Why are some of the gene peptides returned by biomaRt missing an asterisk in the end?

Question

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I am getting peptides using biomaRt library in R for the gene 'BRCA1'. 27 different aminoacid 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? Are all of those valid peptides or not?

Below is the R code I used:

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

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

Answer 1

If it's 3' incomplete that means the evidence used to create it was a fragment. Here's the evidence used to construct BRCA1-214 ENST00000477152.5, a 3' incomplete.

You can see that there's a full length cDNA from EMBL, AK307553.1, which was used to create this model.

The sequence was mapped against the genome sequence to create the transcript model. When searching for the translation, it was found that the open reading frame was started, but there was no stop codon. This suggests that the cDNA AK307553.1 is actually a fragment, that the mRNA was broken or cleaved before it was reverse-transcribed sequenced. We display it in Ensembl in the hope that this will lead someone to identify the full length transcript that it represents.

Many people choose not to work with these incomplete transcripts. You can do this by filtering by Gencode Basic in biomaRt.

Answer 2

If you look at the original data at Ensembl you'll notice that most of these are labeled "CDS 3' incomplete" and have a TSL (transcript support level) of 1, which is as low as it goes. It seems likely that that is simply an incomplete annotation. I'm not surprised that there are a bunch of these for BRCA1, since there was a long time when there were a LOT of legal issues surrounding working on it.