On Mon, Nov 25, 2013 at 3:47 AM, Dave Tang <davetingpongtang@gmail.com>wrote:

> Hello,
>
> I've been using biomaRt to fetch genomic coordinates of RefSeqs (perhaps
> in an incorrect manner?). I found that the RefSeq coordinates don't match
> the coordinates provided at the UCSC Genome Browser (NM_033453 at
> chr20:3190006-3204516):
>
> library("biomaRt")
> ensembl <- useMart("ensembl", dataset="hsapiens_gene_ensembl")
> getBM(attributes=c('refseq_mrna','chromosome_name','
> start_position','end_position','strand'),
> filters = 'refseq_mrna', values = 'NM_033453', mart = ensembl)
>
>     refseq_mrna chromosome_name start_position end_position strand
> 1   NM_033453              20        3189514      3204516      1
>
> The coordinates seem to match this Ensembl transcript (ENST00000483354)
> instead:
>
> getBM(attributes=c('ensembl_transcript_id','chromosome_
> name','start_position','end_position','strand'),
> filters = 'ensembl_transcript_id', values = 'ENST00000483354', mart =
> ensembl)
>
>     ensembl_transcript_id chromosome_name start_position end_position
> strand
> 1       ENST00000483354              20        3189514      3204516      1
>
> Here's another RefSeq model, NM_181493, which should be mapped to
> chr20:3190134-3204516:
>
> getBM(attributes=c('refseq_mrna','chromosome_name','
> start_position','end_position','strand'),
> filters = 'refseq_mrna', values = 'NM_181493', mart = ensembl)
>
>     refseq_mrna chromosome_name start_position end_position strand
> 1   NM_181493              20        3189514      3204516      1
>
> So it seems the RefSeq IDs are mapped to the longest Ensembl transcript
> model that covers the RefSeq model. I searched around the web and looked at
> different available marts but nothing obvious popped out. How should I go
> about obtaining RefSeq coordinates using biomaRt? Or biomaRt is Ensembl
> centric?
>

Hi, Dave.

There may be multiple issues going on here, so you'll have to do some
digging yourself when discrepancies arise like you see here.  Working
through your first example, keep in mind that neither Ensembl or UCSC are
the actual curators of the RefSeq transcripts.  NCBI is the source of that
annotation.  So, if you go to NCBI gene and search for NM_033453 and then
play a bit with the Genomic Sequence Viewer, you'll note that the Gene
(protein NP_258412.1) is mapped with the coordinates given at UCSC while
the mRNA is mapped with the coordinates given by Ensembl.  Add to this
complication that UCSC does its own mapping of the transcripts (even
RefSeq) and you could even have a "unique" set of coordinates given by UCSC
(ie., not the same as NCBI or Ensembl).

Sean

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