Command line: [exonerate -m p2g --showtargetgff -q selenoj1_zf.aa.fa.canviat -t genomeselenoj1_JXSJ01000123.1.fa] Hostname: [ws101100u] C4 Alignment: ------------ Query: SPP00000636_2.0 # Protein # Selenoprotein J1 (SELENOJ1) # Zebrafish Target: JXSJ01000123.1:subseq(305390,55111) Miichthys miiuy scaffold123, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 1364 Query range: 0 -> 341 Target range: 52454 -> 49999 1 : MetAlaLeuAlaLeuSerAsnArgAlaIleGlyAlaIleIleGlySerAlaValAlaAsp : 20 |||||| !||||||:!!:!!||||||||||||||||||:!!|||||||||||||||||| MetAlaAlaAlaLeuAlaAspArgAlaIleGlyAlaIleValGlySerAlaValAlaAsp 52454 : ATGGCTGCAGCTCTGGCCGACAGAGCGATAGGAGCCATCGTAGGATCAGCTGTTGCAGAT : 52397 21 : AlaAla{A} >>>> Target Intron 1 >>>> {la}GlnProLeuHisTrpVal : 29 ||||||{|} 274 bp {||}||||||||| !|||||| AlaAla{A}++ ++{la}GlnProLeuThrTrpVal 52396 : GCAGCA{G}gt.........................ag{CA}CAGCCCCTGACCTGGGTG : 52096 30 : TyrAspLeuSerLysLeuSerValLeuLeuSerGlnSerProGlnProGluPheArgPro : 49 ! !|||||| !!|||||| !! !:!!||||||||| !|||.!.||||||||| !! !! CysAspLeuProLysLeuHisGlyValLeuSerGlnHisProAsnProGluPheCysSer 52095 : TGCGACCTCCCGAAGCTGCATGGGGTTCTGTCTCAGCACCCAAACCCTGAGTTCTGCTCT : 52036 50 : GluSerAlaAsnProPheTyrArgArgAsnThrGlyGlnGlnSerCysTyrGlyAspGln : 69 |||||| !||||||||||||||||||.!.! !|||:!!||||||||||||||||||||| GluSerPheAsnProPheTyrArgArgGlnMetGlyLysGlnSerCysTyrGlyAspGln 52035 : GAATCATTCAACCCTTTCTACAGGAGGCAGATGGGCAAGCAGAGCTGCTACGGGGACCAG : 51976 70 : AlaPheIleLeuLeuGluSerLeuSerGluCysGly{G} >>>> Target Intron : 82 ||||||:!!|||||||||||||||||||||||||||{|} 381 bp AlaPheValLeuLeuGluSerLeuSerGluCysGly{G}++ 51975 : GCGTTTGTCCTGCTGGAATCCTTGTCTGAATGTGGA{G}gt................... : 51934 83 : 2 >>>> {ly}LeuAsnValGluAspPheLysGlnArgThrTyrLysPhePheGlyPro : 98 {||}|||||||||!!:|||.!.|||||||||||| ||||||||||||||| ++{ly}LeuAsnValAspAspLeuLysGlnArgThrLeuLysPhePheGlyPro 51933 : ......ag{GG}CTAAATGTTGACGATCTGAAGCAGCGCACACTGAAGTTCTTTGGCCCT : 51508 99 : GlySerGluTyrAspThrProValAsnAspProTyrArgAspLysGly{A} >>>> Ta : 115 ||||||||||||||||||||||||||||||||||||||||||:::|||{!} GlySerGluTyrAspThrProValAsnAspProTyrArgAspArgGly{G}++ 51507 : GGATCAGAGTATGACACGCCTGTCAATGATCcttacagagacagagga{g}gt....... : 51454 116 : rget Intron 3 >>>> {la}ProArgProGlnLeuProIleGluGlyProTrpArg : 127 104 bp {.!}|||||||||||||||||||||||||||||||||||| ++{ly}ProArgProGlnLeuProIleGluGlyProTrpArg 51453 : ..................ag{GG}CCAAGACCTCAGCTGCCCATTGAAGGACCATGGAGA : 51317 128 : HisAlaSerLeuLysGlyPheIleLysAsnValAspAlaGlyLysGluGluThr{G} > : 146 |||||||||||||||.!!|||:!:||||||||||||||||||||||||||||||{|} HisAlaSerLeuLysSerPheLeuLysAsnValAspAlaGlyLysGluGluThr{G}++ 51316 : CATGCAAGTTTGAAGAGCTTCCTGAAGAATGTGGATGCAGGCAAAGAGGAGACA{G}gt. : 51257 147 : >>> Target Intron 4 >>>> {ly}CysGluThrAspThrGlnIleAspGlyVal : 156 83 bp {||}||||||!.!||| !||||||||||||:!! ++{ly}CysGluAsnAspCysGlnIleAspGlyIle 51256 : ........................ag{GC}TGTGAGAACGACTGTCAGATTGATGGAATA : 51147 157 : ThrLysLeuAlaProIleValAlaCysTyrAlaGlyLysProGluMetLeuGluLysVal : 176 .!!|||||||||||||||||||||! !|||||||||||||||!!:||||||||||||||| AlaLysLeuAlaProIleValAlaPheTyrAlaGlyLysProAspMetLeuGluLysVal 51146 : GCTAAACTGGCTCCTATAGTGGCTTTTTATGCAGGAAAGCCTGACATGCTGGAAAAAGTG : 51087 177 : GluGluAlaValArgValThrGlnAsnAsnAspLeuCysValAlaGluThrLeuAlaAla : 196 |||:!!||||||||||||||||||||||||||| !|||||||||||||||||||||||| GluGlnAlaValArgValThrGlnAsnAsnAspGluCysValAlaGluThrLeuAlaAla 51086 : GAGCAGGCAGTCCGTGTCACCCAGAACAATGATGAATGTGTGGCAGAGACTCTGGCAGCT : 51027 197 : Ala{Ar} >>>> Target Intron 5 >>>> {g}PheLeuGluHisPheIleLeu : 205 |||{||} 254 bp {|}|||||||||:!!||||||||| Ala{Ar}++ ++{g}PheLeuGluTyrPheIleLeu 51026 : GCA{AG}gt.........................ag{G}TTCCTGGAGTATTTCATCCTG : 50746 206 : AsnGlyProAspProLysAlaLeuAspAlaValLeuLysGlnLeuSerAspProGluArg : 225 |||||||||||||||||||||||||||:!!