How to know which is coding gene in GTF File

Question

[lxwgcool]

Hey guys,

I plan to collect all of Coding-Gene and Non-Coding Gene from annotation file (GTF file).

I think those two categories could be addressed by "gene_type". However, i do not really sure which "gene_type" corresponding to coding-gene and which is related to non-coding gene.

I noticed there is a link below shows which "gene_type" is related to non-coding gene:

http://useast.ensembl.org/info/genome/genebuild/ncrna.html

However, i do not think it is the full set of non-coding gene, for example, "sense_intronic" should belongs to non-coding gene, however, it does not be included by this link.

Moreover, i cannot find the link which could show me the full list of "gene_type" of the coding gene.

Could anyone help me to address this problem?

So appreciate for your help

Thanks

Answer 1

[Jean-Karim Heriche]

Since you're using Ensembl, have a look at the GENCODE/Ensembl list of gene/transcript biotypes.

[lxwgcool]

Thanks for reply. Actually i did checked this link before. For my understanding only "protein_coding" related to coding gene, is it correct? thanks so much

[Jean-Karim Heriche]

Yes and no, it depends on what you're after. Genes labelled as protein-coding are those that are usually of interest but they are not the only ones producing polypeptides, for example some pseudogenes can produce proteins, the immunoglobulin genes are protein-coding genes. Pseudogenes generally have inactive products but immunoglobulin genes produce functional peptides.