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Finding gff3 or gtf files for small non-coding RNA
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3.1 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

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

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

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

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@PoGibas hmmm... looks like not!

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13 months ago
PoGibas 4.8k
Vilnius

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
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