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@mauedealiceit-3511
Last seen 10.0 years ago
Unluckily there is no one in our group who has clear idea about these
Biology matter.
We are missing the Biology professor who is still hospitalized.
I asked someone in my group "is there a unique 3UTR region in a gene?"
I was answered "yes".
I know there is plenty of material about these topics on the web.
I really need some very basic reading just to get a grasp of
rudimental concepts.
Best regards,
Maura
-----Messaggio originale-----
Da: Sean Davis [mailto:seandavi@gmail.com]
Inviato: mar 30/06/2009 17.31
A: mauede@alice.it
Cc: Miichael Watson; Steve Lianoglou; Bioconductor List
Oggetto: Re: Found seven 3'UTR sequences attributed to the same
ensembl_gene_id
On Tue, Jun 30, 2009 at 11:28 AM, <mauede@alice.it> wrote:
> 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* ?
>
Hi, Maura.
Genes do not have 3'UTR regions. Only transcripts have 3'UTRs. So,
since a
gene can have multiple transcripts, there will be multiple 3'UTRs
associated
with each gene. So, I think your code is probably fine.
Sean
>
> 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_transcri
pt_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",seqTyp
e="3utr",mart=hmart)
>
> > seq
>
>
> 3utr
> 1
> GGGGCTGGGGCTAGGGGTGGGTGGAGCCCTTTTAAAATACCCTTCCCTTCAACAACTCTCCAGCTCTG
AATGGAGAAACTCTCTAGGCCATCCCCTCTTCTACCTCCTGCAACCCACCCATCCTATTAGCCTCCCACA
TTCAAGGCCCGTGATACAGGGATGAGGTCAGCACCAGCAAACTCTGGACTGGTGGAAGAATTCCCCACCA
GATCTCCTTGAAGCAGAATTAGGGATCAGCATCATTAACACCTTCCCCACCCCCTCCCCCCAGGCAGACA
GTGAAGAGAATCAGAAAACATGATTATGTGTCACTTTAATACAGGAAATTTAGGTGTTTTTTGGTGTTTT
TGTTTTTGTTTTCTTTCCAAAGCTCACCTCGGGGACAATTCCTTGGGCTTCTCCTGAGTCTCGCTCTGTC
GCCAGGCTGGAGTGCAGTGGCGCAGTCTCGGCTCGCTGCAACCTCTGACTCCCTGGTTCAAACGATTCTC
CTGCCTCAGCCTCCCGAGTGGCTGGCATCACCACGCCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGG
TTTCACCATGTTGCCCAGGATGGTCTCGATCTCCTCACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGT
GCTGGGATTACAGGCATGAGCCACCGCGCCCGGCCCCAATCATCTGTTTTTAAACAATCGTTTTTGAGCA
GATAGCTATTCATTCCAGATTTCCGTGTACCCACTCTGTTTCAGGAGCTCTTCTAGGTAAAGCTGAGATC
ACAGGAACAGCAGGTGACAGGCCTAGCTATAGTTAGGAATACACAAGCGGTAAAATCGAGTCCTTACAGC
CATACCACAAGGTACGTCCATTTGGACTACAAGAAGAGCTTCCTTTAAAGTTCCTATTTCAGCATAAAGA
GGCTGTCCTTTTTTTTTAGGAATAGTTTGGACCTTGTGCCTCCTGTGGGAGGCTGAGGACTGCAAGAGGA
GAGCTAGCAGATATGCCTGTTCACCCCTCTCTGGTACTTGTGGCTTGCTAGTATGTTTTTATGATAATCT
CGGGCATTGTTTGCATTGTGTTTATTAATAGGGTTTTGTTTTTATTGTTTCCTTTTTTACAGTAAAGGCT
GAATGACATAAA
> 2
>
> GGGGCTGGGGCTAGGGGTGGGTGGAGCCCTTTTAAAATACCCTTCCCTTCAACAACTCTCCAGCTCTG
AATGGAGAAACTCTCTAGGCCATCCCCTCTTCTACCTCCTGCAACCCACCCATCCTATTAGCCTCCCACA
TTCAAGGCCCGTGATACAGG
> 3
> GGGGCTGGGGCTAGGGGTGGGTGGAGCCCTTTTAAAATACCCTTCCCTTCAACAACTCTCCAGCTCTG
AATGGAGAAACTCTCTAGGCCATCCCCTCTTCTACCTCCTGCAACCCACCCATCCTATTAGCCTCCCACA
TTCAAGGCCCGTGATACAGGGATGAGGTCAGCACCAGCAAACTCTGGACTGGTGGAAGAATTCCCCACCA
GATCTCCTTGAAGCAGAATTAGGGATCAGCATCATTAACACCTTCCCCACCCCCTCCCCCCAGGCAGACA
GTGAAGAGAATCAGAAAACATGATTATGTGTCACTTTAATACAGGAAATTTAGGTGTTTTTTGGTGTTTT
