Command line: [exonerate -m p2g --showtargetgff -q selenoi_zf.aa.fa.canviat -t genomeselenoi_JXSJ01000029.1.fa] Hostname: [ws101100u] C4 Alignment: ------------ Query: SPP00000635_2.0 # Protein # Selenoprotein I (SELENOI) # Zebrafish Target: JXSJ01000029.1:subseq(3454276,105626) Miichthys miiuy scaffold29, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 1643 Query range: 0 -> 397 Target range: 58104 -> 49999 1 : TyrHisTyrValThrGlnGluGlnLeuSerGlyPheAspLysTyrLys >>>> Targe : 17 |||.!.|||||||||||||||||||||:!!|||||||||||||||||| 2 TyrGluTyrValThrGlnGluGlnLeuAlaGlyPheAspLysTyrLys++ 58104 : TACGAATACGTCACTCAGGAGCAGCTTGCGGGCTTCGACAAGTACAAGgt.......... : 58054 18 : t Intron 1 >>>> TyrSerAlaValAspSerAsnProLeuSerIleTyrValMetH : 31 433 bp ||||||||||||||||||||||||||||||:!!|||||||||| ++TyrSerAlaValAspSerAsnProLeuSerValTyrValMetH 58053 : ...............agTACAGCGCAGTGGACTCGAATCCCCTGTCTGTCTACGTCATGC : 55581 32 : isProPheTrpAsnSerValValLys >>>> Target Intron 2 >>>> ValLe : 41 ||||||||||||||! !||||||||| 467 bp !!|| isProPheTrpAsnPheValValLys++ ++PheLe 55580 : ACCCGTTCTGGAACTTTGTGGTGAAGgt.........................agTTTCT : 55084 42 : uProThrTrpLeuAlaProAsnLeuIleThrPheThrGlyPheMetPheLeuValLeuTh : 61 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||!. uProThrTrpLeuAlaProAsnLeuIleThrPheThrGlyPheMetPheLeuValLeuAs 55083 : GCCAACATGGTTGGCTCCAAACCTCATTACGTTTACAGGCTTCATGTTCCTTGTGTTGAA : 55024 62 : rPheThrMetLeuSerPhePheAspPheAspPheTyrAlaSer{G} >>>> Target : 76 !||| !||||||:!!|||!:!|||||||||||| !||||||{!} 69 nPheLeuMetLeuAlaPheTyrAspPheAspPheThrAlaSer{A}++ 55023 : CTTCCTTATGTTGGCCTTCTACGACTTTGACTTCACTGCCTCT{G}gt............ : 54976 77 : Intron 3 >>>> {ly}GluGlyHisThrHisValProSerTrpValTrpIleAlaAl : 90 8 bp {.!}! !|||||| !|||||||||||||||||||||:!!||||| ++{la}AlaGlyHisGluHisValProSerTrpValTrpValAlaAl 54975 : .............ag{CT}GCAGGACATGAACACGTGCCTAGTTGGGTCTGGGTTGCTGC : 54239 91 : aGlyLeuPheAsnPheLeuAlaTyrThrLeu{A} >>>> Target Intron 4 >>> : 101 ||||:!!||||||||||||||||||||||||{|} 1942 bp aGlyIlePheAsnPheLeuAlaTyrThrLeu{A}++ 54238 : AGGGATCTTCAACTTCTTGGCCTATACACTC{G}gt........................ : 54203 102 : > {sp}GlyValAspGlyLysGlnAlaArgArgThrAsnSerSerThrProLeuGlyGl : 119 {||}||||||||||||||||||||||||||||||||||||||||||||||||||||| ++{sp}GlyValAspGlyLysGlnAlaArgArgThrAsnSerSerThrProLeuGlyGl 54202 : .ag{AT}GGTGTTGATGGCAAACAGGCTCGTCGCACCAACTCCTCCACCCCACTAGGGGA : 52210 120 : uLeuPheAspHisGlyLeuAspSerTrpAlaCysValPhePheValAlaThrValTyrSe : 139 ||||||||||||||||||||||||||||||||||:!!||||||||||||||||||||||| uLeuPheAspHisGlyLeuAspSerTrpAlaCysIlePhePheValAlaThrValTyrSe 52209 : GCTGTTTGACCATGGCCTGGACAGTTGGGCGTGCATCTTCTTTGTGGCCACCGTCTACTC : 52150 140 : rValPheGlyArgGlyGluThrGlyValSerValValThrLeuTyrTyrLeuLeuTrpVa : 159 |:!!|||||||||||||||!:!||||||.!!|||!.!||||||||||||:!!|||||||| rIlePheGlyArgGlyGluSerGlyValGlyValAlaThrLeuTyrTyrIleLeuTrpVa 52149 : CATATTTGGGCGTGGGGAAAGCGGCGTAGGTGTCGCTACACTGTACTACATCCTGTGGGT : 52090 160 : lValLeuPheSerPheIleLeuSerHisTrpGluLysTyrAsnThrGlyIleLeuPheLe : 179 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| lValLeuPheSerPheIleLeuSerHisTrpGluLysTyrAsnThrGlyIleLeuPheLe 52089 : GGTGCTGTTCTCGTTCATTCTATCCCACTGGGAGAAATATAACACTGGCATCTTGTTTTT : 52030 180 : uProTrpGlyTyrAspIleSerGlnVal >>>> Target Intron 5 >>>> Thr : 189 |||||||||||||||||||||||||||| 955 bp ||| uProTrpGlyTyrAspIleSerGlnVal++ ++Thr 52029 : GCCGTGGGGATACGACATCAGCCAAGTggt.........................agACC : 51045 190 : IleSerIleValTyrIleIleThrAlaValValGlyValGluThrTrpTyrLysProVal : 209 ||||||:!!