Download the promoter, enchancer, TSS , 3 prime, exon and intron positions of all hg38 genes

Question

[a.james]

Hi All,

I would like to download the promoter enhancer, exon, intron, 3'prime, 5'prime positions of all genes from the human genome hg38 version.

I have seen a couple of information in the ENSEMBLE and FANTOM website, however, the above-mentioned information is not able to find out. For example, here there is peak and representative TSS are mentioned but the other information including an enhancer, intron-exon, etc are not. https://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_latest/extra/CAGE_peaks/breakdown/

I would like to know if it is available as a comprehensive file to download from somewhere. Thanks

[Jean-Karim Heriche]

As far as I know there's no single file with this information. However, you can get the information using the Ensembl perl API.

Answer 1

[Shalu Jhanwar]

Have a look at gencode_regions https://github.com/saketkc/gencode_regions. It has a utility to extract 3'UTR, 5'UTR, CDS, Promoter, and Genes from GTF files.

For enhancers, it depends on which cell-type/tissue you're looking for as the position of enhancers may differ depending on the cell-type/tissue. The site http://enhancer.binf.ku.dk/presets/ contains a repository of enhancers for a wide range of human tissues/cell-types/tissues, including ubiquitous enhancers. Details of the enhancers identified are available on https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5215096/.

[a.james]

Thank you for the detailed reply. I will take a look :)

[Lhl]

For promoters and enhancers, I think Shalu provide a good source. For the rest of the features, I recommend using https://github.com/RacconC/gtftools to extract the latest annotation of certain features from gencode gtf file.