Download the promoter, enchancer, TSS , 3 prime, exon and intron positions of all hg38 genes
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8 months ago
a.james ▴ 220

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

RNA-Seq DNA-seq • 407 views
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As far as I know there's no single file with this information. However, you can get the information using the Ensembl perl API.

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8 months ago
Shalu Jhanwar ▴ 490

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/.

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