Command line: [exonerate -m p2g --showtargetgff -q SBP2n/SBP2n_U.fa -t SBP2n/SUBSEQ/KB229338.1_0_subseq.txt --exhaustive yes] Hostname: [luke] C4 Alignment: ------------ Query: SPP00000054_2.0 # Protein # SECIS binding protein 2 (SBP2) # Human (Homo sapiens) Target: KB229338.1:subseq(1859871,25221) Odobenus rosmarus divergens isolate Ivan unplaced genomic scaffold Scaffold461, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 987 Query range: 631 -> 854 Target range: 25221 -> 18581 632 : TyrCysSerGlnMetLeuSerLysGluValAspAlaCysValThrAspLeuLeuLysGlu : 651 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| TyrCysSerGlnMetLeuSerLysGluValAspAlaCysValThrAspLeuLeuLysGlu 25221 : TACTGCAGCCAGATGCTGAGTAAGGAGGTGGACGCGTGTGTCACGGATCTGCTGAAGGAG : 25164 652 : LeuValArgPheGlnAspArgMetTyrGlnLysAspProValLysAlaLysThrLysArg : 671 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| LeuValArgPheGlnAspArgMetTyrGlnLysAspProValLysAlaLysThrLysArg 25163 : CTGGTGCGCTTCCAAGACCGCATGTACCAGAAAGATCCAGTCAAGGCTAAGACCAAACGC : 25104 672 : ArgLeuValLeuGlyLeuArgGluValLeuLysHisLeuLysLeuLysLysLeuLysCys : 691 |||||||||||||||||||||||||||||||||||||||||||||!:!|||||||||||| ArgLeuValLeuGlyLeuArgGluValLeuLysHisLeuLysLeuArgLysLeuLysCys 25103 : CGACTTGTGCTGGGGCTGCGGGAGGTCCTCAAGCATCTGAAGCTCAGGAAACTCAAGTGC : 25044 692 : ValIleIleSerProAsnCysGluLysIleGlnSerLys{G} >>>> Target Intr : 705 :!!||||||||||||||||||||||||||||||||||||{|} 5471 bp IleIleIleSerProAsnCysGluLysIleGlnSerLys{G}++ 25043 : ATCATCATCTCTCCCAACTGTGAGAAGATCCAGTCGAAA{G}gt................ : 24999 706 : on 1 >>>> {ly}GlyLeuAspAspThrLeuHisThrIleIleAspTyrAlaCysGlu : 720 {||}||||||||||||||||||||||||||||||||||||||||||||| ++{ly}GlyLeuAspAspThrLeuHisThrIleIleAspTyrAlaCysGlu 24998 : .........ag{GT}GGGCTGGATGACACGCTGCACACCATCATTGATTATGCCTGTGAG : 19486 721 : GlnAsnIleProPheValPheAlaLeuAsnArgLysAlaLeuGlyArgSerLeuAsnLys : 740 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GlnAsnIleProPheValPheAlaLeuAsnArgLysAlaLeuGlyArgSerLeuAsnLys 19485 : CAGAACATTCCCTTCGTGTTCGCGCTCAACCGCAAAGCTCTGGGGCGCAGTTTGAACAAG : 19426 741 : AlaValProValSerValValGlyIlePheSerTyrAspGlyAlaGln >>>> Targe : 757 |||||||||||||||||||||||||||||||||||||||||||||||| AlaValProValSerValValGlyIlePheSerTyrAspGlyAlaGln++ 19425 : GCCGTTCCCGTCAGCGTGGTGGGCATCTTCAGCTACGACGGGGCCCAGgt.......... : 19373 758 : t Intron 2 >>>> AspGlnPheHisLysMetValGluLeuThrValAlaAlaArgG : 771 131 bp ||||||||||||!:!|||||||||||||||:!!|||||||||| ++AspGlnPheHisArgMetValGluLeuThrMetAlaAlaArgG 19372 : ...............agGACCAGTTCCACAGGATGGTCGAGCTGACGATGGCCGCCCGGC : 19202 772 : lnAlaTyrLysThrMetLeuGluAsnValGlnGlnGluLeuValGlyGluProArgProG : 791 |||||||||||||||||||||||||||||!::!:!||||||!.!||||||||| !!|||! lnAlaTyrLysThrMetLeuGluAsnValArgArgGluLeuAlaGlyGluProGlyProP 19201 : AGGCGTACAAGACCATGCTGGAGAATGTGCGCCGAGAGCTGGCCGGGGAGCCTGGGCCCC : 19142 792 : lnAlaProProSerLeuProThrGlnGlyProSerCysProAlaGluAspGlyProProA : 811 !|||||| !!.!!! !|||..!|||||||||.!! !! !!|||:!!||||||||||||| roAlaProAlaGlyProProValGlnGlyProGlyGlySerAlaGlnAspGlyProProA 19141 : CGGCTCCGGCCGGCCCGCCCGTGCAGGGCCCCGGCGGCTCGGCGCAGGACGGCCCCCCTG : 19082 812 : la<->LeuLysGluLysGluGluProHisTyr{I} >>>> Target Intron 3 >> : 821 || :!! ! !