Question

to extract the mRNA sequences of the canonical RefSeq genes

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Bogdan ▴ 670

@bogdan-2367

Last seen 13 months ago

Palo Alto, CA, USA

Dear all,

if you do not mind reading or answering a simple question please :

would you please advise, what is the simplest and most reliable way to extract the mRNA sequences of the canonical RefSeq genes in human or mouse genomes ?

thanks a lot,

-- bogdan

Biostrings • 2.0k views

ADD COMMENT • link 4.0 years ago Bogdan ▴ 670

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Dear Bogdan,

This can be done using a combination of useMart and getSequence functions. If you want the mRNA sequence for NM_031419 for example, use:

library(biomaRt)

mart <- useMart('ensembl',
            dataset = 'hsapiens_gene_ensembl',
            host = 'useast.ensembl.org')

cds_seq = getSequence(id = "NM_031419",
                      type = "refseq_mrna",
                      seqType = "coding",
                      mart = mart)
View(cds_seq)

I hope this helps! Best, Heiko

ADD REPLY • link 4.0 years ago heiko_kin ▴ 60

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Dear Heiko, thank you for your suggestions.

shall i aim please to download the transcript sequence of a lincRNA (for example NR_130130), how shall i specify it in the getSequence() ?

thanks :)

ADD REPLY • link 4.0 years ago Bogdan ▴ 670

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Not really a Bioc question, but how about simple downloading the transcriptome fasta files for your reference build and then grep what you need?

ADD REPLY • link 4.0 years ago ATpoint ★ 4.5k

score 3 · Accepted Answer · 2020-12-01

That's not a simple question, unless you are only planning to get only RefSeq Select or MANE Select transcripts, there isn't, so far as I know a 'canonical sequence` for a gene. I mean there are canonical sequences, like RefSeq Select and MANE Select, but so far there aren't that many such transcripts that the powers that be have decided are canonical.

As ATpoint noted, you could download the transcript FASTA files, from here. Or you can do one or more of the suggested things at the bottom of the page here.

And that is restricted to human, not mouse. Given that there are often multiple transcripts per gene, and given that NCBI and EBI/EMBL disagree on the transcripts for many genes (hence MANE), you will have to decide what the 'canonical sequence' is. Once you have decided upon that fraught question, you can easily generate a GRangesList and use getSeq from Biostrings to get the sequence from whatever BSgenome package is relevant.