Command line: [exonerate -m p2g --showtargetgff -q selenoj2_zf.aa.fa.canviat -t genomeselenoj2_JXSJ01000123.1.fa] Hostname: [ws101100u] C4 Alignment: ------------ Query: SPP00000636_2.0 # Protein # Selenoprotein J1 (SELENOJ1) # Zebrafish Target: JXSJ01000123.1:subseq(358337,55376) Miichthys miiuy scaffold123, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 1351 Query range: 0 -> 341 Target range: 5735 -> 2999 1 : MetAlaLeuAlaLeuSerAsnArgAlaIleGlyAlaIleIleGlySerAlaValAlaAspAl : 21 |||||| !||||||:!!:!!||||||||||||||||||:!!|||||||||||||||||||| MetAlaAlaAlaLeuAlaAspArgAlaIleGlyAlaIleValGlySerAlaValAlaAspAl 5735 : ATGGCTGCAGCTCTGGCCGACAGAGCGATAGGAGCCATCGTAGGATCAGCTGTTGCAGATGC : 5675 22 : aAla{A} >>>> Target Intron 1 >>>> {la}GlnProLeuHisTrpValTyrA : 31 ||||{|} 290 bp {||}||||||||| !||||||! !| aAla{A}++ ++{la}GlnProLeuThrTrpValCysA 5674 : AGCA{G}gt.........................ag{CA}CAGCCCCTGACCTGGGTGTGCG : 5355 32 : spLeuSerLysLeuSerValLeuLeuSerGlnSerProGlnProGluPheArgProGluSer : 51 ||||| !!|||||| !! !:!!||||||||| !|||.!.|||||||||!.! !|||||| spLeuProLysLeuHisGlyValLeuSerGlnHisProAsnProGluPheHisPheGluSer 5354 : ACCTCCCGAAGCTGCATGGGGTTCTGTCTCAGCACCCAAACCCTGAGTTCCATTTTGAGTCA : 5295 52 : AlaAsnProPheTyrArgArgAsnThrGlyGlnGlnSerCysTyrGlyAspGlnAlaPheIl : 72 !||||||!:!|||||||||.!.||||||:!!|||||||||!:!|||||||||||||||:! IleAsnProTyrTyrArgArgGluThrGlyLysGlnSerCysPheGlyAspGlnAlaPheVa 5294 : ATCAACCCCTACTACAGGAGGGAGACGGGCAAACAGAGCTGCTTTGGAGACCAGGCATTTGT : 5232 73 : eLeuLeuGluSerLeuSerGluCysGly{G} >>>> Target Intron 2 >>>> {l : 82 !|||||||||||||||||||||||||||{|} 255 bp {| lLeuLeuGluSerLeuSerGluCysGly{G}++ ++{l 5231 : CCTGCTGGAGTCCTTGTCTGAATGTGGA{G}gt.........................ag{G : 4946 83 : y}LeuAsnValGluAspPheLysGlnArgThrTyrLysPhePheGlyProGlySerGluTyr : 102 |}|||||||||!!:|||.!.|||||||||||| ||||||||||||||||||||||||||| y}LeuAsnValAspAspLeuLysGlnArgThrLeuLysPhePheGlyProGlySerGluTyr 4945 : G}CTAAATGTTGATGATCTGAAGCAGCGCACACTGAAGTTCTTTGGCCCTGGATCAGAGTAT : 4887 103 : AspThrProValAsnAspProTyrArgAspLysGly{A} >>>> Target Intron 3 : 115 ||||||||||||||||||||||||||||||||||||{!} 93 bp AspThrProValAsnAspProTyrArgAspLysGly{G}++ 4886 : GACACACCTGTCAATGATCCTTACAGAGACAAAGGA{G}gt..................... : 4845 116 : >>>> {la}ProArgProGlnLeuProIleGluGlyProTrpArgHisAlaSerLeuLysG : 133 {.!}|||! !|||||||||||||||||||||||||||||||||||||||||||||. ++{ly}ProThrProGlnLeuProIleGluGlyProTrpArgHisAlaSerLeuLysS 4844 : ....ag{GG}CCAACACCTCAGCTGCCCATTGAAGGACCATGGAGACATGCAAGTTTGAAGA : 4701 134 : lyPheIleLysAsnValAspAlaGlyLysGluGluThr{G} >>>> Target Intron : 146 !!|||:!:||||||||||||||||||||||||||||||{|} 83 bp erPheLeuLysAsnValAspAlaGlyLysGluGluThr{G}++ 4700 : GCTTCCTGAAGAATGTGGATGCAGGCAAAGAGGAGACA{G}gt................... : 4659 147 : 4 >>>> {ly}CysGluThrAspThrGlnIleAspGlyValThrLysLeuAlaProIleVa : 163 {||}||||||!.!||| !||||||||||||:!!.!!||||||||||||||||| ++{ly}CysGluAsnAspCysGlnIleAspGlyIleAlaLysLeuAlaProIleVa 4658 : ......ag{GC}TGTGAGAACGACTGTCAGATTGATGGAATAGCTAAACTGGCTCCTATAGT : 4528 164 : lAlaCysTyrAlaGlyLysProGluMetLeuGluLysValGluGluAlaValArgValThrG : 184 ||||! !|||||||||||||||!!:||||||||||||:!!|||:!!|||||||||||||||| lAlaPheTyrAlaGlyLysProAspMetLeuGluLysMetGluGlnAlaValArgValThrG 4527 : GGCTTTTTATGCAGGAAAGCCTGACATGCTGGAAAAAATGGAGCAGGCAGTCCGTGTCACCC : 4465 185 : lnAsnAsnAspLeuCysValAlaGluThrLeuAlaAlaAla{Ar} >>>> Target Int : 198 ||||||||||| !|||||||||||||||||||||||||||{||} 462 b lnAsnAsnAspGluCysValAlaGluThrLeuAlaAlaAla{Ar}++ 4464 : AGAACAATGATGAATGTGTGGCAGAGACTCTGGCAGCTGCA{AG}gt............... : 4419 199 : ron 5 >>>> {g}PheLeuGluHisPheIleLeuAsnGlyProAspProLysAlaLeuAs : 214 p {|}|||||||||:!!