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"
                	/pseudogene="unprocessed"
                	/pseudogene="unitary"
                	/pseudogene="allelic"
                	/pseudogene="unknown"

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

processed:
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.
unprocessed:
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.
unitary:
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.
allelic:
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.
unknown:
the submitter does not know the method of pseudogenisation.
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