Command line: [exonerate -m p2g --showtargetgff -q SelU2n/SelU2n_U.fa -t SelU2n/SUBSEQ/KB229214.1_0_subseq.txt --exhaustive yes] Hostname: [luke] C4 Alignment: ------------ Query: SPP00000114_2.0 # Protein # Selenoprotein X2 (SelX2) # Human (Homo sapiens) Target: KB229214.1:subseq(215400,25140) Odobenus rosmarus divergens isolate Ivan unplaced genomic scaffold Scaffold337, whole genome shotgun sequence Model: protein2genome:local Raw score: 823 Query range: 4 -> 185 Target range: 18962 -> 25137 5 : AlaProValThrArgGlnValSerGlyAlaAlaAlaLeuValProAlaProSerGlyPro : 24 !.!|||||||||||||||||||||||| !||||||! !!.! !!!.!|||||||||||| GlyProValThrArgGlnValSerGlyArgAlaAlaProAlaAlaValProSerGlyPro 18963 : GGCCCGGTTACGCGGCAGGTCAGCGGCCGCGCCGCCCCAGCCGCAGTCCCGAGCGGCCCC : 19020 25 : AspSerGlyGlnProLeuAlaAlaAlaValAlaGluLeuProValLeuAspAlaArgGly : 44 !!: !!|||||||||||||||||||||||||||||||||||||||||||||||| !||| GluArgGlyGlnProLeuAlaAlaAlaValAlaGluLeuProValLeuAspAlaSerGly 19021 : GAGCGCGGCCAGCCCCTGGCCGCAGCGGTAGCCGAGCTGCCTGTGCTGGACGCCTCCGGG : 19080 45 : GlnArgValProPheGlyAlaLeuPheArgGluArgArgAlaValValValPheValArg : 64 ::!!:!|||||||||||||||||||||||||||||||||||||||||||||||||||||| ArgGlnValProPheGlyAlaLeuPheArgGluArgArgAlaValValValPheValArg 19081 : AGGCAGGTGCCCTTCGGCGCGCTGTTTCGGGAGCGTCGGGCTGTCGTAGTCTTCGTGCGG : 19140 65 : >>>> Target Intron 1 >>>> HisPheLeuCysTyrIleCysLysGluTyrV : 75 433 bp ||||||||||||||||||||||||||||||| ++ ++HisPheLeuCysTyrIleCysLysGluTyrV 19141 : gt.........................agCATTTCCTGTGTTACATTTGCAAGGAATACG : 19606 76 : alGluAspLeuAlaLysIleProArgSerPheLeuGln >>>> Target Intron 2 : 88 |||||||||||||||||||||||!:!|||||||||||| 887 bp alGluAspLeuAlaLysIleProLysSerPheLeuGln++ 19607 : TAGAAGATCTGGCCAAAATCCCCAAGAGTTTTTTACAAgt.................... : 19647 89 : >>>> GluAlaAsnValThrLeuIleValIleGlyGlnSerSerTyrHisHisIleGl : 105 ||||||:!!|||||||||||||||||||||||||||||||||||||||||||| ++GluAlaAspValThrLeuIleValIleGlyGlnSerSerTyrHisHisIleGl 19648 : .....agGAAGCAGATGTCACCCTAATAGTGATTGGACAGTCATCCTACCATCATATCGA : 20583 106 : u >>>> Target Intron 3 >>>> ProPheCysLysLeuThrGlyTyrSerHis : 115 | 164 bp |||||||||||||||||||||||||||||| u++ ++ProPheCysLysLeuThrGlyTyrSerHis 20584 : Ggt.........................agcCTTTCTGCAAACTGACTGGATATTCTCAT : 20777 116 : GluIleTyrValAspProGluArgGluIleTyrLysArgLeuGlyMetLysArgGlyGlu : 135 ||||||||||||||||||||||||||||||||||||:::||||||||||||||||||||| GluIleTyrValAspProGluArgGluIleTyrLysLysLeuGlyMetLysArgGlyGlu 20778 : GAAATCTATGTTGATCctgagagagaaatttataaaaaattggGAATGAAAAGAGGTGAA : 20837 136 : GluIleAlaSerSer{G} >>>> Target Intron 4 >>>> {ly}GlnSerPro : 144 |||||||||||||||{|} 4148 bp {||}:!!|||||| GluIleAlaSerSer{G}++ ++{ly}LysSerPro 20838 : GAAATTGCCTCCTCA{G}gt.........................ag{GA}AAGAGCCCc : 25012 145 : HisIleLysSerAsnLeuLeuSerGlySerLeuGlnSerLeuTrpArgAlaValThrGly : 164 |||||||||||||||:::||||||||||||:!!!:!