From Gene Names To Sequences/Orthollogs

Question

[bingyu19821270]

Hi all, I have a bunch of gene names (the names are in chaos, some from Refseq, some from CCDS...) in human genome. I can I get the sequences and chromosomal coordinates of these genes? If I finally get them, could some tell me how to fetch the orthologs from other veterbrate species (46 species as I know)? Thanks a million!

Patricia Hsu

[Pierre Lindenbaum]

duplicate of http://www.biostars.org/post/show/7568 . Close ?

[JC]

I didn't see that before, really informative

Answer 1

[Rm]

Follow this similar post https://lists.soe.ucsc.edu/pipermail/genome/2007-April/013402.html and Check the UCSC table browser to download the genes of interest (paste/upload the your list to filter).

For also look here http://hgdownload.cse.ucsc.edu/downloads.html

Answer 2

[JC]

First is better if you homogenize your gene IDs (I prefer Connect the Dots http://prion.systemsbiology.net/page/DotHome *disclaimer: is our local tool) and obtain the stable Ensembl ID.

Then you can use Biomart to query in other species, see: http://www.ensembl.info/blog/2009/01/21/how-to-get-all-the-orthologous-genes-between-two-species/

[bingyu19821270]

Thank you, JC. I tried to homogenize my gene IDs use the tool you suggested, but there are hundreds of genes that have no hits in the database. Does this mean that the database hasn't been updated for a long time or....there is some other reason?

[JC]

I don't know the last update for CTD, but I know is really common to have instable IDs in human genes. You can try UCSC GB or Ensembl to search the missing IDs.