Finding gff3 or gtf files for small non-coding RNA

Question

[y.gladbach]

Hi everyone, Does anyone know where to get gtf or gff3 files for these small RNAs: piRNA, intron-derived miRNA, endogenuous siRNA, linc-RNA, lnc-RNA, sno-RNA, snRNA.

I am especially interested in intron-derived miRNA and endogenuous siRNA.

I know RNACentral, but it only has fasta files. I checked Ensembl as well on the ftp server, but couldn't find them, as well as on GENCODE, lncipedia and MiTranscriptome.

A direct link would be much appriciated. Thanks in advance everyone

[GenoMax]

This has been addressed in: GTF/GFF for non-coding RNA

[Santosh Anand]

Have you looked at the gencode Gene/Transcript Biotypes https://www.gencodegenes.org/gencode_biotypes.html

[PoGibas]

Do they have biotypes intron-derived miRNA or endogenous siRNA?

[Santosh Anand]

@PoGibas hmmm... looks like not!

Answer 1

[PoGibas]

What is wrong with downloading gene annotation from GENCODE and creating intron-derived miRNA by yourself?

1. Download GENCODE GTF
2. dataset A <- Select intron coordinates
3. dataset B <- Select miRNA coordinates
4. intron-derived miRNA <- Overlap datasetA and datasetB