How do I get utr transcript coordinates?
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?
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Salvatore •
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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.
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what have you tried so far?
downloading from biomart genomic coordinates and converting in transcript with genomeTotranscript but it's not that efficient
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.
i mean the counting of the coordinates should start from the start of the transcript (5'utr start then)