How to detect which Ensembl transcript ID corresponds to tRNAs

Question

[nkabo]

Dear all,

I have a list of Ensembl transcript IDs (ENST00000492842, ENST00000495576, ENST00000477740, ENST00000610542 for example). These IDs are obtained after transcript quantification and annotation of RNA-Seq raw data. I would like to find which of these IDs corresponds to tRNAs.

Is it possible to give this list as an input (it includes more than 163000 transcript IDs) and obtain an output, only including Ensembl transcript IDs corresponding tRNAs? Or is there another way for such filtering?

Thanks in advance,

[GenoMax]

Mitochondrially encoded tRNA entries.

chrM    ENSEMBL transcript      577     647     .       +       .       gene_id "ENSG00000210049.1"; transcript_id "ENST00000387314.1"; gene_type "Mt_tRNA"; gene_name "MT-TF"; transcript_type "Mt_tRNA"; transcript_name "MT-TF-201"; level 3; transcript_support_level "NA"; hgnc_id "HGNC:7481"; tag "basic";

[Emily]

There are the MT tRNAs in the gene files, but there are no chromosome-encoded tRNAs with gene IDs

[nkabo]

Thank you for your reply. Is this output retrieved via BioMaRt?

[GenoMax]

It is from GENCODE GTF file for GRCh38 annotation. A simple grep "tRNA" gtf_file will find these entries.

[nkabo]

Thank you very much, it helped a lot

Answer 1

[Emily]

tRNAs don't have Ensembl gene IDs associated with them. They're annotated as part of the repeat-masking process instead of in the gene annotation pipeline.