misc_RNA in Ensembl

Question

[Martombo]

Do you know which are the criteria used to classify a gene as misc_RNA by Ensembl? I couldn't find an answer on the Ensembl page describing non-coding RNA.

A few example of such genes retrieved from BioMart:

• http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000207157;r=13:23726725-23726825;t=ENST00000384428
• http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000242037;r=13:95351479-95351756;t=ENST00000470538
• http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000223298;r=13:95963084-95963209;t=ENST00000411366

These examples show that they are pseudogenes. why aren't they associated to the "pseudogene" gene type? what makes them misc_RNA?

thank you!

Answer 1

[Emily]

misc_RNA is defined as any ncRNA that we can't categorise as anything else.

If you look at your genes of interest here, the word 'pseudogene' is found in the gene name ('RNA, Ro-associated Y3 pseudogene 4 [Source:HGNC Symbol;Acc:42488]'), which we lift directly from HGNC. However, these genes do not fit our definition of pseudogenes so are not classified as such. We can't change the official HGNC name, but we will only annotate genes as what we believe them to be.

[cdsouthan]

There is some cryptic circularity going on here.

For example I can't provenance RNY3P4 as anything. It appears to be a RefSeq prediction of something http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=100873808 and points back to HGNC - but I wasn't aware they did predictions of psedogenes (they might annotate) so where did this come from?

But ENSG00000207157.1 says "No overlapping RefSeq" clips the RefSeq down from 301 to a 101 exon? on the basis of an Rfam model?

But nothing from Havana/Vega in this location?

[Emily]

We got it from an RFam record. And no, no manual annotation on these guys.

[cdsouthan]

We're into serious "what is a gene" territory here... I might pose it as a general question. It's getting crucial as more equivocal automated and manual annotations keep stacking up.

[AlicePsyche]

Thanks for your reply! What is the difference between "type" and "locus_tag". I am looking for all rRNA sequences from GenBank file. I am a little confused why there are many 5S_rRNA are labeled as "misc_RNA"? Such as:

gene            493631..493747
                     /gene=ENSDARG00000085618
                     /locus_tag="5S_rRNA"
                     /note="5S ribosomal RNA [Source:RFAM;Acc:RF00001]"
     misc_RNA        493631..493747
                     /gene="ENSDARG00000085618"
                     /db_xref="RFAM_trans_name:5S_rRNA.1275-201"
                     /note="rRNA"
                     /note="transcript_id=ENSDART00000121018"

Thanks in advance.