_______________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 6e-99 Query name: gi|984109117|ref|XP_015345952.1| PREDICTED: selenoprotein P isoform X1 [Marmota marmota marmota] Query range: 1-371 (total 371) Target: /data/www-rg/seblastian_results/851530411/tempfiles/temptarget.fasta Chromosome: KZ296009.1:subseq_147966,54855_ Strand: - Positions: -Exon 1 31185 31387 -Exon 2 30008 30220 -Exon 3 27849 27966 -Exon 4 24961 25539 Redox box: YES Query MWRSLGLALALCFLPYGGTESQGENFICKQPPDWSIRDQNPMQNSHGSVTVVALLQASUYLCILQASR <---Intron---> LEDLRIKLEKEGYSNI |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| < 964bp > |||||||||||||||| Target MWRSLGLALALCFLPYGGTESQGENFICKQPPDWSIRDQNPMQNSHGSVTVVALLQASUYLCILQASR LEDLRIKLEKEGYSNI ataacgcgcgcttcctggagacggatatacccgtaaagcacacatcgtgagggcccgattctaccgta tggccaatgaggttaa tgggtgtctctgttcaggcagagaattgaaccaggtgaaactaacagctcttcttacggatgttaccg taatgtataaagacat gggcgatcgtcttcctaaagcgtaccttgacacgtaatataggccttagtgttttatcacgctggac agacgaaagaaaatttt * Query SYIVVNHQGISSQLKYIHLKNKVSDHIPVYQQEENQKDVWTLLNGYKDDFLIYDR <---Intron---> CGHLVYHLGLPYSFLTFPYVEDAIKIAYC |||||||||||||||||||||||||||||||||||| |||||||||||||||||| < 2041bp > ||||||||||||||||||||||||||||| Target SYIVVNHQGISSQLKYIHLKNKVSDHIPVYQQEENQTDVWTLLNGYKDDFLIYDR CGHLVYHLGLPYSFLTFPYVEDAIKIAYC ttaggaccgattctataccaaagtgcacgtccggacaggtactagtaggtcatga tgccgtccgtctttcatctggggaaagtt catttaaagtccataatataaatcaatctaaaaaaacatgcttagaaaatttaag ggattaatgtcacttctcataactatcag cttttttaacttaaacattatgtactttttaaaacaatcgacatacatcccatc atcttattttgtcccatcataatctgttct Query EDRCGNCSFR <---Intron---> TLENEDFCRNVSLPTVEKTIEALQPHHHHSHQHLGSSELSKNQQPGAADTPSNPAPLDLHHHKKHKGQYRQGNS |||||||||| < 2309bp > |||||| |||||||||||| |||||||||/|||||||||||||||||||||||||||||||||||||||||||| Target EDRCGNCSFR TLENEDLCRNVSLPTVEKTTEALQPHHHHNHQHLGSSELSKNQQPGAADTPSNPAPLDLHHHKKHKGQYRQGNS ggatgattta acgaggttaagttcaggaaaggcccccccaccccgaagctaacccggggactacgccgccccaacagctacgat aagggagctg ctaaaatggatctcctaaccactacaaaaaaaatgggatcaaaacgccacccaccctataaaaaaagaagagac acatacctcg ttatacatatatgctgaaatgtggatctcctgttgctgtagtgaaaaatttaccttacttctaacgcgtggtca Query ESUQMAGSEGLQLSLAQRKLCQKGCVNQLQCKLFKDPQAASSSCCCHCRHLIFEKRESAITUQCAENLPSLCSUQGLRAEENVIESCQURKPPAAUQRSQ |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||| Target ESUQMAGSEGLQLSLAQRKLCQKGCVNQLQCKLFKDPQAASSSCCCHCRHLIFEKRESAITUQCAENLPSLCSUQGLRAEENVIESCQURMPPAAUQRSQ gatcaggaggtcctcgcaactcagtgactctattagccggtaatttctcccatgaagtgaatctggacctttatcgcagggagagttctcaccggtcaac aggatcggagtatctcagatgaaggtaatagattaacacccgggggaggatttaagacctcgagcaatcctgggagtgcaaattacgaggtccccgagga gcaggaatataatataagaccagatataagtggcatagatttctccttatgataaagtaccagttaccatatcagatgaggtctactgaagtatcaaatg * * * * * Query QLDPTEVGTNUSUKNKAKK ||||||||||||||||||| Target QLDPTEVGTNUSUKNKAKK ccgcagggaatataaagaa ataccatgcagggaaacaa gttcaatcctacaatgaag * * Sequence until next stop: TGA * Distance CDS-SECIS: 283 ; UGA-SECIS: 301 ------- SECIS element -- id:1 -- grade:A ---- Chromosome = KZ296009.1:subseq_147966,54855_ Strand = - Positions = 24677 - 24608 Found by: Infernal (score=25.84) Covels (score=32.57) Stem2 length = 11 Apical loop length = 14 Insertion in stem2 = 0, 0 Free Energy = -10.24 ..(((((((.......(((((((((((((((...............)))))))))))))))........))))))).. model uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc ..((((((.---....{[[{((((((((([(.....-.........)])))))))))