Finding gff3 or gtf files for small non-coding RNA
1
0
Entering edit mode
4.7 years ago
y.gladbach • 0

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

gff gtf small non-coding RNA • 3.3k views
ADD COMMENT
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

@PoGibas hmmm... looks like not!

ADD REPLY
2
Entering edit mode
4.7 years ago
PoGibas 5.0k

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
ADD COMMENT

Login before adding your answer.

Traffic: 2597 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6