|||||| ||||||!:!||||||:!!||| AsnGlyProAspProLysAlaLeuAspSerValLeuAlaGlnLeuAsnAspProLysArg 50745 : AATGGTCCTGATCCAAAAGCCTTGGACTCAGTGCTCGCTCAGCTCAATGACCCAAAGAGA : 50686 226 : LysAsnProGlnGluLeuAspLysAlaValIle{G} >>>> Target Intron 6 > : 237 |||.!.||||||!!:||||||||||||||||||{|} 113 bp LysGlnProGlnAspLeuAspLysAlaValIle{G}++ 50685 : AAGCAGCCTCAGGATCTGGACAAAGCAGTCATT{G}gt...................... : 50647 238 : >>> {ly}HisIleHisGlnValLysAspAsnLeuAsnLysLysProLysGluLeuIle : 254 {||}||||||||||||||||||!!:||||||:::|||! ||||||||||||||| ++{ly}HisIleHisGlnValLysGluAsnLeuSerLysThrProLysGluLeuIle 50646 : ...ag{GG}CACATTCATCAGGTGAAGGAGAATTTATCAAAGACTCCTAAGGAGCTAATT : 50486 255 : ProAlaValPheProAsnThrUnk{G} >>>> Target Intron 7 >>>> {ly} : 263 |||.!!||||||||||||.!! {|} 133 bp {||} ProThrValPheProAsnAla***{G}++ ++{ly} 50485 : CCCACTGTGTTTCCAAATGCATGA{G}gt.........................ag{GT} : 50325 264 : LeuProGlyAlaPheGlnAlaAlaLeuHisGlyValLeuThrAlaSerSerTyrGluGln : 283 |||||||||||||||||||||||||||||||||||||||||||||!.!..!||||||||| LeuProGlyAlaPheGlnAlaAlaLeuHisGlyValLeuThrAlaLysGlnTyrGluGln 50324 : TTGCCAGGTGCGTTCCAAGCAGCGCTGCATGGAGTCCTGACAGCTAAGCAATATGAGCAG : 50266 284 : AlaValArgAspThrMetSerCysGlyGlyCysThrCysSerArgSerSerPheIleGly : 303 |||:!!||||||!.!||||||||||||||||||||||||||||||.!!|||||||||||| AlaIleArgAspAsnMetSerCysGlyGlyCysThrCysSerArgGlySerPheIleGly 50265 : GCTATTAGAGACAACATGAGCTGTGGAGGATGCACCTGTAGCAGAGGGTCCTTCATTGGA : 50206 304 : AlaCysIleGlyAlaGln >>>> Target Intron 8 >>>> ValGlyLeuGluG : 314 ||||||:!!||||||||| 90 bp :!!|||!!!|||| AlaCysLeuGlyAlaGln++ ++IleGlyPheGluG 50205 : GCCTGTCTTGGGGCTCAGgt.........................agATTGGATTTGAGG : 50083 315 : lyIleProAlaSerTrpLysSerLysThrLeuArgCysAsnThrLeuLeuAspLeuSerA : 334 |||||||||||||||||!:!|||||||||||| !!! !:!!.!!:!!|||!!:! !:!!! lyIleProAlaSerTrpArgSerLysThrLeuCysTyrAspAlaValLeuGluHisAlaL 50082 : GAATTCCAGCTTCCTGGAGATCCAAAACTCTGTGTTATGACGCAGTGTTGGAGCATGCCA : 50023 335 : rgLysValValAlaLeuGlnGln : 341 :!|||:!!..! !! !!!.||| ysLysIleThrLysHisHisGln 50022 : AGAAGATAACCAAACACCACCAG : 50000 vulgar: SPP00000636_2.0 0 341 . JXSJ01000123.1:subseq(305390,55111) 52454 49999 - 1364 M 22 66 S 0 1 5 0 2 I 0 270 3 0 2 S 1 2 M 58 174 S 0 1 5 0 2 I 0 377 3 0 2 S 1 2 M 32 96 S 0 1 5 0 2 I 0 100 3 0 2 S 1 2 M 30 90 S 0 1 5 0 2 I 0 79 3 0 2 S 1 2 M 51 153 S 0 2 5 0 2 I 0 250 3 0 2 S 1 1 M 38 114 S 0 1 5 0 2 I 0 109 3 0 2 S 1 2 M 25 75 S 0 1 5 0 2 I 0 129 3 0 2 S 1 2 M 46 138 5 0 2 I 0 86 3 0 2 M 32 96 # --- 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 # JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local gene 50000 52454 1364 - . gene_id 1 ; sequence SPP00000636_2.0 ; gene_orientation + JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local cds 52388 52454 . - . JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local exon 52388 52454 . - . insertions 0 ; deletions 0 JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local splice5 52386 52387 . - . intron_id 1 ; splice_site "GT" JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local intron 52114 52387 . - . intron_id 1 JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local splice3 52114 52115 . - . intron_id 0 ; splice_site "AG" JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local cds 51937 52113 . - . JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local exon 51937 52113 . - . insertions 0 ; deletions 0 JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local splice5 51935 51936 . - . intron_id 2 ; splice_site "GT" JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local intron 51556 51936 . - . intron_id 2 JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local splice3 51556 51557 . - . intron_id 