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.