGGAGACCGGG : 106243 181 : yArgArgGlyProSerSerGlyGly : 188 ||||||||||||||||||||||||| yArgArgGlyProSerSerGlyGly 106244 : GCGCAGGGGCCCATCATCTGGTGGA : 106269 vulgar: SPP00000115_1.0 0 188 . PVKD010001728.1:subseq(36210,192112) 98068 106269 + 838 M 25 75 S 0 1 5 0 2 I 0 547 3 0 2 S 1 2 M 44 132 S 0 1 5 0 2 I 0 1175 3 0 2 S 1 2 M 35 105 5 0 2 I 0 3163 3 0 2 M 30 90 5 0 2 I 0 148 3 0 2 M 26 78 S 0 1 5 0 2 I 0 2584 3 0 2 S 1 2 M 25 75 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2019-11-20 ##type DNA # # # seqname source feature start end score strand frame attributes # PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local gene 98069 106269 838 + . gene_id 1 ; sequence SPP00000115_1.0 ; gene_orientation + PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local cds 98069 98144 . + . PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local exon 98069 98144 . + . insertions 0 ; deletions 0 PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local splice5 98145 98146 . + . intron_id 1 ; splice_site "GT" PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local intron 98145 98695 . + . intron_id 1 PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local splice3 98694 98695 . + . intron_id 0 ; splice_site "ag" PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local cds 98696 98830 . + . PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local exon 98696 98830 . + . insertions 0 ; deletions 0 PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local splice5 98831 98832 . + . intron_id 2 ; splice_site "GT" PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local intron 98831 100009 . + . intron_id 2 PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local splice3 100008 100009 . + . intron_id 1 ; splice_site "ag" PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local cds 100010 100116 . + . PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local exon 100010 100116 . + . insertions 0 ; deletions 0 PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local splice5 100117 100118 . + . intron_id 3 ; splice_site "GT" PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local intron 100117 103283 . + . intron_id 3 PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local splice3 103282 103283 . + . intron_id 2 ; splice_site "AG" PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local cds 103284 103373 . + . PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local exon 103284 103373 . + . insertions 0 ; deletions 0 PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local splice5 103374 103375 . + . intron_id 4 ; splice_site "GT" PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local intron 103374 103525 . + . intron_id 4 PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local splice3 103524 103525 . + . intron_id 3 ; splice_site "AG" PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local cds 103526 103604 . + . PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local exon 103526 103604 . + . insertions 0 ; deletions 0 PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local splice5 103605 103606 . + . intron_id 5 ; splice_site "GT" PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local intron 103605 106192 . + . intron_id 5 PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local splice3 106191 106192 . + . intron_id 4 ; splice_site "AG" PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local cds 106193 106269 . + . PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local exon 106193 106269 . + . insertions 0 ; deletions 0 PVKD010001728.1:subseq(36210,192112) exonerate:protein2genome:local similarity 98069 106269 838 + . alignment_id 1 ; Query SPP00000115_1.0 ; Align 98069 1 75 ; Align 98698 27 132 ; Align 100012 72 105 ; Align 103284 107 90 ; Align 103526 137 78 ; Align 106195 164 75 # --- END OF GFF DUMP --- # -- completed exonerate analysis