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@mauedealiceit-3511
Last seen 10.5 years ago
I found seven 3'UTR sequences attributed to the same ensembl_gene_id.
Naively, I wonder whether it is possible, or it is
the consequence of a logic bug in my code. Can the same gene have more
than one 3'UTR region ?
In the following is is what I have extracted running just the first
iteration of a nested loop.
Is that *real* ?
Thank you for your attention.
Maura
hmart <- useMart('ensembl', dataset='hsapiens_gene_ensembl')
> enst
[1] "ENST00000376439"
> rec <- getBM(attributes=c('hgnc_symbol','ensembl_gene_id','ensembl_t
ranscript_id','refseq_dna'),
+ filters='ensembl_transcript_id', values=enst, mart=hmart)
> rec
hgnc_symbol ensembl_gene_id ensembl_transcript_id refseq_dna
1 RABL2A ENSG00000144134 ENST00000376439 NA
> rec[,"ensembl_gene_id"]
[1] "ENSG00000144134"
> seq = getSequence(id=rec[,"ensembl_gene_id"],type="ensembl_gene_id",
seqType="3utr",mart=hmart)
> seq
3utr
1
GGGGCTGGGGCTAGGGGTGGGTGGAGCCCTTTTAAAATACCCTTCCCTTCAACAACTCTCCAGCTCTGAA
TGGAGAAACTCTCTAGGCCATCCCCTCTTCTACCTCCTGCAACCCACCCATCCTATTAGCCTCCCACATT
CAAGGCCCGTGATACAGGGATGAGGTCAGCACCAGCAAACTCTGGACTGGTGGAAGAATTCCCCACCAGA
TCTCCTTGAAGCAGAATTAGGGATCAGCATCATTAACACCTTCCCCACCCCCTCCCCCCAGGCAGACAGT
GAAGAGAATCAGAAAACATGATTATGTGTCACTTTAATACAGGAAATTTAGGTGTTTTTTGGTGTTTTTG
TTTTTGTTTTCTTTCCAAAGCTCACCTCGGGGACAATTCCTTGGGCTTCTCCTGAGTCTCGCTCTGTCGC
CAGGCTGGAGTGCAGTGGCGCAGTCTCGGCTCGCTGCAACCTCTGACTCCCTGGTTCAAACGATTCTCCT
GCCTCAGCCTCCCGAGTGGCTGGCATCACCACGCCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGTT
TCACCATGTTGCCCAGGATGGTCTCGATCTCCTCACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGC
TGGGATTACAGGCATGAGCCACCGCGCCCGGCCCCAATCATCTGTTTTTAAACAATCGTTTTTGAGCAGA
TAGCTATTCATTCCAGATTTCCGTGTACCCACTCTGTTTCAGGAGCTCTTCTAGGTAAAGCTGAGATCAC
AGGAACAGCAGGTGACAGGCCTAGCTATAGTTAGGAATACACAAGCGGTAAAATCGAGTCCTTACAGCCA
TACCACAAGGTACGTCCATTTGGACTACAAGAAGAGCTTCCTTTAAAGTTCCTATTTCAGCATAAAGAGG
CTGTCCTTTTTTTTTAGGAATAGTTTGGACCTTGTGCCTCCTGTGGGAGGCTGAGGACTGCAAGAGGAGA
GCTAGCAGATATGCCTGTTCACCCCTCTCTGGTACTTGTGGCTTGCTAGTATGTTTTTATGATAATCTCG
GGCATTGTTTGCATTGTGTTTATTAATAGGGTTTTGTTTTTATTGTTTCCTTTTTTACAGTAAAGGCTGA
ATGACATAAA
2
GGGGCTGGGGCTAGGGGTGGGTGGAGCCCTTTTAAAATACCCTTCCCTTCAACAACTCTCCAGCTCTGAA
TGGAGAAACTCTCTAGGCCATCCCCTCTTCTACCTCCTGCAACCCACCCATCCTATTAGCCTCCCACATT
CAAGGCCCGTGATACAGG
3
GGGGCTGGGGCTAGGGGTGGGTGGAGCCCTTTTAAAATACCCTTCCCTTCAACAACTCTCCAGCTCTGAA
TGGAGAAACTCTCTAGGCCATCCCCTCTTCTACCTCCTGCAACCCACCCATCCTATTAGCCTCCCACATT
