I'm trying to translate TF name from transfac to Ensembl gene names, and I get terms such as: bmal2-xbb1, lrh1-xbb1 etc.
Hi Lilach,
I contacted Biobase, the company that curates the TRANSFAC database about the xbb1 suffix. Here is their response:
The suffix xbb1, xbb2, xbb3, etc. denotes an isoform (splice variants etc.), for which the protein sequence was given in a publication, but for which the protein sequence did not fit to an isoform in Uniprot.
In the given case, the protein sequence for this mouse Sox2 (variant) goes back to EMBO J. 1995 July 17; 14(14): 3510–3519.
The sequence given in this publication is three amino acids shorter than the one given in UniProt.
Therefore the entry was labeled as a potentially different isoform.
Although, we may need to re-check if a separate entry is still justified based on latest knowledge.
Best regards,
Volker
Thanks Biobase and Volker for the quick response.
Jason
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