Rfam Family Types

Question

[int11ap1]

Good afternoon from Barcelona,

I would like to ask a little question that I cannot find on the Internet. As fas as i know, there are these Rfam family types:

Cis-reg;

Cis-reg; frameshift_element;

Cis-reg; IRES;

Cis-reg; leader;

Cis-reg; riboswitch;

Cis-reg; thermoregulator;

Gene;

Gene; antisense;

Gene; antitoxin;

Gene; CRISPR;

Gene; lncRNA;

Gene; miRNA;

Gene; ribozyme;

Gene; rRNA;

Gene; snRNA;

Gene; snRNA; snoRNA; CD-box;

Gene; snRNA; snoRNA; HACA-box;

Gene; snRNA; snoRNA; scaRNA;

Gene; snRNA; splicing;

Gene; sRNA;

Gene; tRNA;

Intron;

Can somebody explain what is the meaning of one RNA sequence being classified as "Gene", and only "Gene"?

What about the Intron-type?

The Cis-reg RNAs could be classified as well as lncRNA, couldn't they?

[Hamish]

Probably worth contacting the Rfam folks for this, see http://rfam.sanger.ac.uk/help#tabview=tab12

Answer 1

[Neilfws]

1. I would guess that the terms following the semi-colon are sub-types of the type "Gene". So those entries classed only as "Gene" are not known to belong to any of the sub-types.

As Hamish said, Rfam help is the place for specific queries.

1. The Intron type includes RNAs such as Group I catalytic intron (ribozymes). See the Wikipedia entry.

2. Are all Cis-reg RNAs also lncRNAs? If not, then no.