|||||||||||||||||||||||| HisIleLysSerAsnIleLeuSerGlySerIleArgSerLeuTrpArgAlaValThrGly 25013 : catataaaatcaaatatactcTCAGGAAGCATTCGGAGCCTGTGGAGGGCAGTGACTGGC : 25072 165 : ProLeuPheAspPheGlnGlyAspProAlaGlnGlnGlyGlyThrLeuIleLeuGlyPro : 184 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ProLeuPheAspPheGlnGlyAspProAlaGlnGlnGlyGlyThrLeuIleLeuGlyPro 25073 : CCTCTTTTTGATTTTCAAGGAGACCCTGCTCAGCAAGGCGGAACCCTCATCTTAGGTCCA : 25132 185 : Gly : 185 ||| Gly 25133 : GGT : 25137 vulgar: SPP00000114_2.0 4 185 . KB229214.1:subseq(215400,25140) 18962 25137 + 823 M 60 180 5 0 2 I 0 429 3 0 2 M 23 69 5 0 2 I 0 883 3 0 2 M 18 54 5 0 2 I 0 160 3 0 2 M 35 105 S 0 1 5 0 2 I 0 4144 3 0 2 S 1 2 M 44 132 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2015-11-25 ##type DNA # # # seqname source feature start end score strand frame attributes # KB229214.1:subseq(215400,25140) exonerate:protein2genome:local gene 18963 25137 823 + . gene_id 1 ; sequence SPP00000114_2.0 ; gene_orientation + KB229214.1:subseq(215400,25140) exonerate:protein2genome:local cds 18963 19142 . + . KB229214.1:subseq(215400,25140) exonerate:protein2genome:local exon 18963 19142 . + . insertions 0 ; deletions 0 KB229214.1:subseq(215400,25140) exonerate:protein2genome:local splice5 19143 19144 . + . intron_id 1 ; splice_site "GT" KB229214.1:subseq(215400,25140) exonerate:protein2genome:local intron 19143 19575 . + . intron_id 1 KB229214.1:subseq(215400,25140) exonerate:protein2genome:local splice3 19574 19575 . + . intron_id 0 ; splice_site "AG" KB229214.1:subseq(215400,25140) exonerate:protein2genome:local cds 19576 19644 . + . KB229214.1:subseq(215400,25140) exonerate:protein2genome:local exon 19576 19644 . + . insertions 0 ; deletions 0 KB229214.1:subseq(215400,25140) exonerate:protein2genome:local splice5 19645 19646 . + . intron_id 2 ; splice_site "GT" KB229214.1:subseq(215400,25140) exonerate:protein2genome:local intron 19645 20531 . + . intron_id 2 KB229214.1:subseq(215400,25140) exonerate:protein2genome:local splice3 20530 20531 . + . intron_id 1 ; splice_site "AG" KB229214.1:subseq(215400,25140) exonerate:protein2genome:local cds 20532 20585 . + . KB229214.1:subseq(215400,25140) exonerate:protein2genome:local exon 20532 20585 . + . insertions 0 ; deletions 0 KB229214.1:subseq(215400,25140) exonerate:protein2genome:local splice5 20586 20587 . + . intron_id 3 ; splice_site "GT" KB229214.1:subseq(215400,25140) exonerate:protein2genome:local intron 20586 20749 . + . intron_id 3 KB229214.1:subseq(215400,25140) exonerate:protein2genome:local splice3 20748 20749 . + . intron_id 2 ; splice_site "ag" KB229214.1:subseq(215400,25140) exonerate:protein2genome:local cds 20750 20855 . + . KB229214.1:subseq(215400,25140) exonerate:protein2genome:local exon 20750 20855 . + . insertions 0 ; deletions 0 KB229214.1:subseq(215400,25140) exonerate:protein2genome:local splice5 20856 20857 . + . intron_id 4 ; splice_site "GT" KB229214.1:subseq(215400,25140) exonerate:protein2genome:local intron 20856 25003 . + . intron_id 4 KB229214.1:subseq(215400,25140) exonerate:protein2genome:local splice3 25002 25003 . + . intron_id 3 ; splice_site "AG" KB229214.1:subseq(215400,25140) exonerate:protein2genome:local cds 25004 25137 . + . KB229214.1:subseq(215400,25140) exonerate:protein2genome:local exon 25004 25137 . + . insertions 0 ; deletions 0 KB229214.1:subseq(215400,25140) exonerate:protein2genome:local similarity 18963 25137 823 + . alignment_id 1 ; Query SPP00000114_2.0 ; Align 18963 5 180 ; Align 19576 65 69 ; Align 20532 88 54 ; Align 20750 106 105 ; Align 25006 142 132 # --- END OF GFF DUMP --- # -- completed exonerate analysis