• BioProject locus tag prefix 予約機能の不具合

DDBJ Annotated/Assembled Sequences

  • Home
  • Submission
    • 塩基配列の登録
    • Web 版塩基配列登録システム
    • Mass Submission System
    • 登録データの修正・更新
  • Search
    • getentry
    • ARSA
  • Flat file
    • Feature key の定義
    • Qualifier key の定義
    • Organism qualifier に記載する生物名
    • Location の記述法
    • タンパク質コード配列
    • The Genetic Codes
    • 配列の記載に用いる略号
    • 登録の見本
  • Data categories
    • Genome project のデータ登録
    • Pseudohaplotype
    • WGS
    • Finished level genomic sequences
    • メタゲノムアセンブリ
    • Single amplified genome
    • CON
    • GSS
    • HTG
    • Environmental sequence の登録
    • ENV
    • TLS
    • Transcriptome Project のデータ登録
    • TSA
    • EST
    • HTC
    • Third Party Data (TPA)
  • FAQ
  • Other
    • Patent
    • MGA
  • ホーム
  • ddbj
  • Controlled vocabulary for /pseudogene qualifier

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.