I'm having troubles with the IDs in miRbase-context file. In particular, I have a list of around 300 miRNAs with a miRbase ID (i.e. hsa-mir-100). All I want to know is their genomic location: 3'UTR, Intron, Exon or 5'UTR. To do so, I downloaded from the FTP site of miRbase the file miRNA_context. This is how it looks like:
82087 ENSACAT00000008610 + exon 11 HGNC_trans_name 82088 ENSACAT00000013598 + 3UTR 11 miRBase_trans_name 82089 ENSACAT00000003614 + exon 11 HGNC_trans_name 82092 ENSACAT00000019163 + exon 1 miRBase_trans_name 82094 ENSACAT00000020806 + exon 1 miRBase_trans_name 82096 ENSACAT00000004565 + intron 58 HGNC_trans_name
And here a brief explanation of the file from miRbase FAQs: "... Once open, you will see that there are numerous columns corresponding to (left to right): miRNA ID, transcript ID, + or - (according whether the sequence lies on the sense or antisense strand, respectively, of a stem-loop structure), where the miRNA originates (i.e. intron, exon, 5' UTR or 3'UTR), the number of the exon or intron from which the miRNA originates, the transcript source, and the transcript name."
Next, I converted my "miRbase ID" in "Transcript stable ID" using Biomart. But then, when I try to intersect these two lists using the transcript IDs, I only find 3 in common.
Does anyone have an idea which could be the problem?
Thank you in advance