Command line: [exonerate -m p2g --showtargetgff -q SelU3n/SelU3n_U.fa -t SelU3n/SUBSEQ/KB229213.1_0_subseq.txt --exhaustive yes] Hostname: [luke] C4 Alignment: ------------ Query: SPP00000117_2.0 # Protein # Selenoprotein X3 (SelX3) # Human (Homo sapiens) Target: KB229213.1:subseq(991624,25206) Odobenus rosmarus divergens isolate Ivan unplaced genomic scaffold Scaffold336, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 660 Query range: 50 -> 228 Target range: 25206 -> 16880 51 : GluAlaValGluLeuArgSerLeuTrpArgGluHisAlaCysValValAlaGlyLeuArg : 70 :!!||||||||||||||||||||||||||||||!!.|||||||||||||||||||||||| GlnAlaValGluLeuArgSerLeuTrpArgGluGlnAlaCysValValAlaGlyLeuArg 25206 : CAGGCCGTGGAGCTGCGGAGTCTGTGGCGGGAGCAGGCGTGCGTGGTGGCCGGCCTGCGG : 25149 71 : ArgPheGlyCysValValCysArgTrpIleAlaGlnAspLeuSerSerLeuAlaGlyLeu : 90 |||||||||||| !|||||||||||||||||||||||||||||||||||| !|||||| ArgPheGlyCysSerValCysArgTrpIleAlaGlnAspLeuSerSerLeuArgGlyLeu 25148 : CGCTTCGGCTGCTCGGTGTGTCGCTGGATCGCCCAGGACCTCAGCAGCCTCAGGGGGCTA : 25089 91 : LeuAspGlnHisGlyValArgLeuValGlyValGlyProGluAlaLeuGlyLeuGlnGlu : 110 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| LeuAspGlnHisGlyValArgLeuValGlyValGlyProGluAlaLeuGlyLeuGlnGlu 25088 : CTGGACCAGCATGGCGTGCGCCTGGTGGGCGTGGGGCCCGAGGCCCTGGGCCTGCAGGAG : 25029 111 : PheLeuAspGlyAspTyrPheAlaGly{G} >>>> Target Intron 1 >>>> { : 120 ||||||||||||! !||||||||||||{|} 575 bp { PheLeuAspGlyGlyTyrPheAlaGly{G}++ +-{ 25028 : TTCCTGGACGGGGGCTACTTCGCAGGA{G}gt.........................ac{ : 24423 121 : lu}LeuTyrLeuAspGluSerLysGlnLeuTyrLysGluLeuGlyPheLys{Ar} >>> : 137 ||}||||||||||||||||||||||||!!!|||!:!||||||||||||!:!{||} lu}LeuTyrLeuAspGluSerLysGlnPheTyrArgGluLeuGlyPheArg{Ar}++ 24422 : AG}CTCTACCTGGATGAAAGCAAGCAGTTCTACAGGGAGCTGGGCTTCAGA{CG}gt... : 24369 138 : > Target Intron 2 >>>> {g}Leu{T} >>>> Target Intron 3 >>>> : 139 318 bp {|}! !{|} 168 bp ++{g}Ser{T}-+ 24368 : ......................ag{G}TCT{T}ct......................... : 24046 140 : {rp}ThrGlnAlaSerProGluPheGlyGlnAlaThrTrpCysLeuArgArgTyrAsn : 157 {||} !||| !.!! !!..! ! !! ! ! ! !|||||| !!|||! !||| ++{rp}LeuGlnArgGlyAlaArgAlaTrpThrArgGlnLeuCysLeuCysArgCysAsn 24045 : ag{GG}CTTCAGAGAGGAGCCAGAGCCTGGACAAGGCAGCTGTGTCTTTGCAGGTGCAAC : 23827 158 : SerLeuSerIleLeuProAlaAlaLeuGlyLysProValArgAspValAlaAlaLys > : 177 !!!|||||||||:!!|||||||||||||||||||||||||||||||||||| !||| ArgLeuSerIleValProAlaAlaLeuGlyLysProValArgAspValAlaLeuLys++ 23826 : AGATTGAGCATTGTGCCTGCTGCCCTGGGGAAGCCTGTGCGCGATGTGGCCCTCAAGgt. : 23765 178 : >>> Target Intron 4 >>>> AlaLysAlaValGlyIleGlnGlyAsnLeuSerG : 188 84 bp |||||||||||||||||||||||||||||||||| ++AlaLysAlaValGlyIleGlnGlyAsnLeuSerG 23764 : ........................agGCTAAAGCTGTTGGCATCCAGGGCAACCTGTCGG : 23650 189 : lyAspLeuLeuGlnSerGlyGlyLeuLeuValValSerLys{G} >>>> Target In : 202 |||||||||||||||||||||||||||||||||||!!!|||{|} 321 lyAspLeuLeuGlnSerGlyGlyLeuLeuValValThrLys{G}++ 23649 : GGGACTTGCTGCAGAGTGGAGGGCTGCTGGTGGTTACCAAA{G}gt.............. : 23605 203 : tron 5 >>>> {lu}ValProArgArgLeuArgProGlnGlyAlaHisProAlaGlyP : 217 bp {||}|||||| !! !!||| !! !!! !|||! !||||||||||||| ++{lu}ValProGly***LeuCysSerProGlyGluHisProAlaGlyP 23604 : ...........ag{AA}GTCCCCGGGTGACTATGTTCCCCAGGAGAGCATCCTGCAGGCC : 23242 218 : roGlyHisLeuCysGlyGlyLeuCys{Gl} >>>> Target Intron 6 >>>> { : 226 ||||||||||||||||||||||||||{||} 6326 bp { roGlyHisLeuCysGlyGlyLeuCys{Gl}++ ++{ 23241 : CTGGGCATCTCTGCGGAGGGCTGTGC{CA}gt.........................ag{ : 16887 227 : n}ArgPro : 228 |}!:!