Command line: [exonerate --exhaustive yes -m p2g --showtargetgff -q ../TR1-human.fa -t TR1-NIVO01039896.1.subseq] Hostname: [sitdoc] C4 Alignment: ------------ Query: SPP00000034_1.0 # Protein # Thioredoxin reductase 1 (TR1) # Homo sapiens # Complete Target: NIVO01039896.1:subseq(857893,163183) Ammotragus lervia isolate NAZ scaffold2252_len1020358_cov73, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 2396 Query range: 0 -> 499 Target range: 87380 -> 49999 1 : MetAsnGlyProGluAspLeuProLysSerTyrAspTyrAspLeuIleIleIleGlyGly : 20 ||||||||| !!:!!|||||||||:!! !!|||||||||||||||||||||||||||||| MetAsnGlySerLysAspLeuProGluProTyrAspTyrAspLeuIleIleIleGlyGly 87380 : atgaatggCTCCAAGGATCTCCCGGAGCCCTATGACTACGACCTCATCATCATTGGAGGG : 87323 21 : GlySerGlyGlyLeuAlaAlaAlaLys >>>> Target Intron 1 >>>> GluA : 31 ||||||||||||||||||||||||||| 260 bp |||| GlySerGlyGlyLeuAlaAlaAlaLys+- ++GluA 87322 : GGTTCTGGAGGACTGGCAGCCGCCAAGgc.........................aggAGG : 87030 32 : laAlaGlnTyrGlyLysLysValMetValLeuAspPheValThrProThrProLeuGlyT : 51 |||||:!!|||! !|||||||||||||||||||||||||||||||||||||||||||||| laAlaLysTyrAspLysLysValMetValLeuAspPheValThrProThrProLeuGlyT 87029 : CAGCCAAATATGACAAGAAGGTGATGGTTCTGGATTTTGTCACTCCAACCCCTCTTGGAA : 86970 52 : hrArgTrp{G} >>>> Target Intron 2 >>>> {ly}LeuGlyGlyThrCysV : 60 ||||||||{|} 2400 bp {||}|||||||||||||||| hrArgTrp{G}++ ++{ly}LeuGlyGlyThrCysV 86969 : CTAGATGG{G}gt.........................ag{GT}CTTGGAGGAACGTGTG : 84543 61 : alAsnValGlyCysIleProLysLysLeuMetHisGlnAlaAlaLeuLeuGlyGlnAlaL : 80 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| alAsnValGlyCysIleProLysLysLeuMetHisGlnAlaAlaLeuLeuGlyGlnAlaL 84542 : TGAATGTGGGTTGCATACCTAAAAAACTGATGCACCAAGCAGCGTTGTTAGGACAAGCCC : 84483 81 : euGlnAspSerArgAsnTyrGlyTrpLysValGluGluThr{V} >>>> Target In : 94 ||!:!|||||||||||||||||||||!!.||||||||||||{|} 8672 euArgAspSerArgAsnTyrGlyTrpAsnValGluGluThr{V}++ 84482 : TACGAGACTCTCGAAACTACGGGTGGAACGTCGAGGAGACA{G}gt.............. : 84438 95 : tron 3 >>>> {al}LysHisAspTrpAspArgMetIleGluAlaValGlnAsnHisI : 109 bp {||}||||||||||||!!:||||||! !||||||||||||||||||| ++{al}LysHisAspTrpGluArgMetThrGluAlaValGlnAsnHisI 84437 : ...........ag{TT}AAGCATGACTGGGAGAGAATGACAGAGGCGGTCCAGAACCACA : 75724 110 : leGlySerLeuAsnTrpGlyTyrArgValAlaLeuArgGluLysLysValValTyrGluA : 129 ||||||||||||||||||||||||||||||||||||||||||||||||||..!||||||| leGlySerLeuAsnTrpGlyTyrArgValAlaLeuArgGluLysLysValThrTyrGluA 75723 : TTGGCTCTCTCAACTGGGGCTACCGCGTGGCCCTGCGGGAGAAAAAGGTCACCTACGAGA : 75664 130 : snAlaTyrGlyGlnPheIleGlyProHisArgIleLys >>>> Target Intron 4 : 142 ||:!!||||||:!!|||:!:|||||||||||||||||| 386 bp snSerTyrGlyGluPheValGlyProHisArgIleLys++ 75663 : ACTCGTACGGGGAGTTTGTGGGGCCTCACAGGATTAAGgt.................... : 75623 143 : >>>> AlaThrAsnAsnLysGlyLysGluLysIleTyrSerAlaGluArgPheLeuIl : 159 ||||||||||||||||||||||||||||||||||||||||||||||||||||| ++AlaThrAsnAsnLysGlyLysGluLysIleTyrSerAlaGluArgPheLeuIl 75622 : .....agGCAACAAATAATAAAGGCAAAGAGAAGATTTACTCAGCAGAGAGATTTCTCAT : 75188 160 : eAlaThrGlyGluArgProArgTyrLeuGlyIleProGlyAspLysGluTyrCysIleSe : 179 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| eAlaThrGlyGluArgProArgTyrLeuGlyIleProGlyAspLysGluTyrCysIleSe 