How do I get utr transcript coordinates?

Question

[Salvatore]

Do you know any way to retrieve 3'UTR transcript coordinate (0 is the start of the 5'UTR) without considering introns but just the mature mRNA?

[jv]

what have you tried so far?

[Salvatore]

downloading from biomart genomic coordinates and converting in transcript with genomeTotranscript but it's not that efficient

[rpolicastro]

What do you mean exactly by "0 is the start of the 5'UTR". The 3` UTR is from the end of the ORF to the end of the last exon, so the wording is a little confusing at the moment.

[Salvatore]

i mean the counting of the coordinates should start from the start of the transcript (5'utr start then)

Answer 1

[Darked89]

There may be different approaches depending on the existing gene/transcript annotation. For example one can parse Genbank file containing given sequence: mouse p53 gene :

CDS             102..1274

The more generic approach is to search for the longest ORF in a full transcript sequence using tools form EMBOSS like getorf Some scripting may be required if you want to process non-trivial number of transcripts.