Gene annotation from genomic features

Question

[chiefcat]

Hi guys,

I've a got basic question regarding gene annotation.

What kind of genomic features can be assigned to genes (other than TSS, TTS, exon, intron, enhancer)? Thanks!

Kylie

Answer 1

[Alex Reynolds]

The GFF3 site offers a specification document with 1916 feature type categories and their descriptions/definitions.

For example:

[Term]
id: SO:0000188
name: intron
def: "A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
xref: http://en.wikipedia.org/wiki/Intron "wiki"
is_a: SO:0000835 ! primary_transcript_region

Or:

[Term]
id: SO:0000198
name: noncoding_exon
def: "An exon that does not contain any codons." [SO:ke]
subset: SOFA
synonym: "noncoding exon" EXACT []
is_a: SO:0000147 ! exon

Etc.

I suppose the real answer is that it depends on what format of gene annotation data you're working with. Anything goes, so long as people agree to use your standard.

Answer 2

[Jean-Karim Heriche]

From the top my head: promoters, enhancers, chromatin states, DNA modifications (e.g. methylation), variations (SNPs, CNVs), gene type (e.g. coding/non-coding ...). There's probably more. Just look at annotated genomes in Ensembl to get ideas.