To predict/find human homolog in the yeast (Sac-Cere)

Question

[mycrspr]

I want to predict/find human homolog of the following protein in the yeast saccharomyces cerevisiae (Sac-cere). Please suggest how can I go for it, tools or steps I should follow? There are different isoforms which one should I use?

Thanks

http://www.uniprot.org/uniprot/Q9BQL6

[ahmedakhokhar]

Either this link can help you:

http://www.ncbi.nlm.nih.gov/homologene/?term=FERMT1%5Byeast%5D

Or follow the old thread with the same topic:

Homolog Finding

[GenoMax]

The gene linked is involved in keratinocyte migration so I am not sure how that is immediately relevant in yeast. Not every gene has to have a homolog in distant organisms.

To complicate things further it appears that URP1 is an alias shared by Human FERMT1 gene and RPL21A (ribosomal 60S subunit protein gene in yeast).

[Denise CS]

Yes, that's correct. Not every gene has to have a homolog in distantly related organisms or otherwise. Besides "absence of evidence os not evidence of absence". All of this needs to be taken in consideration. At any rate, as it stands, no ortholog of human Q9BQL6 has been found in yeast, as far as annotation goes.

Answer 1

[Denise CS]

It seems the 'yeast' term was ignored in the NCBI link above. So the results do not take that organism into account. As far as I can see, there is no yeast homolog to Q9BQL6 in NCBI, Ensembl or UCSC. Although UniProt lists four sequences (alternative isoforms due to common alternatively splicing of most human multi-exon genes), you may want to focus on the longest one. This is the approach used by Ensembl when identifying homologues in human and any other species (Protein tree and orthologies). This longest isoform can be named by some as the canonical sequence although this term should be used with great care. If you have a list of genes (or proteins) in human and want to find out their orthologues in yeast, try BioMart as explained by one of the links found the thread given above.