Command line: [/mnt/NFS_UPF/soft/exonerate/exonerate-2.2.0-x86_64/bin/exonerate -m p2g --showtargetgff --exhaustive yes -q query5 -t q_subseq] Hostname: [am30332-131235u] C4 Alignment: ------------ Query: SPP00000102_1.0 # Protein # Glutathione peroxidase 5 (GPx5) # Mus musculus # Complete Target: PVKD010003030.1:subseq(1,165951) Cricetomys gambianus isolate US082 CriGam_scaffold_6056, whole genome shotgun sequence Model: protein2genome:local Raw score: 792 Query range: 3 -> 236 Target range: 56694 -> 129038 4 : AspCysArgPro{Se} >>>> Target Intron 1 >>>> {r}AspGlnLysS : 12 .!.||| !|||{||} 19089 bp {|}.!.||||||| GlnCysSerPro{Se}++ ++{r}GlnGlnLysS 56695 : CAATGTTCTCCC{AG}gt.........................ag{T}CAGCAGAAGT : 75808 13 : erAla{Va} >>>> Target Intron 2 >>>> {l}LeuValMetValThrGl : 20 ||!.!{:!} 44231 bp {!} !!.!|||!.! !:! erGly{Il}++ ++{e}ThrAlaMetAlaLeuGl 75809 : CAGGA{AT}gt.........................ag{T}ACAGCCATGGCCCTGCA : 120063 21 : uLeuArgValPheTyrLeuValProLeuLeuLeuAlaSerTyrValGlnThrThrPro : 39 !!!! !!!.!! !! !||| !!||||||!!!||||||:!!! !.!||| !|||! ! nPheTrpAlaSerCysLeuPheProLeuPheLeuAlaAlaLeuAlaGlnGluThrLeu 120064 : GTTCTGGGCCTCCTGTCTTTTCCCATTGTTTCTGGCTGCCTTGGCTCAGGAGACTCTG : 120120 40 : ArgProGluLysMetLys >>>> Target Intron 3 >>>> MetAspCysTy : 49 !.!|||:!!||| !||| 1308 bp :!:|||||| ! AsnProGlnLysAlaLys++ ++ValAspCysAs 120121 : AATCCTCAAAAAGCGAAGgt.........................agGTAGATTGCAA : 121458 50 : rLysAspValLysGlyThrIleTyrAspTyrGluAlaLeuSerLeuAsnGlyLysGlu : 68 !|||! ||| ||||||||||||!!:|||! !||| !!!!||||||||| !||| nLysGlyValAlaGlyThrIleTyrGluTyrGlyAlaLysThrLeuAsnGlyGlyGlu 121459 : CAAAGGGGTGGCTGGCACCATCTATGAGTATGGAGCGAAGACCCTGAATGGTGGGGAG : 121515 69 : HisIleProPheLysGlnTyrAlaGlyLysHisValLeuPheValAsnValAlaThrT : 88 :!!|||! !|||:!!|||||||||||||||||||||||||||||||||||||||:!!! TyrIleGlnPheGlnGlnTyrAlaGlyLysHisValLeuPheValAsnValAlaSerP 121516 : TATATCCAGTTCCAGCAGTATGCAGGAAAGCATGTCCTCTTTGTCAATGTGGCATCCT : 121575 89 : yrCysGlyLeuThrIleGlnTyrPro{G} >>>> Target Intron 4 >>>> : 97 :!|||||||||||| ! ||||||{|} 4834 bp heCysGlyLeuThrAlaThrTyrPro{G}++ ++ 121576 : TCTGTGGCCTGACAGCTACTTATCCT{G}gt.........................ag : 126435 98 : {lu}LeuAsnAlaLeuGlnGluAspLeuLysProPheGlyLeuValIleLeuGlyPhe : 115 {||}|||||| !|||||||||!!:||||||! !|||..!:!!:!!:!!||||||||| {lu}LeuAsnLysLeuGlnGluGluLeuLysGlnPheAsnValIleValLeuGlyPhe 126436 : {AA}CTGAACAAACTGCAGGAGGAGCTGAAGCAGTTCAATGTCATTGTTTTGGGCTTT : 126490 116 : ProCysAsnGlnPheGlyLysGlnGluProGlyAspAsnLeuGluIleLeuProGlyL : 135 ||||||||||||||||||||||||||||||!.. ||| ||||||||| |||| ProCysAsnGlnPheGlyLysGlnGluProAlaArgAsnSerGluIleLeuLeuGlyL 126491 : CCTTGCAACCAGTTTGGAAAACAAGAACCTGcaaggaactcagagatcctccttgGAC : 126550 136 : eu{Ly} >>>> Target Intron 5 >>>> {s}TyrValArgProGlyLysGl : 143 ||{||} 463 bp {|}||||||||||||||| || eu{Ly}++ ++{s}TyrValArgProGlyGlyGl 126551 : TC{AA}gt.........................ag{A}TATGTGCGTCCAGGTGGTGG : 127037 144 : yPheLeuProAsnPheGlnLeuPheAlaLysGlyAspValAsnGlyGluAsnGluGln : 162 |!:!:!!||||||||||||||||||! !|||||||||||||||||||||||||||||| yTyrValProAsnPheGlnLeuPheGluLysGlyAspValAsnGlyGluAsnGluGln 127038 : ATATGTCCCCAATTTCCAGCTCTTTGAGAAAGGGGATGTGAATGGAGAAAACGAACAA : 127094 163 : LysIlePheThrPheLeuLys >>>> Target Intron 6 >>>> ArgSerCy : 172 |||:!!