Hi there,
I'd like to know why a microRNA could correspond to multiple ensembl gene IDs? For examples, we can see "hsa-mir-1302-2" corresponds to 4 ensembl gene IDs:
ensembl_gene_id gene_biotype ensembl_transcript_id mirbase_id
ENSG00000284332 miRNA ENST00000607096 hsa-mir-1302-2
ENSG00000284557 miRNA ENST00000408734 hsa-mir-1302-2
ENSG00000283921 miRNA ENST00000408365 hsa-mir-1302-2
ENSG00000283801 miRNA ENST00000408051 hsa-mir-1302-2
The GTF file is downloaded from: ftp://ftp.ensembl.org/pub/release-90/gtf/homo_sapiens/
Could any one please tell me why? I want to get the sequence length for each miRNA and it seems that I should not add up the length of all the transcripts together.
2 answers
There are all paralogues:
Really thanks for you help. I am wondering if there is any attribute that can tell the miRNA I required with those paralogs apart when using the getBM() function from the R package biomaRt? To be more precise, I found that for each of the four miRNAs: hsa-mir-1302-2, hsa-mir-1302-9, hsa-mir-1302-10, hsa-mir-1302-11, the getBM() function will return the same information including all the four miRNAs. That seems to be quite tedious. The R code is as follows:
mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
miRNA_res <- getBM(attributes=c("ensembl_gene_id", "gene_biotype", "ensembl_transcript_id", "mirbase_id"), mart=mart)
The following four commands will get the same results :
miRNA_res[miRNA_res$mirbase_id=="hsa-mir-1302-2",]
miRNA_res[miRNA_res$mirbase_id=="hsa-mir-1302-9",]
miRNA_res[miRNA_res$mirbase_id=="hsa-mir-1302-10",]
miRNA_res[miRNA_res$mirbase_id=="hsa-mir-1302-11",]
Any hint would be really appreciated.
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