Hi I was using mirbase to get the genomic positions for each mirna. However i have noticed that for few mirna multiple genomic positions were provided eg: mmu-mir-9-5p. i am little confused about this and dont know which one to take into consideration for my downstream analysis
mmu-mir-9-5p should be found at 3 different locations on the genome (chr3, chr7, and chr13). It is because you can find the exact same miRNA sequence duplicated in the genome. But they do not necessarily arise from the same precursor.
To avoid this ambiguity, you should use the other IDs that are given in the gff file (ftp://mirbase.org/pub/mirbase/CURRENT/genomes/mmu.gff3) and that should be unique.
For your mmu-mir-9-5p, the IDs are MIMAT0000142_1, MIMAT0000142_2, and MIMAT0000142_3.
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Thank you for the useful reply. If i want to find the location of pri-mirna (in mirbase they have only given the precurssor-mirna location) where can i get it? Are there any databases available for that? my model organism is mouse. I want to see TFBS at the promoter region of the mirna
I do not know about databases of pri-mirna. Figuring out what are the potential regulators is not trivial. For your TFBSs search, I would create several data sets depending on their location. First, if you have a miRNA which is intergenic and "alone", you could look in the upstream and downstream regions considering them as the potential promoters. If your miRNA is intronic, then I guess that it is transcribed with its host gene and so you wanna focus on the promoter of the gene. Finally, you can have miRNAs that cluster together and might be transcribed as a unique transcript unit. So you would have to look at upstream and downstream regions. But this is just a potential avenue from my first thoughts that would need to be refined. It is far from an easy question since you have so many different cases.
ya we have actually divided the mirna based on intergenic and intragenic criteria also how about overlaying the methylation patterns and dnase1 chip-seq to identify the promoter regions? i am troubled with the false positives here however.
DNase I hypersensitive sites are not only to be found in promoters. And I am not familiar wiith methylation data.