||||||||||||||| 1720 bp !.!||||| LysValPheThrPheLeuLys++ ++AsnSerCy 127095 : AAGGTTTTCACTTTTCTGAAGgt.........................agAATTCCTG : 128844 173 : sProHisProSerGluThrValValMetSerLysHisThrPheTrpGluProIleLys : 191 ||||! ! !!|||||| !:!!! ! |||:!!:!! !||||||!!:||||||||| sProProThrSerGluLeuLeuGlySerSerGluTyrLeuPheTrpAspProIleLys 128845 : CCCTCCCACCTCTGAACTTTTGGGCTCTTCAGAATATCTCTTCTGGGATCCTATAAAG : 128901 192 : ValHisAspIleArgTrpAsnPheGluLysPheLeuValGlyProAspGlyIleProV : 211 |||||||||||||||||||||||||||||||||||||||||| !!..!|||:!!|||| ValHisAspIleArgTrpAsnPheGluLysPheLeuValGlySerSerGlyValProV 128902 : GTCCATGACATTCGCTGGAACTTTGAAAAGTTCCTGGTGGGGTCCAGTGGAGTCCCTG : 128961 212 : alMetArgTrpPheHisGlnAlaProValSerThrValLysSerAspIleMetAlaTy : 230 |||||||||||||||||:!!.!!|||||||||..!|||:!!|||||||||!!:! !|| alMetArgTrpPheHisLysThrProValSerValValGlnSerAspIleIleGluTy 128962 : TCATGCGCTGGTTCCACAAGACTCCTGTCAGCGTTGTCCAGTCGGATATTATAGAGTA : 129018 231 : rLeuSerHisPheLysThr : 236 ||||!:!!!.! ! ! ||| rLeuAsnGlnSerHisThr 129019 : CCTAAACCAGTCCCATACC : 129038 vulgar: SPP00000102_1.0 3 236 . PVKD010003030.1:subseq(1,165951) 56694 129038 + 792 M 4 12 S 0 2 5 0 2 I 0 19085 3 0 2 S 1 1 M 5 15 S 0 2 5 0 2 I 0 44227 3 0 2 S 1 1 M 31 93 5 0 2 I 0 1304 3 0 2 M 51 153 S 0 1 5 0 2 I 0 4830 3 0 2 S 1 2 M 38 114 S 0 2 5 0 2 I 0 459 3 0 2 S 1 1 M 33 99 5 0 2 I 0 1716 3 0 2 M 67 201 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2019-11-22 ##type DNA # # # seqname source feature start end score strand frame attributes # PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local gene 56695 129038 792 + . gene_id 1 ; sequence SPP00000102_1.0 ; gene_orientation + PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local cds 56695 56708 . + . PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local exon 56695 56708 . + . insertions 0 ; deletions 0 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local splice5 56709 56710 . + . intron_id 1 ; splice_site "GT" PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local intron 56709 75797 . + . intron_id 1 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local splice3 75796 75797 . + . intron_id 0 ; splice_site "AG" PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local cds 75798 75815 . + . PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local exon 75798 75815 . + . insertions 0 ; deletions 0 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local splice5 75816 75817 . + . intron_id 2 ; splice_site "GT" PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local intron 75816 120046 . + . intron_id 2 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local splice3 120045 120046 . + . intron_id 1 ; splice_site "AG" PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local cds 120047 120140 . + . PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local exon 120047 120140 . + . insertions 0 ; deletions 0 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local splice5 120141 120142 . + . intron_id 3 ; splice_site "GT" PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local intron 120141 121448 . + . intron_id 3 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local splice3 121447 121448 . + . intron_id 2 ; splice_site "AG" PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local cds 121449 121602 . + . PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local exon 121449 121602 . + . insertions 0 ; deletions 0 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local splice5 121603 121604 . + . intron_id 4 ; splice_site "GT" PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local intron 121603 126436 . + . intron_id 4 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local splice3 126435 126436 . + . intron_id 3 ; splice_site "AG" PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local cds 126437 126554 . + . PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local exon 126437 126554 . + . insertions 0 ; deletions 0 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local splice5 126555 126556 . + . intron_id 5 ; splice_site "GT" PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local intron 126555 127017 . + . intron_id 5 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local splice3 127016 127017 . + . intron_id 4 ; splice_site "AG" PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local cds 127018 127117 . + . PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local exon 127018 127117 . + . insertions 0 ; deletions 0 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local splice5 127118 127119 . + . intron_id 6 ; splice_site "GT" PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local intron 127118 128837 . + . intron_id 6 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local splice3 128836 128837 . + . intron_id 5 ; splice_site "AG" PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local cds 128838 129038 . + . PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local exon 128838 129038 . + . insertions 0 ; deletions 0 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local similarity 56695 129038 792 + . alignment_id 1 ; Query SPP00000102_1.0 ; Align 56695 4 12 ; Align 75799 9 15 ; Align 120048 15 93 ; Align 121449 46 153 ; Align 126439 98 114 ; Align 127019 137 99 ; Align 128838 170 201 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000102_1.0 # Protein # Glutathione peroxidase 5 (GPx5) # Mus musculus # Complete Target: PVKD010003030.1:subseq(1,165951) Cricetomys gambianus isolate US082 CriGam_scaffold_6056, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 948 Query range: 0 -> 236 Target range: 100514 -> 93949 1 : MetSerLysAspCysArgProSerAspGlnLysSerAlaValLeuValMetValThrG : 20 |||!:!||||||! !!!! !!|||||||||:::|||...::: ...|||..!! ! MetAsnLysAspPheSerAlaSerAspGlnArgSerValIleProAlaMetAlaMetT 100514 : ATGAACAAAGACTTCAGTGCCTCAGACCAGcgatctgtaatcccagctatggCTATGT : 100457 21 : luLeuArgValPheTyrLeuValProLeuLeuLeuAlaSerTyrValGlnThrThrPr : 39 !!!!||||||! !|||||||||||| ||||||||||||||||||||||||||||| rpPheArgValCysTyrLeuValPro---LeuLeuAlaSerTyrValGlnThrThrPr 100456 : GGTTTAGAGTTTGCTATCTTGTCCCA---CTCCTAGCCAGCTATGTGCAGACAACTCC : 100403 40 : oArgProGluLysMetLys >>>> Target Intron 1 >>>> MetAspCysT : 49 |!:!! !