I'm in interested in the start and stop locations for the coding
DNA sequence.  For example, for the reference squence for
AKT1, NM_001014431, the cds location in NCBI is reported as 341..1783
(see also http://www.ncbi.nlm.nih.gov/nuccore/62241012).

I'm now working using biomaRt and using the Ensembl accession
number ENST00000349310 as follows:

library('biomaRt')
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
getBM(attributes=c('cds_start'),
filters='ensembl_transcript_id', values='ENST00000349310', mart=ensembl)
getBM(attributes=c('transcript_start'), filters='ensembl_transcript_id',
values='ENST00000349310', mart=ensembl)

However, these give me results with respect to the genomic coordinates.  Is
there a way to give the start of the cds with respect to the transcript?

Thanks,
Andrew

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