||||||:!::!!||||||||||||||||||||||||||||||:!!|||:!! IleSerLeuValTyrLeuValThrAlaValValGlyValGluThrTrpTyrGlnProIle 51044 : ATTTCCCTCGTTTACTTGGTCACTGCTGTGGTCGGCGTGGAAACATGGTACCAGCCAATC : 50985 210 : PheLeuAsnIleHisTyrArgAspLeuPheThrValMetIleIle{G} >>>> Targe : 225 .!.|||:!!.!!! !|||||||||||||||||| !!|||||||||{!} LeuLeuHisPheLeuTyrArgAspLeuPheThrPheMetIleIle{A}++ 50984 : CTGTTGCACTTCCTCTATAGAGACCTTTTCACCTTTATGATCATC{G}gt.......... : 50934 226 : t Intron 6 >>>> {ly}CysLeuPheValValThrLeuProMetSerLeuTyrAsn : 238 79 bp {.!}|||! !|||..!||||||||||||||||||||||||||| ++{la}CysSerPheThrValThrLeuProMetSerLeuTyrAsn 50933 : ...............ag{CC}TGTTCCTTTACTGTGACCTTACCCATGAGCCTCTACAAC : 50819 239 : ValPhe{Ly} >>>> Target Intron 7 >>>> {s}AlaTyrArgAsnAsnThr : 247 |||.!.{||} 89 bp {|}!.!:!!|||!:!|||||| ValLeu{Ly}++ ++{s}GlyHisArgSerAsnThr 50818 : GTCCTG{AA}gt.........................ag{A}GGTCACCGCAGTAACACT : 50703 248 : LeuLysHisSerSerLeuTyrGluAlaLeuLeuProPhePheSerProValLeuLeuPhe : 267 |||||||||||||||||||||||||||!!!|||||||||...|||||| ||||||||| LeuLysHisSerSerLeuTyrGluAlaPheLeuProPheLeuSerProPheLeuLeuPhe 50702 : CTGAAGCACAGCAGCCTGTACGAAGCCTTCCtgcccttcctctctcctttcctcctcttt : 50643 268 : ValLeuSerThrLeuTrpIleSerPheSerProThrAsnIleValGlnLysGlnProArg : 287 ::!|||||||||:!!|||:!: !!:!||||||:!!||||||:!!:!! !||||||||| IleLeuSerThrIleTrpValValTyrSerProSerAsnIleLeuGluLeuGlnProArg 50642 : atCTTGTCCACAATTTGGGTGGTCTACTCTCCATCCAACATCCTCGAGCTGCAGCCCAGG : 50583 288 : IlePheTyrLeuMetValGlyThrAlaPheSerAsnValThr >>>> Target Intr : 302 ! !|||||||||||||||||||||||||||:!!||||||||| 94 bp ThrPheTyrLeuMetValGlyThrAlaPheAlaAsnValThr++ 50582 : ACCTTCTACCTCATGGTGGGGACAGCCTTCGCTAATGTCACGgt................ : 50536 303 : on 8 >>>> CysLysLeuIleValCysGlnMetSerAsnThrArgCysLysProLeuS : 318 |||||||||||||||||||||||||||||||||||||||:!! !!|||| ++CysLysLeuIleValCysGlnMetSerAsnThrArgCysGlnAlaLeuS 50535 : .........agTGTAAGCTGATTGTGTGTCAGATGAGTAACACGCGTTGCCAGGCGctca : 50396 319 : erLeuLeuLeuLeuProMetSerIleValValLeuLeuValIleSerGlyThrValGlnG : 338 || |||||||||||||||!!! !||||||||||||!.!:!:!!!||| ||| ! erTrpLeuLeuLeuProMetThrProValValLeuLeuAlaValThrGly---ValPheA 50395 : gctggctgctgctgcccatGACGCCAGTGGTGTTGTTGGCGGTGACCGGG---GTGTTCG : 50339 339 : lyGlyGluSerLeuValLeuPheIleTrpThrAlaValValLeuLeuThrHisIleHisT : 358 .!..!|||!!!|||:!!|||!:!:!:|||||||||!.!|||:!!|||.!!|||||||||| laAsnGluThrLeuLeuLeuTyrLeuTrpThrAlaAlaValIleLeuAlaHisIleHisT 50338 : CTAACGAGACCTTACTGCTTTATCTGTGGACAGCTGCTGTCATACTAGCACACATACACT : 50279 359 : yrGlyValSerVal >>>> Target Intron 9 >>>> ValLysGlnLeuSerAs : 368 |||||||||||||| 157 bp |||:!!|||||||||! yrGlyValSerVal++ ++ValGlnGlnLeuSerGl 50278 : ACGGTGTATCAGTGgt.........................agGTACAACAGCTCAGCGG : 50092 369 : pHisPheAsnIlePheAlaPheSerLeuLysLysProAsnSerAsp<->UnkGlnAspGl : 387 !||||||||||||.!!