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Refseq Mrna Position To Genomic Position

I am trying to find out genomic coordinates for a couple of refseq mrna ids, but a question posted here says that the mapping would be imperfect, but what I see in this file is that the corresponding gene co-ordinates are assigned to refseq ids. This information is really conflicting. Is it okay to carry on and assign the gene co-ordinates to refseq ids since this information is directly from NCBI databases itself ?

[edited part]

What I am trying to do is to see whether it is possible to map dbsnp genomic positions to a corresponding position in the refseq sequence. I know some groups have done it successfully for human, but I am looking for a non model organism (pig to be infact).

refseq mrna genomics position
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updated by gresserT • gresserT • written by Sudeep Sudeep

2 answers

It is true that genomic coordinates are sometimes ambiguous, but that is most often the edge case rather than the norm. The coordinates you will find in the file you linked to are "best guesses", and they're more than likely good enough for your purpose.

Eventually, it boils down to how much uncertainty your analysis can bear, and that is not something we can ascertain unless you give us more information about what you intend to do with these coordinates.

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written by Eric Fournier Eric Fournier

Thank you for this clarification, I have edited my question.

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written by Sudeep Sudeep

For your given purpose, you can probably go ahead and used mapped coordinates.

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written by Eric Fournier Eric Fournier

There is a mapping table from UCSC.
http://genome.ucsc.edu/cgi-bin/hgTables

You can download it in the table browser:
http://genome.ucsc.edu/cgi-bin/hgTables

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written by gresserT • gresserT

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