Last updated:2013.8.28.

Controlled vocabulary for /pseudogene qualifier

The original site; Controlled vocabulary for /pseudogene qualifier 2012.08.15 version

A new qualifier was introduced in version 10.1 (May 2012) of the Feature table definitions: /pseudogene. This qualifier is used to annotate pseudogenes only.

The text below outlines the format and the present list of allowed controlled vocabulary.

Qualifier:       	/pseudogene=
Definition:      	indicates that this feature is a pseudogene of the 
                 	element named by the feature key
Value format:   	"TYPE"		
                 	where TYPE is one of the following:
                 	processed, unprocessed, unitary, allelic, unknown
Examples:        	/pseudogene="processed"

Comment: TYPE is a term taken from the INSDC controlled vocabulary for pseudogenes:

the pseudogene has arisen by reverse transcription of a mRNA into cDNA, followed by reintegration into the genome. Therefore, it has lost any intron/exon structure, and it might have a pseudo-polyA-tail.
the pseudogene has arisen from a copy of the parent gene by duplication followed by accumulation of random mutation. The changes, compared to their functional homolog, include insertions, deletions, premature stop codons, frameshifts and a higher proportion of non-synonymous versus synonymous substitutions.
the pseudogene has no parent. It is the original gene, which is functional in some species but disrupted in some way (indels, mutation, recombination) in another species or strain.
a (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes.
the submitter does not know the method of pseudogenisation.