75187 : TGCCACTGGTGAAAGGCCGCGTTATTTGGGTATCCCTGGTGACAAAGAATACTGTATCAG : 75128 180 : r{Se} >>>> Target Intron 5 >>>> {r}AspAspLeuPheSerLeuProTy : 188 |{||} 1647 bp {|}||||||||||||||||||||||| r{Se}++ ++{r}AspAspLeuPheSerLeuProTy 75127 : C{AG}gt.........................ag{t}gatgatCTTTTCTCTTTACCTTA : 73454 189 : rCysProGlyLysThrLeuValValGlyAlaSerTyrValAlaLeuGluCysAlaGlyPh : 208 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| rCysProGlyLysThrLeuValValGlyAlaSerTyrValAlaLeuGluCysAlaGlyPh 73453 : TTGCCCGGGTAAGACCCTGGTGGTCGGAGCATCCTATGTTGCTTTGGAATGTGCTGGATT : 73394 209 : eLeuAlaGlyIleGlyLeuAspValThrValMetValArgSerIleLeuLeuArgGlyPh : 228 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| eLeuAlaGlyIleGlyLeuAspValThrValMetValArgSerIleLeuLeuArgGlyPh 73393 : TCTTGCTGGTATTGGTTTAGACGTCACTGTTATGGTACGATCCATTCTCCTAAGAGGATT : 73334 229 : eAspGlnAspMetAlaAsnLysIleGlyGluHisMetGluGluHisGlyIleLysPheIl : 248 |||||||||||||||||||||||||||||||||||||:!!|||||||||||||||||||| eAspGlnAspMetAlaAsnLysIleGlyGluHisMetGlnGluHisGlyIleLysPheIl 73333 : TGACCAGGACATGGCCAACAAAATTGGTGAACATATGCAAGAACATGGTATCAAGTTCAT : 73274 249 : eArgGlnPheValProIleLys >>>> Target Intron 6 >>>> ValGluGln : 258 ||||:!!||||||||||||||| 1675 bp ||||||||| eArgGluPheValProIleLys++ ++ValGluGln 73273 : AAGAGAGTTTGTACCAATAAAGgt.........................agGTTGAACAA : 71569 259 : IleGluAlaGlyThrProGlyArgLeuArgValValAlaGlnSerThrAsnSerGluGlu : 278 |||||||||||||||||||||||||||||||||||||||:!!|||||||||.!!!!::!! IleGluAlaGlyThrProGlyArgLeuArgValValAlaLysSerThrAsnGlyAspGln 71568 : ATTGAAGCAGGGACACCAGGCCGACTGAGAGTGGTAGCTAAGTCCACTAATGGTGACCAA : 71509 279 : IleIleGluGlyGluTyrAsnThr >>>> Target Intron 7 >>>> ValMetL : 289 ! !||||||||||||||||||||| 574 bp |||:!!| ThrIleGluGlyGluTyrAsnThr++ ++ValLeuL 71508 : ACCATCGAAGGAGAGTATAATACGgt.........................agGTATTGC : 70902 290 : euAlaIleGlyArgAspAlaCysThrArgLysIleGlyLeuGluThrValGlyValLysI : 309 ||||||||||||||||||||||||||||||||||||||||||||!.!||||||||||||| euAlaIleGlyArgAspAlaCysThrArgLysIleGlyLeuGluAsnValGlyValLysI 70901 : TGGCAATAGGTAGAGATGCTTGCACGAGAAAAATTGGCTTAGAAAACGTGGGagtaaaga : 70842 310 : leAsnGlu{Ly} >>>> Target Intron 8 >>>> {s}ThrGlyLysIleProV : 318 ||||||||{||} 1492 bp {|}|||||||||||||||| leAsnGlu{Ly}++ ++{s}ThrGlyLysIleProV 70841 : taaatgaa{aa}gt.........................ag{g}actggaaaaatacCTG : 69323 319 : alThrAspGluGluGlnThrAsnValProTyrIleTyrAlaIleGlyAspIleLeuGluA : 338 |||||!!:|||||||||||||||||||||||||||||||||||||||||||||||||||! alThrGluGluGluGlnThrAsnValProTyrIleTyrAlaIleGlyAspIleLeuGluG 69322 : TCACAGAGGAAGAGCAGACCAACGTGCCTTACATCTATGCCATCGGTGATATATTAGAGG : 69263 339 : spLysValGluLeuThrProValAlaIleGlnAlaGlyArgLeuLeuAlaGlnArgLeuT : 358 |||:!!|||||||||||||||||||||||||||||||||||||||||||||||||||| lyLysLeuGluLeuThrProValAlaIleGlnAlaGlyArgLeuLeuAlaGlnArgLeuT 69262 : GGAAGCTGGAGCTCACCCCCGTGGCCATCCAGGCAGGAAggctgctggctcagaggttgT : 69203 359 : yrAlaGlySerThrValLys >>>> Target Intron 9 >>>> CysAspTyrGl : 368 ||!.!||||||||||||||| 6753 bp ||||||||||| yrGlyGlySerThrValLys++ ++CysAspTyrGl 69202 : ATGGTGGCTCCACCGTCAAGgt.........................agTGCGACTATGA : 62420 369 : uAsnValProThrThrValPheThrProLeuGluTyrGlyAlaCysGlyLeuSerGluGl : 388 ||||||||||||||||||||||||||||||||||||||||:!!