CAAGGCCCGTGATACAGGGATGAGGTCAGCACCAGCAAACTCTGGACTGGTGGAAGAATTCCCCACCAGA
TCTCCTTGAAGCAGAATTAGGGATCAGCATCATTAACACCTTCCCCACCCCCTCCCCCCAGGCAGACAGT
GAAGAGAATCAGAAAACATGATTATGTGTCACTTTAATACAGGAAATTTAGGTGTTTTTTGGTGTTTTTG
TTTTTGTTTTCTTTCCAAAGCTCACCTCGGGGACAATTCCTTGGGCTTCTCCTGAGGTAATGATTACCCC
CCCACCCACAGCTGAGTCTGTGAGGCCCCATCCTTTCCCTACGTTTTCTCCCATCTTTTTTCCTCTTCAA
TCTCCCAGTCATCTGGTTTGTTTGTTTCTTTGTTCGTCCTGAGACGGAGTCTCGCTCTGTCGCCAGGCTG
GAGTGCAGTGGCGCAGTCTCGGCTCGCTGCAACCTCTGACTCCCTGGTTCAAACGATTCTCCTGCCTCAG
CCTCCCGAGTGGCTGGCATCACCACGCCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCAT
GTTGCCCAGGATGGTCTCGATCTCCTCACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATT
ACAGGCATGAGCCACCGCGCCCGGCCCCAATCATCTGTTTTTAAACAATCGTTTTTGAGCAGATAGCTAT
TCATTCCAGATTTCCGTGTACCCACTCTGTTTCAGGAGCTCTTCTAGGTAAAGCTGAGATCACAGGAACA
GCAGGTGACAGGCCTAGCTATAGTTAGGAATACACAAGCGGTAAAATCGAGTCCTTACAGCCATACCACA
AGGTACGTCCATTTGGACTACAAGAAGAGCTTCCTTTAAAGTTCCTATTTCAGCATAAAGAGGCTGTCCT
TTTTTTTTAGGAATAGTTTGGACCTTGTGCCTCCTGTGGGAGGCTGAGGACTGCAAGAGGAGAGCTAGCA
GATATGCCTGTTCACCCCTCTCTGGTACTTGTGGCTTGCTAGTATGTTTTTATGATAATCTCGGGCATTG
TTTGCATTGTGTTTATTAATAGGGTTTTGTTTTTATTGTTTCCTTTTTTACAGTAAAGGCTGAATGACAT
4
GGGGCTGGGGCTAGGGGTGGGTGGAGCCCTTTTAAAATACCCTTCCCTTCAACAACTCTCCAGCTCTGAA
TGGAGAAACTCTCTAGGCCATCCCCTCTTCTACCTCCTGCAACCCACCCATCCTATTAGCCTCCCACATT
CAAGGCCCGTGATACAGGGATGAGGTCAGCACCAGCAAACTCTGGACTGGTGGAAGAATTCCCCACCAGA
TCTCCTTGAAGCAGAATTAGGGATCAGCATCATTAACACCTTCCCCACCCCCTCCCCCCAGGCAGACAGT
GAAGAGAATCAGAAAACATGATTATGTGTCACTTTAATACAGGAAATTTAGGTGTTTTTTGGTGTTTTTG
TTTTTGTTTTCTTTCCAAAGCTCACCTCGGGGACAATTCCTTGGGCTTCTCCTGAGGTAATGATTACCCC
CCCACCCACAGCTGAGTCTGTGAGGCCCCATCCTTTCCCTACGTTTTCTCCCATCTTTTTTCCTCTTCAA
TCTCCCAGTCATCTGGTTTGTTTGTTTCTTTGTTCGTCCTGAGACGGAGTCTCGCTCTGTCGCCAGGCTG
GAGTGCAGTGGCGCAGTCTCGGCTCGCTGCAACCTCTGACTCCCTGGTTCAAACGATTCTCCTGCCTCAG
CCTCCCGAGTGGCTGGCATCACCACGCCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCAT
GTTGCCCAGGATGGTCTCGATCTCCTCACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATT
ACAGGCATGAGCCACCGCGCCCGGCCCCAATCATCTGTTTTTAAACAATCGTTTTTGAGCAGATAGCTAT
TCATTCCAGATTTCCGTGTACCCACTCTGTTTCAGGAGCTCTTCTAGGTAAAGCTGAGATCACAGGAACA
GCAGGTGACAGGCCTAGCTATAGTTAGGAATACACAAGCGGTAAAATCGAGTCCTTACAGCCATACCACA
AGGTACGTCCATTTGGACTACAAGAAGAGCTTCCTTTAAAGTTCCTATTTCAGCATAAAGAGGCTGTCCT
TTTTTTTTAGGAATAGTTTGGACCTTGTGCCTCCTGTGGGAGGCTGAGGACTGCAAGAGGAGAGCTAGCA
GATATGCCTGTTCACCCCTCTCTGGTACTTGTGGCTTGCTAGTATGTTTTTATGATAATCTCGGGCATTG
TTTGCATTGTGTTTATTAATAGGGTTTTGTTTTTATTGTTTCCTTTTTTACAGTAAAGGCTGAATGACAT
AAA
5 CTGCTTCCTGCATCTGCTGCATCTCCGTGGGCTCCCCTCAGACCCTCTTCTGAAGGCCTGGGGTGTCT