}]]}----.....)))))).. target CUAUUUGCA---UUGAUGAGAACAGAAACAUAAACU-AUGACCUAGGGGUUUCUGUUGGAU----AGUUAGUAAAUUA **** ^^^ **** _________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:2 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 6e-99 Query name: gi|984109117|ref|XP_015345952.1| PREDICTED: selenoprotein P isoform X1 [Marmota marmota marmota] Query range: 1-371 (total 371) Target: /data/www-rg/seblastian_results/851530411/tempfiles/temptarget.fasta Chromosome: KZ296009.1:subseq_147966,54855_ Strand: - Positions: -Exon 1 31185 31387 -Exon 2 30008 30220 -Exon 3 27849 27966 -Exon 4 24961 25539 Redox box: YES Query MWRSLGLALALCFLPYGGTESQGENFICKQPPDWSIRDQNPMQNSHGSVTVVALLQASUYLCILQASR <---Intron---> LEDLRIKLEKEGYSNI |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| < 964bp > |||||||||||||||| Target MWRSLGLALALCFLPYGGTESQGENFICKQPPDWSIRDQNPMQNSHGSVTVVALLQASUYLCILQASR LEDLRIKLEKEGYSNI ataacgcgcgcttcctggagacggatatacccgtaaagcacacatcgtgagggcccgattctaccgta tggccaatgaggttaa tgggtgtctctgttcaggcagagaattgaaccaggtgaaactaacagctcttcttacggatgttaccg taatgtataaagacat gggcgatcgtcttcctaaagcgtaccttgacacgtaatataggccttagtgttttatcacgctggac agacgaaagaaaatttt * Query SYIVVNHQGISSQLKYIHLKNKVSDHIPVYQQEENQKDVWTLLNGYKDDFLIYDR <---Intron---> CGHLVYHLGLPYSFLTFPYVEDAIKIAYC |||||||||||||||||||||||||||||||||||| |||||||||||||||||| < 2041bp > ||||||||||||||||||||||||||||| Target SYIVVNHQGISSQLKYIHLKNKVSDHIPVYQQEENQTDVWTLLNGYKDDFLIYDR CGHLVYHLGLPYSFLTFPYVEDAIKIAYC ttaggaccgattctataccaaagtgcacgtccggacaggtactagtaggtcatga tgccgtccgtctttcatctggggaaagtt catttaaagtccataatataaatcaatctaaaaaaacatgcttagaaaatttaag ggattaatgtcacttctcataactatcag cttttttaacttaaacattatgtactttttaaaacaatcgacatacatcccatc atcttattttgtcccatcataatctgttct Query EDRCGNCSFR <---Intron---> TLENEDFCRNVSLPTVEKTIEALQPHHHHSHQHLGSSELSKNQQPGAADTPSNPAPLDLHHHKKHKGQYRQGNS |||||||||| < 2309bp > |||||| |||||||||||| |||||||||/|||||||||||||||||||||||||||||||||||||||||||| Target EDRCGNCSFR TLENEDLCRNVSLPTVEKTTEALQPHHHHNHQHLGSSELSKNQQPGAADTPSNPAPLDLHHHKKHKGQYRQGNS ggatgattta acgaggttaagttcaggaaaggcccccccaccccgaagctaacccggggactacgccgccccaacagctacgat aagggagctg ctaaaatggatctcctaaccactacaaaaaaaatgggatcaaaacgccacccaccctataaaaaaagaagagac acatacctcg ttatacatatatgctgaaatgtggatctcctgttgctgtagtgaaaaatttaccttacttctaacgcgtggtca Query ESUQMAGSEGLQLSLAQRKLCQKGCVNQLQCKLFKDPQAASSSCCCHCRHLIFEKRESAITUQCAENLPSLCSUQGLRAEENVIESCQURKPPAAUQRSQ |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||| Target ESUQMAGSEGLQLSLAQRKLCQKGCVNQLQCKLFKDPQAASSSCCCHCRHLIFEKRESAITUQCAENLPSLCSUQGLRAEENVIESCQURMPPAAUQRSQ gatcaggaggtcctcgcaactcagtgactctattagccggtaatttctcccatgaagtgaatctggacctttatcgcagggagagttctcaccggtcaac aggatcggagtatctcagatgaaggtaatagattaacacccgggggaggatttaagacctcgagcaatcctgggagtgcaaattacgaggtccccgagga gcaggaatataatataagaccagatataagtggcatagatttctccttatgataaagtaccagttaccatatcagatgaggtctactgaagtatcaaatg * * * * * Query QLDPTEVGTNUSUKNKAKK ||||||||||||||||||| Target QLDPTEVGTNUSUKNKAKK ccgcagggaatataaagaa ataccatgcagggaaacaa gttcaatcctacaatgaag * * Sequence until next stop: TGA * Distance CDS-SECIS: 715 ; UGA-SECIS: 733 ------- SECIS element -- id:2 -- grade:A ---- Chromosome = KZ296009.1:subseq_147966,54855_ Strand = - Positions = 24245 - 24180 Found by: Infernal (score=24.86) Covels (score=16.28) Stem2 length = 10 Apical loop length = 8 Insertion in stem2 = 1, 0 Free Energy = -15.3 ..(((((((.......((((((((((.(((((...............)))))))))))))))........))))))).. model uucggucaugcgUuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc ..(((((((---....([[{((((((.{((((.....--.-----..))))}))))))}]])..--..-.))))))).. target UUUCCAUAG---UCAAUGAUGGUUUAAUAGGGAAAUU--A-----AACCCUCUAAACUUGAACU--CC-UUUAUGGAUA **** ^^^ ****