||||||||||||||||| uAsnValProThrThrValPheThrProLeuGluTyrGlySerCysGlyLeuSerGluGl 62419 : AAACGTTCCGACGACTGTTTTCACTCCTTTGGAATATGGGTCTTGTGGTCTTTCTGAGGA : 62360 389 : uLysAlaValGluLysPheGlyGluGluAsnIleGlu >>>> Target Intron 10 : 401 |||||||||||||||||||||||||||||||:::||| 2382 bp uLysAlaValGluLysPheGlyGluGluAsnValGlu++ 62359 : GAAAGCTGTGGAgaaatttggggaagaaaatgttGAGgt..................... : 62319 402 : >>>> ValTyrHisSerTyrPheTrpProLeuGluTrpThrIleProSerArgAspAs : 418 ||||||||||||||||||||||||||||||||||||||||||||||||||||| ++ValTyrHisSerTyrPheTrpProLeuGluTrpThrIleProSerArgAspAs 62318 : .....agGTTTACCATAGTTACTTTTGGCCATTGGAATGGACGATTCCGTCAAGAGATAA : 59888 419 : nAsnLysCysTyrAlaLysIleIleCysAsnThrLysAspAsn >>>> Target Int : 433 |||||||||||||||||||:!!:!!||||||! !||||||||| 4059 nAsnLysCysTyrAlaLysValValCysAsnIleLysAspAsn++ 59887 : CAACAAATGTTATGCAAAAGTAGTCTGCAATATCAAAGACAATgt............... : 59841 434 : ron 11 >>>> GluArgValValGlyPheHisValLeuGlyProAsnAlaGlyGluVa : 448 bp |||||||||||||||||||||:!!||||||||||||||||||||||| ++GluArgValValGlyPheHisIleLeuGlyProAsnAlaGlyGluVa 59840 : ...........agGAACGTGTTGTGGGCTTCCACATACTGGGtccaaatgctggagaggt : 55739 449 : lThrGlnGlyPheAlaAlaAlaLeuLysCysGlyLeuThrLysLysGlnLeuAspSerTh : 468 ||||||||||||||||||||||||||||||||||||||||||| ! |||||||||||||| lThrGlnGlyPheAlaAlaAlaLeuLysCysGlyLeuThrLysAspGlnLeuAspSerTh 55738 : gacCCAGGGGTTCGCAGCAGCACTCAAATGTGGGCTGACCAAGGACCAGCTGGACAGCAC : 55679 469 : rIleGlyIleHisProValCysAlaGlu >>>> Target Intron 12 >>>> Va : 478 |||||||||||||||||||||||||||| 5584 bp || rIleGlyIleHisProValCysAlaGlu++ ++Va 55678 : CATCGGGATCCACCCTGTTTGTGCAGAGgt..........................agGT : 50065 479 : lPheThrThrLeuSerValThrLysArgSerGlyAlaSerIleLeuGlnAlaGlyCysUn : 498 ||||||||||||||||||||||||||||||||||!.!!:!|||||||||.!!|||||| lPheThrThrLeuSerValThrLysArgSerGlyGlyAsnIleLeuGlnThrGlyCys** 50064 : GTTCACGACTCTGTCGGTGACCAAGCGCTCCGGGGGAAACATCCTCCAGACCGGTTGCTG : 50005 499 : kGly : 499 ||| *Gly 50004 : AGGT : 50000 vulgar: SPP00000034_1.0 0 499 . NIVO01039896.1:subseq(857893,163183) 87380 49999 - 2396 M 29 87 5 0 2 I 0 256 3 0 2 M 24 72 S 0 1 5 0 2 I 0 2396 3 0 2 S 1 2 M 39 117 S 0 1 5 0 2 I 0 8668 3 0 2 S 1 2 M 47 141 5 0 2 I 0 382 3 0 2 M 38 114 S 0 2 5 0 2 I 0 1643 3 0 2 S 1 1 M 75 225 5 0 2 I 0 1671 3 0 2 M 31 93 5 0 2 I 0 570 3 0 2 M 25 75 S 0 2 5 0 2 I 0 1488 3 0 2 S 1 1 M 52 156 5 0 2 I 0 6749 3 0 2 M 36 108 5 0 2 I 0 2378 3 0 2 M 32 96 5 0 2 I 0 4055 3 0 2 M 45 135 5 0 2 I 0 5580 3 0 2 M 22 66 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-17 ##type DNA # # # seqname source feature start end score strand frame attributes # NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local gene 50000 87380 2396 - . gene_id 1 ; sequence SPP00000034_1.0 ; gene_orientation + NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local cds 87294 87380 . - . NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local exon 87294 87380 . - . insertions 0 ; deletions 0 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice5 87292 87293 . - . intron_id 1 ; splice_site "GC" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local