Why some of the gene peptides returned by biomaRt do not have an asterisk in the end?

Question

[ebrudermanver]

I am using biomaRt tool to get the peptides for BRCA1 using below code:

library(biomaRt)
mart = useMart('ensembl', dataset='hsapiens_gene_ensembl')
seq = getSequence(id='BRCA1', type='hgnc_symbol', seqType='peptide', mart = mart)

27 different sequences are returned, and 12 of those have an asterisk (*) in the end, while 15 do not. What does that mean? I know that asterisk is used to indicate stop codon. So, does that mean the peptides without an asterisk do not have a stop codon? Is that possible at all?

MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKVLLCCPSWSTVVRS* is an example sequence with an asterisk in the end. MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKSLQESTRFSQLVEEL‌​LKIICAFQLDTGLEYANSYN‌​FAKKENNSPEHLKDEVSI is an example without an asterisk.

[Devon Ryan]

Hello ebrudermanver!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/2300/why-some-of-the-gene-peptides-returned-by-biomart-do-not-have-an-asterisk-in-the

This is typically not recommended as it runs the risk of annoying people in both communities.

Answer 1

[Emily]

The ones without an asterisk don't have a stop codon because they are 3' incomplete: http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000012048;r=17:43044295-43170245