||||||||||||||||||{|} 366 bp laSerValProGlyLysGluGluProHisTyr{I}++ 19081 : CCTCCGTGCCTGGGAAAGAAGAGCCGCACTAC{A}gt....................... : 19046 822 : >> {le}GluIleTrpLysLysHisLeuGluAlaTyrSerGlyCysThrLeuGluLeuG : 839 {||}|||||||||!:!!:!|||||||||!.!|||||| !!|||.!!|||||||||| ++{le}GluIleTrpArgArgHisLeuGluValTyrSerArgCysAlaLeuGluLeuG 19045 : ..ag{TT}GAAATCTGGAGAAGACACCTGGAAGTGTACAGTCGCTGTGCTCTGGAGCTGG : 18629 840 : luGluSerLeuGluAlaSerThrSerGlnMetMetAsnLeuAsnLeu : 854 ||!!:|||||||||||||||||||||||||||||||||||||||||| luAspSerLeuGluAlaSerThrSerGlnMetMetAsnLeuAsnLeu 18628 : AAGACTCGCTGGAGGCTTCAACCTCTCAGATGATGAACCTGAATTTA : 18582 vulgar: SPP00000054_2.0 631 854 . KB229338.1:subseq(1859871,25221) 25221 18581 - 987 M 73 219 S 0 1 5 0 2 I 0 5467 3 0 2 S 1 2 M 51 153 5 0 2 I 0 127 3 0 2 M 55 165 G 0 3 M 9 27 S 0 1 5 0 2 I 0 362 3 0 2 S 1 2 M 33 99 # --- 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 # KB229338.1:subseq(1859871,25221) exonerate:protein2genome:local gene 18582 25221 987 - . gene_id 1 ; sequence SPP00000054_2.0 ; gene_orientation + KB229338.1:subseq(1859871,25221) exonerate:protein2genome:local cds 25002 25221 . - . KB229338.1:subseq(1859871,25221) exonerate:protein2genome:local exon 25002 25221 . - . insertions 0 ; deletions 0 KB229338.1:subseq(1859871,25221) exonerate:protein2genome:local splice5 25000 25001 . - . intron_id 1 ; splice_site "GT" KB229338.1:subseq(1859871,25221) exonerate:protein2genome:local intron 19531 25001 . - . intron_id 1 KB229338.1:subseq(1859871,25221) exonerate:protein2genome:local splice3 19531 19532 . - . intron_id 0 ; splice_site "AG" KB229338.1:subseq(1859871,25221) exonerate:protein2genome:local cds 19376 19530 . - . KB229338.1:subseq(1859871,25221) exonerate:protein2genome:local exon 19376 19530 . - . insertions 0 ; deletions 0 KB229338.1:subseq(1859871,25221) exonerate:protein2genome:local splice5 19374 19375 . - . intron_id 2 ; splice_site "GT" KB229338.1:subseq(1859871,25221) exonerate:protein2genome:local intron 19245 19375 . - . intron_id 2 KB229338.1:subseq(1859871,25221) exonerate:protein2genome:local splice3 19245 19246 . - . intron_id 1 ; splice_site "AG" KB229338.1:subseq(1859871,25221) exonerate:protein2genome:local cds 19049 19244 . - . KB229338.1:subseq(1859871,25221) exonerate:protein2genome:local exon 19049 19244 . - . insertions 3 ; deletions 0 KB229338.1:subseq(1859871,25221) exonerate:protein2genome:local splice5 19047 19048 . - . intron_id 3 ; splice_site "GT" KB229338.1:subseq(1859871,25221) exonerate:protein2genome:local intron 18683 19048 . - . intron_id 3 KB229338.1:subseq(1859871,25221) exonerate:protein2genome:local splice3 18683 18684 . - . intron_id 2 ; splice_site "AG" KB229338.1:subseq(1859871,25221) exonerate:protein2genome:local cds 18582 18682 . - . KB229338.1:subseq(1859871,25221) exonerate:protein2genome:local exon 18582 18682 . - . insertions 0 ; deletions 0 KB229338.1:subseq(1859871,25221) exonerate:protein2genome:local similarity 18582 25221 987 - . alignment_id 1 ; Query SPP00000054_2.0 ; Align 25222 632 219 ; Align 19529 706 153 ; Align 19245 757 165 ; Align 19077 812 27 ; Align 18681 822 99 # --- END OF GFF DUMP --- # -- completed exonerate analysis