TGTTTTTGTTTTCTTTCCAAAGCTCACCTCGGGGACAATTCCTTGGGCTTCTCCTGAGGTAATGATTACC
CCCCCACCCACAGCTGAGTCTGTGAGGCCCCATCCTTTCCCTACGTTTTCTCCCATCTTTTTTCCTCTTC
AATCTCCCAGTCATCTGGTTTGTTTGTTTCTTTGTTCGTCCTGAGACGGAGTCTCGCTCTGTCGCCAGGC
TGGAGTGCAGTGGCGCAGTCTCGGCTCGCTGCAACCTCTGACTCCCTGGTTCAAACGATTCTCCTGCCTC
AGCCTCCCGAGTGGCTGGCATCACCACGCCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACC
ATGTTGCCCAGGATGGTCTCGATCTCCTCACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGA
TTACAGGCATGAGCCACCGCGCCCGGCCCCAATCATCTGTTTTTAAACAATCGTTTTTGAGCAGATAGCT
ATTCATTCCAGATTTCCGTGTACCCACTCTGTTTCAGGAGCTCTTCTAGGTAAAGCTGAGATCACAGGAA
CAGCAGGTGACAGGCCTAGCTATAGTTAGGAATACACAAGCGGTAAAATCGAGTCCTTACAGCCATACCA
CAAGGTACGTCCATTTGGACTACAAGAAGAGCTTCCTTTAAAGTTCCTATTTCAGCATAAAGAGGCTGTC
CTTTTTTTTTAGGAATAGTTTGGACCTTGTGCCTCCTGTGGGAGGCTGAGGACTGCAAGAGGAGAGCTAG
CAGATATGCCTGTTCACCCCTCTCTGGTACTTGTGGCTTGCTAGTATGTTTTTATGATAATCTCGGGCAT
TGTTTGCATTGTGTTTATTAATAGGGTTTTGTTTTTATTGTTTCCTTTTTTACAGTAAAGGCTGAATGAC
AT
> 4
> GGGGCTGGGGCTAGGGGTGGGTGGAGCCCTTTTAAAATACCCTTCCCTTCAACAACTCTCCAGCTCTG
AATGGAGAAACTCTCTAGGCCATCCCCTCTTCTACCTCCTGCAACCCACCCATCCTATTAGCCTCCCACA
TTCAAGGCCCGTGATACAGGGATGAGGTCAGCACCAGCAAACTCTGGACTGGTGGAAGAATTCCCCACCA
GATCTCCTTGAAGCAGAATTAGGGATCAGCATCATTAACACCTTCCCCACCCCCTCCCCCCAGGCAGACA
GTGAAGAGAATCAGAAAACATGATTATGTGTCACTTTAATACAGGAAATTTAGGTGTTTTTTGGTGTTTT
TGTTTTTGTTTTCTTTCCAAAGCTCACCTCGGGGACAATTCCTTGGGCTTCTCCTGAGGTAATGATTACC
CCCCCACCCACAGCTGAGTCTGTGAGGCCCCATCCTTTCCCTACGTTTTCTCCCATCTTTTTTCCTCTTC
AATCTCCCAGTCATCTGGTTTGTTTGTTTCTTTGTTCGTCCTGAGACGGAGTCTCGCTCTGTCGCCAGGC
TGGAGTGCAGTGGCGCAGTCTCGGCTCGCTGCAACCTCTGACTCCCTGGTTCAAACGATTCTCCTGCCTC
AGCCTCCCGAGTGGCTGGCATCACCACGCCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACC
ATGTTGCCCAGGATGGTCTCGATCTCCTCACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGA
TTACAGGCATGAGCCACCGCGCCCGGCCCCAATCATCTGTTTTTAAACAATCGTTTTTGAGCAGATAGCT
ATTCATTCCAGATTTCCGTGTACCCACTCTGTTTCAGGAGCTCTTCTAGGTAAAGCTGAGATCACAGGAA
CAGCAGGTGACAGGCCTAGCTATAGTTAGGAATACACAAGCGGTAAAATCGAGTCCTTACAGCCATACCA
CAAGGTACGTCCATTTGGACTACAAGAAGAGCTTCCTTTAAAGTTCCTATTTCAGCATAAAGAGGCTGTC
CTTTTTTTTTAGGAATAGTTTGGACCTTGTGCCTCCTGTGGGAGGCTGAGGACTGCAAGAGGAGAGCTAG
CAGATATGCCTGTTCACCCCTCTCTGGTACTTGTGGCTTGCTAGTATGTTTTTATGATAATCTCGGGCAT
TGTTTGCATTGTGTTTATTAATAGGGTTTTGTTTTTATTGTTTCCTTTTTTACAGTAAAGGCTGAATGAC
ATAAA
> 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
>
> GGGGCTGGGGCTAGGGGAATAGTTTGGACCTTGTGCCTCCTGTGGGAGGCTGAGGACTGCAAGAGGAG
AGCTAGCAGATATGCCTGTTCACCCCTCTCTGGTACTTGTGGCTTGCTAGTATGTTTTTATGATAATCTC
GGGCATTGTTTGCATTGTGTTTATTAATAGGGTTTTGTTTTTATTGTTTCCTTTTTTACAGTAAAGGCTG
AATGACATAA
> 7
>
> GGGGCTGGGGCTAGGGGAATAGTTTGGACCTTGTGCCTCCTGTGGGAGGCTGAGGACTGCAAGAGGAG
AGCTAGCAGATATGCCTGTTCACCCCTCTCTGGTACTTGTGGCTTGCTAGTATGTTTTTATGATAATCTC
GGGCATTGTTTGCATTGTGTTTATTAATAGGGTTTTGTTTTTATTGTTTCCTTTTTTACAGTAAAGGCTG
AATGACAT
> ensembl_gene_id
> 1 ENSG00000144134
> 2 ENSG00000144134
> 3 ENSG00000144134
> 4 ENSG00000144134
> 5 ENSG00000144134
> 6 ENSG00000144134
> 7 ENSG00000144134
>
>
>
>
>
>
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