There are certain miRNA originated from the intron of genes.
I could not found such tabulated form in which genes and respective miRNA are given
Can anyone provide the same.
First question: which species are we talking about? I assume you could find such files for human or mouse as a supplementary information for some papers, not sure for other species. To make sure that the annotations are up to date, I would recommend to compile the tab file yourself in 3 relatively easy steps.
- download miRNA gff file for the species you are interested in from miRBase (http://mirbase.org/ftp.shtml)
- download gene annotation for your species (the same genome version as used in miRBase) from ensembl (http://www.ensembl.org/biomart/martview/ab0fc52b7dde5284de84d8eee7469039)
-intersect two files using bedtools (use -s and -wa, depending what exactly you are interested in, manual for the command can be found here: http://bedtools.readthedocs.org/en/latest/content/tools/intersect.html).
Good luck!
THANKS Kataryzna,
We are currently studying mouse model for B lymphocyte differentiation,
I will follow as above mentioned.
If you use R to do your analysis I hope that the following can be helpful for you:
- You can use the two following libraries:
library(biomaRt)
library(GenomicRanges)
- You can select the last assembly version of Ensembl! of the organism of your interest as:
ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
- You can load the mirna from miRBase in a R object.
In this example you are getting all mirna annotated in mirbase on the chromosome 13 of the hsapiens_gene_ensembl
miRNA
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