Question: Retrieving The Sequences Of The Human Snorna, Lncrna, Etc...
gravatar for Pierre Lindenbaum
6.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

Hi all,

do you know a way to download the fasta sequences of all the non-'classical' Human RNA (!= rRNA, mRNA, rRNA) ?

Thank you,


rna • 2.9k views
ADD COMMENTlink modified 6.8 years ago by PoGibas4.8k • written 6.8 years ago by Pierre Lindenbaum129k
gravatar for JC
6.8 years ago by
JC11k wrote:

You can get all these from Ensembl:

ADD COMMENTlink written 6.8 years ago by JC11k

thank you. I also awk-ed && found some candidates in

ADD REPLYlink written 6.8 years ago by Pierre Lindenbaum129k
gravatar for PoGibas
6.8 years ago by
PoGibas4.8k wrote:

Pierre, there are several lncRNA annotations for human (of course there is overlap between them).

Annotations that have exon/intron coordinates:

  1. Derrien et al., 2012 - The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression;
  2. Cabili et al., 2011 - Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses;
  3. Kelley D., Rinn J., 2012 - Transposable elements reveal a stem cell specific class of long noncoding;
  4. NONCODEv4 (See edit 13.11.28).
  5. Necsulea et al., 2014 - The evolution of lncRNA repertoires and expression patterns in tetrapods;

Annotations that have only locus coordinates:

  1. Sigova et al., 2013 - Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells;
  2. Orom et al., 2010 - Long noncoding RNAs with enhancer-like function in human cells (lots of overlap with Gencode);
  3. Hangauer et al., 2013 - Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs;
  4. Laurent et al., 2013 - VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer.

I would suggest using Gencode annotation (Cabili annotation is "popular" too).

There are ~19k non-overlapping lncRNA genes that have exon/intron coordinates.

Also there is:

  • LNCipedia - a comprehensive compendium of long non-coding RNAs;

Edit 13.11.28 NONCODEv4 NONCODEv4: exploring the world of long non-coding RNA genes, Nucleic Acids Research, 2013 Nov., (Chinese Academy of Sciences, Beijing).

"210831 lncRNA from eukaryotes, eubacteria, archebacteria, and viral and viroids"

"Human lncRNA: 56018 genes & 95135 transcripts"

"Mouse lncRNA: 46475 genes & 67628 transcripts"

"Expression profile of lncRNAs for human and mouse, as well as predict functions of these lncRNA genes"

ADD COMMENTlink modified 7 months ago by RamRS28k • written 6.8 years ago by PoGibas4.8k

Edit about NONCODEv4 was made.

ADD REPLYlink written 6.7 years ago by PoGibas4.8k

thank-you for that new information.

ADD REPLYlink modified 6.7 years ago • written 6.7 years ago by Pierre Lindenbaum129k
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