|||||||||||| 2944 bp |||||||||| oLysLeuGluLysMetLys++ ++MetAspCysT 100402 : CAAGCTGGAAAAGATGAAGgt.........................agATGGATTGCT : 97429 50 : yrLysAspValLysGlyThrIleTyrAspTyrGluAlaLeuSerLeuAsnGlyLysGl : 68 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||!! yrLysAspValLysGlyThrIleTyrAspTyrGluAlaLeuSerLeuAsnGlyLysAs 97428 : ACAAAGATGTGAAAGGCACCATCTATGACTACGAGGCGCTCTCTCTTAATGGGAAGGA : 97372 69 : uHisIleProPheLysGlnTyrAlaGlyLysHisValLeuPheValAsnValAlaThr : 87 :!.!|||! !||||||||||||:!!|||!!.! !:!!||||||||||||||||||||| pArgIleGlnPheLysGlnTyrSerGlyAsnLeuIleLeuPheValAsnValAlaThr 97371 : TCGTATTCAATTCAAACAGTATTCAGGCAACCTCATCCTCTTTGTCAACGTGGCTACC : 97315 88 : TyrCysGlyLeuThrIleGlnTyrPro{G} >>>> Target Intron 2 >>>> : 97 ||||||.!!|||||| !|||||||||{|} 1372 bp TyrCysSerLeuThrAlaGlnTyrPro{G}++ + 97314 : TATTGCAGTCTGACAGCTCAGTACCCT{G}gt.........................a : 95914 98 : {lu}LeuAsnAlaLeuGlnGluAspLeuLysProPheGlyLeuValIleLeuGlyPh : 115 {||}|||||||||||||||:!!!!:|||||||||.!.|||||||||:!!|||||||| +{lu}LeuAsnAlaLeuGlnLysGluLeuLysProLeuGlyLeuValValLeuGlyPh 95913 : g{AG}CTGAATGCACTTCAGAAGGAGTTGAAGCCACTGGGCTTGGTTGTACTAGGCTT : 95859 116 : eProCysAsnGlnPheGlyLysGlnGluProGlyAspAsnLeuGluIleLeuProGly : 134 ||||||||||||||||||||||||||||||||||||||||! !||||||||| !!||| eProCysAsnGlnPheGlyLysGlnGluProGlyAspAsnSerGluIleLeuSerGly 95858 : TCCCTGCAACCAGTTTGGGAAGCAAGAACCCGGAGACAACTCAGAGATTCTTTCTGGG : 95802 135 : Leu{Ly} >>>> Target Intron 3 >>>> {s}TyrValArgProGlyLysG : 143 |||{||} 461 bp {|}||||||||||||||| !! Leu{Ly}++ ++{s}TyrValArgProGlyGlyG 95801 : CTC{AA}gt.........................ag{G}TATGTTCGTCCAGGAGGAG : 95314 144 : lyPheLeuProAsnPheGlnLeuPheAlaLysGlyAspValAsnGlyGluAsnGluGl : 162 !!:!:!!||||||||||||||||||||||||||||||||||||||||||...||||| luTyrValProAsnPheGlnLeuPheAlaLysGlyAspValAsnGlyGluLysGluGl 95313 : AATATGTACCTAATTTCCAACTGTTTGCCAAAGGGGATGTGAAtggtgaaaaagaaca : 95257 163 : nLysIlePheThrPheLeuLys >>>> Target Intron 4 >>>> ArgSerC : 172 |||||||||||||||||||||| 1083 bp !:!|||| nLysIlePheThrPheLeuLys++ ++GlnSerC 95256 : gaaaatcttCACCTTCTTGAAGgt.........................agCAATCCT : 94144 173 : ysProHisProSerGluThrValValMetSerLysHisThrPheTrpGluProIleLy : 191 ||||||||||||||||| |||!.!! !! !||||||! !! !|||||||||:!!|| ysProHisProSerGluIleValAlaThrPheLysHisIleSerTrpGluProValLy 94143 : gtcctcacccctcagagattgTAGCCACGTTCAAACACATCTCCTGGGAGCCGGTAAA : 94087 192 : sValHisAspIleArgTrpAsnPheGluLysPheLeuValGlyProAspGlyIlePro : 210 ||||:!!|||||||||||||||||||||||||||||||||||||||:!!|||:!!||| sValAsnAspIleArgTrpAsnPheGluLysPheLeuValGlyProAsnGlyValPro 94086 : AGTCAATGACATCCGCTGGAACTTCGAAAAGTTCCTGGTGGGACCCAATGGTGTCCCT : 94030 211 : ValMetArgTrpPheHisGlnAlaProValSerThrValLysSerAspIleMetAlaT : 230 |||||||||||||||||||||.!!|||:!!||||||||||||:!!||||||:!!|||| ValMetArgTrpPheHisGlnThrProIleSerThrValLysAlaAspIleLeuAlaT 94029 : GTCATGCGCTGGTTCCACCAGACTCCCATCAGCACTGTCAAAGCTGATATCCTGGCAT : 93970 231 : yrLeuSerHisPheLysThr : 236 |||||!.!!..! !