Gff3 Format - Human Genome

Question

[toni]

Hi all,

Does exist a place where I can easily download a GFF3 file of hg19 human annotations ?

Cheers,

T.

[Jeremy Leipzig]

Good question. UCSC has always been weirdly hostile to gbrowse: "There is no GFF3 format (yet) for complicated reasons." https://lists.soe.ucsc.edu/pipermail/genome/2009-June/019228.html

[Casbon]

Ensembl have GTF (which is GFF 2.5 or something). But I want this too.

Answer 1

[Alex]

Check this url

Data type:
gff3
Build:
hg19

[Gww]

That's a really nice link, thanks.

[toni]

Absolutely, that's a great link. Very helpful ! thank you very much.

[Casbon]

Is there a spec on what is in and what is out feature wise? There are UTRs which must be inferred by the translation, right?

Answer 2

[Travis]

It should be noted that the files linked in the top answer are Ensembl annotations and the chromosome identifiers have NOT been altered to refer to the UCSC hg19 genome.

Answer 3

[Felix]

You can also get all Ensembl data including gene annotation GTFs (which you can convert to GFF3) from here: http://www.ensembl.org/info/data/ftp/index.html.
Through their BioMart you can customize your search and download e.g. a CVS file.