Question: Retrieving The Sequences Of The Human Snorna, Lncrna, Etc...
3
gravatar for Pierre Lindenbaum
5.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k 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,

Pierre

rna • 2.4k views
ADD COMMENTlink modified 5.4 years ago by PoGibas4.8k • written 5.4 years ago by Pierre Lindenbaum118k
3
gravatar for JC
5.4 years ago by
JC7.7k
Mexico
JC7.7k wrote:

You can get all these from Ensembl: ftp://ftp.ensembl.org/pub/current_fasta/homo_sapiens/ncrna/

ADD COMMENTlink written 5.4 years ago by JC7.7k

thank you. I also awk-ed && found some candidates in ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/H_sapiens/RNA/rna.fa.gz

ADD REPLYlink written 5.4 years ago by Pierre Lindenbaum118k
3
gravatar for PoGibas
5.4 years ago by
PoGibas4.8k
Vilnius
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 4.9 years ago • written 5.4 years ago by PoGibas4.8k

Edit about NONCODEv4 was made.

ADD REPLYlink written 5.4 years ago by PoGibas4.8k

thank-you for that new information.

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by Pierre Lindenbaum118k
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