||| n}LysPro 16886 : G}AAGCCC : 16881 vulgar: SPP00000117_2.0 50 228 . KB229213.1:subseq(991624,25206) 25206 16880 - 660 M 69 207 S 0 1 5 0 2 I 0 571 3 0 2 S 1 2 M 16 48 S 0 2 5 0 2 I 0 314 3 0 2 S 1 1 M 1 3 S 0 1 5 0 2 I 0 164 3 0 2 S 1 2 M 37 111 5 0 2 I 0 80 3 0 2 M 25 75 S 0 1 5 0 2 I 0 317 3 0 2 S 1 2 M 23 69 S 0 2 5 0 2 I 0 6322 3 0 2 S 1 1 M 2 6 # --- 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 # KB229213.1:subseq(991624,25206) exonerate:protein2genome:local gene 16881 25206 660 - . gene_id 1 ; sequence SPP00000117_2.0 ; gene_orientation + KB229213.1:subseq(991624,25206) exonerate:protein2genome:local cds 24999 25206 . - . KB229213.1:subseq(991624,25206) exonerate:protein2genome:local exon 24999 25206 . - . insertions 0 ; deletions 0 KB229213.1:subseq(991624,25206) exonerate:protein2genome:local splice5 24997 24998 . - . intron_id 1 ; splice_site "GT" KB229213.1:subseq(991624,25206) exonerate:protein2genome:local intron 24424 24998 . - . intron_id 1 KB229213.1:subseq(991624,25206) exonerate:protein2genome:local splice3 24424 24425 . - . intron_id 0 ; splice_site "AC" KB229213.1:subseq(991624,25206) exonerate:protein2genome:local cds 24372 24423 . - . KB229213.1:subseq(991624,25206) exonerate:protein2genome:local exon 24372 24423 . - . insertions 0 ; deletions 0 KB229213.1:subseq(991624,25206) exonerate:protein2genome:local splice5 24370 24371 . - . intron_id 2 ; splice_site "GT" KB229213.1:subseq(991624,25206) exonerate:protein2genome:local intron 24054 24371 . - . intron_id 2 KB229213.1:subseq(991624,25206) exonerate:protein2genome:local splice3 24054 24055 . - . intron_id 1 ; splice_site "AG" KB229213.1:subseq(991624,25206) exonerate:protein2genome:local cds 24049 24053 . - . KB229213.1:subseq(991624,25206) exonerate:protein2genome:local exon 24049 24053 . - . insertions 0 ; deletions 0 KB229213.1:subseq(991624,25206) exonerate:protein2genome:local splice5 24047 24048 . - . intron_id 3 ; splice_site "CT" KB229213.1:subseq(991624,25206) exonerate:protein2genome:local intron 23881 24048 . - . intron_id 3 KB229213.1:subseq(991624,25206) exonerate:protein2genome:local splice3 23881 23882 . - . intron_id 2 ; splice_site "AG" KB229213.1:subseq(991624,25206) exonerate:protein2genome:local cds 23768 23880 . - . KB229213.1:subseq(991624,25206) exonerate:protein2genome:local exon 23768 23880 . - . insertions 0 ; deletions 0 KB229213.1:subseq(991624,25206) exonerate:protein2genome:local splice5 23766 23767 . - . intron_id 4 ; splice_site "GT" KB229213.1:subseq(991624,25206) exonerate:protein2genome:local intron 23684 23767 . - . intron_id 4 KB229213.1:subseq(991624,25206) exonerate:protein2genome:local splice3 23684 23685 . - . intron_id 3 ; splice_site "AG" KB229213.1:subseq(991624,25206) exonerate:protein2genome:local cds 23608 23683 . - . KB229213.1:subseq(991624,25206) exonerate:protein2genome:local exon 23608 23683 . - . insertions 0 ; deletions 0 KB229213.1:subseq(991624,25206) exonerate:protein2genome:local splice5 23606 23607 . - . intron_id 5 ; splice_site "GT" KB229213.1:subseq(991624,25206) exonerate:protein2genome:local intron 23287 23607 . - . intron_id 5 KB229213.1:subseq(991624,25206) exonerate:protein2genome:local splice3 23287 23288 . - . intron_id 4 ; splice_site "AG" KB229213.1:subseq(991624,25206) exonerate:protein2genome:local cds 23214 23286 . - . KB229213.1:subseq(991624,25206) exonerate:protein2genome:local exon 23214 23286 . - . insertions 0 ; deletions 0 KB229213.1:subseq(991624,25206) exonerate:protein2genome:local splice5 23212 23213 . - . intron_id 6 ; splice_site "GT" KB229213.1:subseq(991624,25206) exonerate:protein2genome:local intron 16888 23213 . - . intron_id 6 KB229213.1:subseq(991624,25206) exonerate:protein2genome:local splice3 16888 16889 . - . intron_id 5 ; splice_site "AG" KB229213.1:subseq(991624,25206) exonerate:protein2genome:local cds 16881 16887 . - . KB229213.1:subseq(991624,25206) exonerate:protein2genome:local exon 16881 16887 . - . insertions 0 ; deletions 0 KB229213.1:subseq(991624,25206) exonerate:protein2genome:local similarity 16881 25206 660 - . alignment_id 1 ; Query SPP00000117_2.0 ; Align 25207 51 207 ; Align 24422 121 48 ; Align 24053 138 3 ; Align 23879 140 111 ; Align 23684 177 75 ; Align 23285 203 69 ; Align 16887 227 6 # --- END OF GFF DUMP --- # -- completed exonerate analysis