1 ; splice_site "AG" JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local cds 51457 51555 . - . JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local exon 51457 51555 . - . insertions 0 ; deletions 0 JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local splice5 51455 51456 . - . intron_id 3 ; splice_site "gt" JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local intron 51353 51456 . - . intron_id 3 JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local splice3 51353 51354 . - . intron_id 2 ; splice_site "AG" JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local cds 51260 51352 . - . JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local exon 51260 51352 . - . insertions 0 ; deletions 0 JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local splice5 51258 51259 . - . intron_id 4 ; splice_site "GT" JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local intron 51177 51259 . - . intron_id 4 JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local splice3 51177 51178 . - . intron_id 3 ; splice_site "AG" JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local cds 51020 51176 . - . JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local exon 51020 51176 . - . insertions 0 ; deletions 0 JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local splice5 51018 51019 . - . intron_id 5 ; splice_site "GT" JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local intron 50766 51019 . - . intron_id 5 JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local splice3 50766 50767 . - . intron_id 4 ; splice_site "AG" JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local cds 50650 50765 . - . JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local exon 50650 50765 . - . insertions 0 ; deletions 0 JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local splice5 50648 50649 . - . intron_id 6 ; splice_site "GT" JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local intron 50537 50649 . - . intron_id 6 JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local splice3 50537 50538 . - . intron_id 5 ; splice_site "AG" JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local cds 50459 50536 . - . JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local exon 50459 50536 . - . insertions 0 ; deletions 0 JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local splice5 50457 50458 . - . intron_id 7 ; splice_site "GT" JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local intron 50326 50458 . - . intron_id 7 JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local splice3 50326 50327 . - . intron_id 6 ; splice_site "AG" JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local cds 50186 50325 . - . JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local exon 50186 50325 . - . insertions 0 ; deletions 0 JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local splice5 50184 50185 . - . intron_id 8 ; splice_site "GT" JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local intron 50096 50185 . - . intron_id 8 JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local splice3 50096 50097 . - . intron_id 7 ; splice_site "AG" JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local cds 50000 50095 . - . JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local exon 50000 50095 . - . insertions 0 ; deletions 0 JXSJ01000123.1:subseq(305390,55111) exonerate:protein2genome:local similarity 50000 52454 1364 - . alignment_id 1 ; Query SPP00000636_2.0 ; Align 52455 1 66 ; Align 52112 24 174 ; Align 51554 83 96 ; Align 51351 116 90 ; Align 51175 147 153 ; Align 50765 199 114 ; Align 50535 238 75 ; Align 50324 264 138 ; Align 50096 310 96 # --- END OF GFF DUMP --- # -- completed exonerate analysis