CTCCTGCCACCATGCCTGTGTCTGCAGGTGCCTGCCACCAGCCCCAGTCTGCTGCACGGGCCCTGGCAAG
TAGAAAGCACTTGCCTTCTGACCACACGGGGAGCTGAGGGTCAGAGACGGAACCAGGGCTCGACCCTCCA
CCTTGAAACCTTGAGATGGGGATGCTCCTCATTCTAGCCAGTTCCTCCTCAGCTCTCAAAACAAGGAACA
GATGCTCAGGAAACCAGATCTGGACAAAAGTCATCTGAGCCTGGTGTGAGGCAGATTCCAGAAGTTTAGT
TACAGACATCCTTTATAAGGAGACTTCATCGGGAATTCAAGACAACCTGGTGATTCATTGAAATTTGCCT
GTGAAAGAGAATCTACATAGACTTCCTGCCACCTCTTGAGATGTGACAGTTGCTGACCCTCCCGCCACCA
CACAGGGCGAGCCCCTAGCCCTGAGCTTGAACCATGTTGCTTGCACAAATAGCTGGGTGATTTAGAAGTG
AGGTCAGCTGTGCCAGCAGTTACAGGGTGGTGGTTGTCTGTAACTTTAATCCACTGACTGTTGTACTAGG
GCAGTTTGGGCTAGACACTTTGGAGGAGCTCCTGTGAAGGGCATGAAGGCTCACTGTAGCAGCAGCTCAG
TTGTCTTTCAGAGTTCTGCCCTTAGAGCTGGTTTGCAGTGCTCATCCTTCTTGCTGATATTTTAAAATAG
GTAGAAACAGGCTGGGCGCGGTGACTCATGCCTTTAATCCCAGTACTTTGGGAGGCCTAGGTGGGCAGAT
CACCTGAGGTCAGGAGTTCGAGACCAGCCTGACCAACATGTTGAAACCCCGTCTCTACTAGAAATACAAA
AATTAGCCAGGCGTGGTGGCGCGCACCTGTAATCCAGCTACTCAGGAGGCTGAGACAGGAGAATCGTTTG
AAGACAGGAGAATCGTTTGAACCCAGGAGGTGGAGGTTGCAGTGGCAGTGAGCCAAGATACCGCCACTGC
ACTCTAGCCTGGGCAACAGAGCAAGACTCCATCTCAAAATAAATAAATAAATAAAAATAAAATAGGTAAA
AACAAATTATAAAGTAATACAATTATGAACTGCAAATAATAAAACATAAAAATTACTTTAAAAAAATTTA
AAGAGGCCGGGCACAGTGGCTTATGCCTGTAATCCCAGAAATTTGGGAGGCCGAGGCAGGAGGATCACTT
GAGCCCGGGAGTCCAAGACCAGCCTCGTTAATATAATGAGAGCTTATCATCTCTACAAAAAATAAACAAA
ATTAGCCAGGCATGGTGGCATGTGCCTGTAGTTCCAGCTACTCAGGAGGCTGAGGTAGGAGGATCACTGG
AGCCCAGGGGGTGGAGGAGCAGTAAGCCAAGATTCTGCCACTGCACTCCAGCCTGGCTGACAGAGTAAGA
CCCTATCTCAAAAAACAAAAAGCAGAAAGAACAAAGAAGTAAACAAAAGCTTAAAAGTAAATCAGCCAGG
TGCAGTAGCTCATGCCTGTAATCCCAGTACTTTGGGAGGCCTAGGCAGGCAGATTACTGCAGGTCAAGAG
TTTGAGACCAGCCTGGCCAACATGATGAAACCCTGTCTCTACTAAAACTACAAAAATTAGCCAGGCATGG
TGGTGCGCACCTGTAATCCCAGCTACTCCGGAGGCTGAGACAAGAGAATCGCTTGAACCTAGGAAGTGGA
GGTTGCAGTGGCAGTGAGCCAAGATAGCGCCACTGCACTCCAGCCTGGGCAACAGAGCAAGACTCCATAT
ATGGAGATCCCTTGAGATCAAGAGTTCGAGACCAGCCTGGCCAACACGGCAAAACCCTGTCTCTACTAAA
AATAAAAAAA
6
GGGGCTGGGGCTAGGGGAATAGTTTGGACCTTGTGCCTCCTGTGGGAGGCTGAGGACTGCAAGAGGAGAG
CTAGCAGATATGCCTGTTCACCCCTCTCTGGTACTTGTGGCTTGCTAGTATGTTTTTATGATAATCTCGG
GCATTGTTTGCATTGTGTTTATTAATAGGGTTTTGTTTTTATTGTTTCCTTTTTTACAGTAAAGGCTGAA
TGACATAA
7
GGGGCTGGGGCTAGGGGAATAGTTTGGACCTTGTGCCTCCTGTGGGAGGCTGAGGACTGCAAGAGGAGAG
CTAGCAGATATGCCTGTTCACCCCTCTCTGGTACTTGTGGCTTGCTAGTATGTTTTTATGATAATCTCGG
GCATTGTTTGCATTGTGTTTATTAATAGGGTTTTGTTTTTATTGTTTCCTTTTTTACAGTAAAGGCTGAA
TGACAT
ensembl_gene_id
1 ENSG00000144134
2 ENSG00000144134
3 ENSG00000144134
4 ENSG00000144134
5 ENSG00000144134
6 ENSG00000144134
7 ENSG00000144134
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