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Identify lncRNA in list of Ensembl ID's

Hi all,

I have a list of ~17000 transcripts in the form of Ensembl IDs (although this can be converted to any other form of ID needed), and I am looking to figure out which of the ~17000 are coding and which are non-coding RNAs.

Ensembl itself obviously tells you if it is coding or non-coding when you search the ensembl ID, but is it not feasible to do this by hand for so many transcripts. I have also found lncRNA databases but again they seem to be searched one by one.

Does anyone know how can I run the whole list against an existing database to give me a non-coding or coding for each of the transcripts?

Any help much appreciated!

Thanks! Laura

genome gene ensembl
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updated by EagleEye EagleEye • written by Laura • Laura

3 answers

this you could do it using Ensemble biomart. You can upload all the transcript id in the filter option and using Attribute you can select transcript type or gene type at what level you want to see.

I guess this solves the purpose

• 1 views • link
written by Prasad Prasad

There's a help video to get you started with BioMart.

• 1 views • link
written by Emily Emily

That worked beautifully. Thank you!

• 1 views • link
written by Laura • Laura

Thanks! Managed, saved me lots and lots of time

• 1 views • link
written by Laura • Laura

You can just download ensemble gtf and map transcript ids to their biotype.

Or upload your list to biomart and get all associated attributes.

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written by poisonAlien poisonAlien

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