Controlled vocabulary for /pseudogene qualifier

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.