|||||| yrLeuLysArgSerLysThr 93969 : ATCTGAAGCGGTCCAAGACC : 93950 vulgar: SPP00000102_1.0 0 236 . PVKD010003030.1:subseq(1,165951) 100514 93949 - 948 M 28 84 G 1 0 M 16 48 5 0 2 I 0 2940 3 0 2 M 51 153 S 0 1 5 0 2 I 0 1368 3 0 2 S 1 2 M 38 114 S 0 2 5 0 2 I 0 457 3 0 2 S 1 1 M 33 99 5 0 2 I 0 1079 3 0 2 M 67 201 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2019-11-22 ##type DNA # # # seqname source feature start end score strand frame attributes # PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local gene 93950 100514 948 - . gene_id 1 ; sequence SPP00000102_1.0 ; gene_orientation + PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local cds 100383 100514 . - . PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local exon 100383 100514 . - . insertions 0 ; deletions 1 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local splice5 100381 100382 . - . intron_id 1 ; splice_site "GT" PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local intron 97439 100382 . - . intron_id 1 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local splice3 97439 97440 . - . intron_id 0 ; splice_site "AG" PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local cds 97285 97438 . - . PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local exon 97285 97438 . - . insertions 0 ; deletions 0 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local splice5 97283 97284 . - . intron_id 2 ; splice_site "GT" PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local intron 95913 97284 . - . intron_id 2 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local splice3 95913 95914 . - . intron_id 1 ; splice_site "AG" PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local cds 95795 95912 . - . PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local exon 95795 95912 . - . insertions 0 ; deletions 0 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local splice5 95793 95794 . - . intron_id 3 ; splice_site "GT" PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local intron 95334 95794 . - . intron_id 3 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local splice3 95334 95335 . - . intron_id 2 ; splice_site "AG" PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local cds 95234 95333 . - . PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local exon 95234 95333 . - . insertions 0 ; deletions 0 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local splice5 95232 95233 . - . intron_id 4 ; splice_site "GT" PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local intron 94151 95233 . - . intron_id 4 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local splice3 94151 94152 . - . intron_id 3 ; splice_site "AG" PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local cds 93950 94150 . - . PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local exon 93950 94150 . - . insertions 0 ; deletions 0 PVKD010003030.1:subseq(1,165951) exonerate:protein2genome:local similarity 93950 100514 948 - . alignment_id 1 ; Query SPP00000102_1.0 ; Align 100515 1 84 ; Align 100431 30 48 ; Align 97439 46 153 ; Align 95911 98 114 ; Align 95333 137 99 ; Align 94151 170 201 # --- END OF GFF DUMP --- # -- completed exonerate analysis