intron 87034 87293 . - . intron_id 1 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice3 87034 87035 . - . intron_id 0 ; splice_site "ag" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local cds 86961 87033 . - . NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local exon 86961 87033 . - . insertions 0 ; deletions 0 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice5 86959 86960 . - . intron_id 2 ; splice_site "GT" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local intron 84561 86960 . - . intron_id 2 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice3 84561 84562 . - . intron_id 1 ; splice_site "AG" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local cds 84441 84560 . - . NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local exon 84441 84560 . - . insertions 0 ; deletions 0 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice5 84439 84440 . - . intron_id 3 ; splice_site "GT" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local intron 75769 84440 . - . intron_id 3 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice3 75769 75770 . - . intron_id 2 ; splice_site "AG" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local cds 75626 75768 . - . NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local exon 75626 75768 . - . insertions 0 ; deletions 0 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice5 75624 75625 . - . intron_id 4 ; splice_site "GT" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local intron 75240 75625 . - . intron_id 4 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice3 75240 75241 . - . intron_id 3 ; splice_site "AG" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local cds 75124 75239 . - . NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local exon 75124 75239 . - . insertions 0 ; deletions 0 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice5 75122 75123 . - . intron_id 5 ; splice_site "GT" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local intron 73477 75123 . - . intron_id 5 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice3 73477 73478 . - . intron_id 4 ; splice_site "ag" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local cds 73251 73476 . - . NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local exon 73251 73476 . - . insertions 0 ; deletions 0 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice5 73249 73250 . - . intron_id 6 ; splice_site "GT" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local intron 71576 73250 . - . intron_id 6 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice3 71576 71577 . - . intron_id 5 ; splice_site "AG" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local cds 71483 71575 . - . NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local exon 71483 71575 . - . insertions 0 ; deletions 0 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice5 71481 71482 . - . intron_id 7 ; splice_site "GT" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local intron 70909 71482 . - . intron_id 7 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice3 70909 70910 . - . intron_id 6 ; splice_site "AG" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local cds 70832 70908 . - . NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local exon 70832 70908 . - . insertions 0 ; deletions 0 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice5 70830 70831 . - . intron_id 8 ; splice_site "gt" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local intron 69340 70831 . - . intron_id 8 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice3 69340 69341 . - . intron_id 7 ; splice_site "ag" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local cds 69183 69339 . - . NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local exon 69183 69339 . - . insertions 0 ; deletions 0 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice5 69181 69182 . - . intron_id 9 ; splice_site "GT" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local intron 62430 69182 . - . intron_id 9 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice3 62430 62431 . - . intron_id 8 ; splice_site "AG" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local cds 62322 62429 . - . NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local exon 62322 62429 . - . insertions 0 ; deletions 0 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice5 62320 62321 . - . intron_id 10 ; splice_site "GT" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local intron 59940 62321 . - . intron_id 10 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice3 59940 59941 . - . intron_id 9 ; splice_site "AG" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local cds 59844 59939 . - . NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local exon 59844 59939 . - . insertions 0 ; deletions 0 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice5 59842 59843 . - . intron_id 11 ; splice_site "GT" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local intron 55785 59843 . - . intron_id 11 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice3 55785 55786 . - . intron_id 10 ; splice_site "AG" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local cds 55650 55784 . - . NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local exon 55650 55784 . - . insertions 0 ; deletions 0 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice5 55648 55649 . - . intron_id 12 ; splice_site "GT" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local intron 50066 55649 . - . intron_id 12 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local splice3 50066 50067 . - . intron_id 11 ; splice_site "AG" NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local cds 50000 50065 . - . NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local exon 50000 50065 . - . insertions 0 ; deletions 0 NIVO01039896.1:subseq(857893,163183) exonerate:protein2genome:local similarity 50000 87380 2396 - . alignment_id 1 ; Query SPP00000034_1.0 ; Align 87381 1 87 ; Align 87034 30 72 ; Align 84559 55 117 ; Align 75767 95 141 ; Align 75240 142 114 ; Align 73476 181 225 ; Align 71576 256 93 ; Align 70909 287 75 ; Align 69339 313 156 ; Align 62430 365 108 ; Align 59940 401 96 ; Align 55785 433 135 ; Align 50066 478 66 # --- END OF GFF DUMP --- # -- completed exonerate analysis