Where To Download Hg19 Gene Annotation, Transcript Annotation And Cdna Fasta Files?

Question

[Shaojiang Cai]

Hi, I am hanging around to look for hg19 transcript annotations together with cDNA fasta files.

From UCSC, I can download the gene annotation, but without transcripts. I know that I can infer from the genome once I get the transcript annotation, but is there any place where I can download the transcript annotation and cDNA Fasta files?

I also would like to know the correspondence between the genes and transcripts. Say, transcripts A, B and C are from gene G.

Thanks

[jaqx008]

This is old but I found the GTF https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/genes/

[Ram]

There was no need to add this as an answer. The question clearly says they can already do this.

From UCSC, I can download the gene annotation, but without transcripts.

Answer 1

[Nicolas Rosewick]

Everything is available here: http://www.ensembl.org/info/data/ftp/index.html

Answer 2

[aebmad]

For the transcript annotation file, I use the genePredToGtf script from UCSC which allows you to create a GTF annotation file. You can find a detailed explanation of how to download and use the script here: http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format

Alex

[pjmaguire3]

Just to clarify in case anyone in the future uses genePredToGtf, in the 2nd step the section "region should be set to "position" instead of genome" should only be followed for the example and not for the actual GTF derivation. Leave it as "genome" when actually deriving a GTF file in this manner.

Answer 3

[sgujja]

Hi,

I came across your post while looking to download hg19 Transcript Annotation file with correspondence between transcripts and gene.

Could you please let me know where you were able to download it from.

Thanks
Sharvari