Conservation between mouse and human genes: form ensembl gene id?

Question

[piyushjo]

Hi,

I want to know if there is an easy way to find if a particular gene id (ensembl) is conserved between human and mouse. For individual genes I can try blast, but I actually have 3000+ genes (lncRNA), and I want to know what is the status of conservation and what is its human counterpart gene id.

Thanks!

Answer 1

[finswimmer]

Hello,

does BioMart give you the information you need?

• As Databasechoose Ensembl Genes 93
• As Dataset choose Human Genes
• Under Attributes activate the radio button Homologues
• In the area Gene select Gene stable ID and in Homolegues the gene stable IDof the speciese of interested
• Under Filters->Gene->Input external references ID list you can paste your gene ids

fin swimmer

[piyushjo]

Not working for long noncoding RNAs. :(

[Erin Haskell | ELIXIR]

Hi!

This should work for ncRNAs, but requires you to be very specific (BioMart is not very smart!). It's really important to make sure the format of the IDs submitted matches exactly what is shown in the drop-down menu above the submission box 'Input external references ID list'. By default it is Ensembl IDs e.g. ENSG00000223784, but it also supports RefSeq or MirBase IDs and many more but you have to choose the right format.

I published a short video about how to use BioMart to find homologues between species just last week. Skip to 1min 50 to look at the gene submission part. It should show you how to do what you want! It also explains the difference in using filters and attributes to get homologues.

[piyushjo]

Hi Erin!

I tried using the mouse id ENSMUSG00000097336. This is for mouse gene Fendrr. A human lncRNA FENDRR also exists, but when I try to search for it it doesn't show it. I also see that on the ensembl page the ortholog block doesn't get activated in Comparative genomics section.

[Erin Haskell | ELIXIR]

Hello,

Sorry for the delay in response. So while I said we have data for ncRNAs, unfortunately at present this does not include lincRNAs. There are apparently some complications with patchy alignments and as a result we cannot use our homology calling pipeline with lincRNAs. We do have this data available for other non-coding RNAs, for example this snoRNA ENSG00000207047.

Sorry that we do not have this data available in Ensembl, hopefully we'll be able to run analyses on these in the future.