Identify lncRNA in list of Ensembl ID's

Question

[Laura]

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

Answer 1

[Prasad]

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

[Emily]

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

[Laura]

That worked beautifully. Thank you!

Answer 2

[EagleEye]

Also try UCSC table browser

A: I need to download a list of all human genes with their respective Esemble gene

https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=501155603_yl6KfgoSdqSze5XAqTkDy4Gp4pMA&hgta_doSchemaDb=hg19&hgta_doSchemaTable=ensemblSource

[Laura]

Thanks! Managed, saved me lots and lots of time

Answer 3

[poisonAlien]

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

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