|||||||||||||||||||||||||||||| ::::::|| yHisPheAsnIleLeuAlaPheSerLeuLysLysProAsnSerAsp***GlnGluGluGl 50091 : CCACTTCAACATCCTCGCCTTCTCCCTGAAAAAGCCCAACAGTgactgacaggaggagga : 50032 388 : uGluLysIleGlyLeuLysAlaAlaGluVal : 397 ||||:::||||||||||||! !||||||||| uGluArgIleGlyLeuLysGluAlaGluVal 50031 : agaacgaATCGGCTTGAAAGAAGCGGAGGTT : 50000 vulgar: SPP00000635_2.0 0 397 . JXSJ01000029.1:subseq(3454276,105626) 58104 49999 - 1643 M 16 48 5 0 2 I 0 2429 3 0 2 M 23 69 5 0 2 I 0 463 3 0 2 M 36 108 S 0 1 5 0 2 I 0 694 3 0 2 S 1 2 M 24 72 S 0 1 5 0 2 I 0 1938 3 0 2 S 1 2 M 87 261 5 0 2 I 0 951 3 0 2 M 36 108 S 0 1 5 0 2 I 0 75 3 0 2 S 1 2 M 15 45 S 0 2 5 0 2 I 0 85 3 0 2 S 1 1 M 60 180 5 0 2 I 0 90 3 0 2 M 33 99 G 1 0 M 27 81 5 0 2 I 0 153 3 0 2 M 21 63 G 0 3 M 14 42 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-16 ##type DNA # # # seqname source feature start end score strand frame attributes # JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local gene 50000 58104 1643 - . gene_id 1 ; sequence SPP00000635_2.0 ; gene_orientation + JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local cds 58057 58104 . - . JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local exon 58057 58104 . - . insertions 0 ; deletions 0 JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local splice5 58055 58056 . - . intron_id 1 ; splice_site "GT" JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local intron 55624 58056 . - . intron_id 1 JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local splice3 55624 55625 . - . intron_id 0 ; splice_site "ag" JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local cds 55555 55623 . - . JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local exon 55555 55623 . - . insertions 0 ; deletions 0 JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local splice5 55553 55554 . - . intron_id 2 ; splice_site "GT" JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local intron 55088 55554 . - . intron_id 2 JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local splice3 55088 55089 . - . intron_id 1 ; splice_site "AG" JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local cds 54979 55087 . - . JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local exon 54979 55087 . - . insertions 0 ; deletions 0 JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local splice5 54977 54978 . - . intron_id 3 ; splice_site "GT" JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local intron 54281 54978 . - . intron_id 3 JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local splice3 54281 54282 . - . intron_id 2 ; splice_site "AG" JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local cds 54206 54280 . - . JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local exon 54206 54280 . - . insertions 0 ; deletions 0 JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local splice5 54204 54205 . - . intron_id 4 ; splice_site "GT" JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local intron 52264 54205 . - . intron_id 4 JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local splice3 52264 52265 . - . intron_id 3 ; splice_site "AG" JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local cds 52001 52263 . - . JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local exon 52001 52263 . - . insertions 0 ; deletions 0 JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local splice5 51999 52000 . - . intron_id 5 ; splice_site "gt" JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local intron 51046 52000 . - . intron_id 5 JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local splice3 51046 51047 . - . intron_id 4 ; splice_site "AG" JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local cds 50937 51045 . - . JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local exon 50937 51045 . - . insertions 0 ; deletions 0 JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local splice5 50935 50936 . - . intron_id 6 ; splice_site "GT" JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local intron 50858 50936 . - . intron_id 6 JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local splice3 50858 50859 . - . intron_id 5 ; splice_site "AG" JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local cds 50809 50857 . - . JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local exon 50809 50857 . - . insertions 0 ; deletions 0 JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local splice5 50807 50808 . - . intron_id 7 ; splice_site "GT" JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local intron 50720 50808 . - . intron_id 7 JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local splice3 50720 50721 . - . intron_id 6 ; splice_site "AG" JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local cds 50539 50719 . - . JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local exon 50539 50719 . - . insertions 0 ; deletions 0 JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local splice5 50537 50538 . - . intron_id 8 ; splice_site "GT" JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local intron 50445 50538 . - . intron_id 8 JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local splice3 50445 50446 . - . intron_id 7 ; splice_site "AG" JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local cds 50265 50444 . - . JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local exon 50265 50444 . - . insertions 0 ; deletions 1 JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local splice5 50263 50264 . - . intron_id 9 ; splice_site "GT" JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local intron 50108 50264 . - . intron_id 9 JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local splice3 50108 50109 . - . intron_id 8 ; splice_site "AG" JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local cds 50000 50107 . - . JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local exon 50000 50107 . - . insertions 3 ; deletions 0 JXSJ01000029.1:subseq(3454276,105626) exonerate:protein2genome:local similarity 50000 58104 1643 - . alignment_id 1 ; Query SPP00000635_2.0 ; Align 58105 1 48 ; Align 55624 17 69 ; Align 55088 40 108 ; Align 54279 77 72 ; Align 52262 102 261 ; Align 51046 189 108 ; Align 50856 226 45 ; Align 50719 242 180 ; Align 50445 302 99 ; Align 50346 336 81 ; Align 50108 363 63 ; Align 50042 384 42 # --- END OF GFF DUMP --- # -- completed exonerate analysis