||||||||||||||||||||||||||||||||||| ++{g}PheLeuGluTyrPheIleLeuAsnGlyProAspProLysAlaLeuAs 4418 : ..........ag{G}TTCCTGGAGTATTTTATCCTGAATGGTCCTGATCCAAAAGCCTTGGA : 3913 215 : pAlaValLeuLysGlnLeuSerAspProGluArgLysAsnProGlnGluLeuAspLysAlaV : 235 |:!!|||||| ||||||!:!||||||:!!||||||.!.||||||!!:||||||||||||| pSerValLeuAlaGlnLeuAsnAspProLysArgLysGlnProGlnAspLeuAspLysAlaV 3912 : CTCAGTGCTCGCTCAGCTCAATGACCCAAAGAGAAAGCAGCCTCAGGATCTGGACAAAGCAG : 3850 236 : alIle{G} >>>> Target Intron 6 >>>> {ly}HisIleHisGlnValLysAsp : 244 |||||{|} 261 bp {||}||||||||||||||||||!!: alIle{G}++ ++{ly}HisIleHisGlnValLysGlu 3849 : TCATT{G}gt.........................ag{GG}CACATTCATCAGGTGAAGGAG : 3562 245 : AsnLeuAsnLysLysProLysGluLeuIleProAlaValPheProAsnThrUnk{G} >>> : 263 ||||||:::|||! |||:!!||||||||||||.!!|||||| !!|||:!! {|} AsnLeuSerLysThrProGlnGluLeuIleProThrValPheSerAsnSer***{G}++ 3561 : AATTTATCAAAGACTCCTCAGGAGCTAATCCCCACTGTATTTTCAAACTCCTGA{G}gt... : 3502 264 : > Target Intron 7 >>>> {ly}LeuProGlyAlaPheGlnAlaAlaLeuHisGlyV : 275 179 bp {||}|||||||||||||||||||||||||||||||||| ++{ly}LeuProGlyAlaPheGlnAlaAlaLeuHisGlyV 3501 : ......................ag{GT}TTGCCAGGTGCGTTCCAAGCAGCGCTGCATGGAG : 3290 276 : alLeuThrAlaSerSerTyrGluGlnAlaValArgAspThrMetSerCysGlyGlyCysThr : 295 |||||||||||!.!..!||||||||||||:!!||||||!.!||||||||||||||||||||| alLeuThrAlaLysGlnTyrGluGlnAlaIleArgAspAsnMetSerCysGlyGlyCysThr 3289 : TCCTGACAGCTAAGCAATATGAGCAGGCTATTAGAGACAACATGAGCTGTGGAGGATGCACC : 3230 296 : CysSerArgSerSerPheIleGlyAlaCysIleGlyAlaGln >>>> Target Intron : 310 |||||||||.!!||||||||||||||||||:!!||||||||| 90 bp CysSerArgGlySerPheIleGlyAlaCysLeuGlyAlaGln++ 3229 : TGTAGCAGAGGGTCCTTCATTGGAGCCTGTCTTGGGGCTCAGgt.................. : 3183 311 : 8 >>>> ValGlyLeuGluGlyIleProAlaSerTrpLysSerLysThrLeuArgCysAs : 327 :!!|||!!!|||||||||||||||||||||!:!|||||||||||| !!! !:! ++IleGlyPheGluGlyIleProAlaSerTrpArgSerLysThrLeuCysTyrAs 3182 : .......agATTGGATTTGAGGGAATTCCAGCTTCCTGGAGATCCAAAACTCTGTGTTATGA : 3044 328 : nThrLeuLeuAspLeuSerArgLysValValAlaLeuGlnGln : 341 !.!!:!!|||!!:! !:!!!:!|||:!!..! !! !!!.||| pAlaValLeuGluHisAlaLysLysIleThrLysHisHisGln 3043 : CGCAGTGTTGGAGCATGCCAAGAAGATAACCAAACATCACCAG : 3000 vulgar: SPP00000636_2.0 0 341 . JXSJ01000123.1:subseq(358337,55376) 5735 2999 - 1351 M 22 66 S 0 1 5 0 2 I 0 286 3 0 2 S 1 2 M 58 174 S 0 1 5 0 2 I 0 251 3 0 2 S 1 2 M 32 96 S 0 1 5 0 2 I 0 89 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 0 458 3 0 2 S 1 1 M 38 114 S 0 1 5 0 2 I 0 257 3 0 2 S 1 2 M 25 75 S 0 1 5 0 2 I 0 175 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(358337,55376) exonerate:protein2genome:local gene 3000 5735 1351 - . gene_id 1 ; sequence SPP00000636_2.0 ; gene_orientation + JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local cds 5669 5735 . - . JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local exon 5669 5735 . - . insertions 0 ; deletions 0 JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local splice5 5667 5668 . - . intron_id 1 ; splice_site "GT" JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local intron 5379 5668 . - . intron_id 1 JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local splice3 5379 5380 . - . intron_id 0 ; splice_site "AG" JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local cds 5202 5378 . - . JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local exon 5202 5378 . - . insertions 0 ; deletions 0 JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local splice5 5200 5201 . - . intron_id 2 ; splice_site "GT" JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local intron 4947 5201 . - . intron_id 2 JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local splice3 4947 4948 . - . intron_id 1 ; splice_site "AG" JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local cds 4848 4946 . - . JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local exon 4848 4946 . - . insertions 0 ; deletions 0 JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local splice5 4846 4847 . - . intron_id 3 ; splice_site "GT" JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local intron 4755 4847 . - . intron_id 3 JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local splice3 4755 4756 . - . intron_id 2 ; splice_site "AG" JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local cds 4662 4754 . - . JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local exon 4662 4754 . - . insertions 0 ; deletions 0 JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local splice5 4660 4661 . - . intron_id 4 ; splice_site "GT" JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local intron 4579 4661 . - . intron_id 4 JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local splice3 4579 4580 . - . intron_id 3 ; splice_site "AG" JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local cds 4422 4578 . - . JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local exon 4422 4578 . - . insertions 0 ; deletions 0 JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local splice5 4420 4421 . - . intron_id 5 ; splice_site "GT" JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local intron 3960 4421 . - . intron_id 5 JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local splice3 3960 3961 . - . intron_id 4 ; splice_site "AG" JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local cds 3844 3959 . - . JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local exon 3844 3959 . - . insertions 0 ; deletions 0 JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local splice5 3842 3843 . - . intron_id 6 ; splice_site "GT" JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local intron 3583 3843 . - . intron_id 6 JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local splice3 3583 3584 . - . intron_id 5 ; splice_site "AG" JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local cds 3505 3582 . - . JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local exon 3505 3582 . - . insertions 0 ; deletions 0 JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local splice5 3503 3504 . - . intron_id 7 ; splice_site "GT" JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local intron 3326 3504 . - . intron_id 7 JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local splice3 3326 3327 . - . intron_id 6 ; splice_site "AG" JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local cds 3186 3325 . - . JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local exon 3186 3325 . - . insertions 0 ; deletions 0 JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local splice5 3184 3185 . - . intron_id 8 ; splice_site "GT" JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local intron 3096 3185 . - . intron_id 8 JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local splice3 3096 3097 . - . intron_id 7 ; splice_site "AG" JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local cds 3000 3095 . - . JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local exon 3000 3095 . - . insertions 0 ; deletions 0 JXSJ01000123.1:subseq(358337,55376) exonerate:protein2genome:local similarity 3000 5735 1351 - . alignment_id 1 ; Query SPP00000636_2.0 ; Align 5736 1 66 ; Align 5377 24 174 ; Align 4945 83 96 ; Align 4753 116 90 ; Align 4577 147 153 ; Align 3959 199 114 ; Align 3581 238 75 ; Align 3324 264 138 ; Align 3096 310 96 # --- END OF GFF DUMP --- # -- completed exonerate analysis