{"id":56,"date":"2022-06-20T14:25:23","date_gmt":"2022-06-20T13:25:23","guid":{"rendered":"https:\/\/insdc.org\/?page_id=56"},"modified":"2022-07-21T14:50:25","modified_gmt":"2022-07-21T13:50:25","slug":"pseudogene-qualifier-vocabulary","status":"publish","type":"page","link":"https:\/\/www.insdc.org\/submitting-standards\/pseudogene-qualifier-vocabulary\/","title":{"rendered":"Controlled vocabulary for \/pseudogene qualifier"},"content":{"rendered":"<p>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.<\/p>\n<p>The text below outlines the format and the present list of allowed controlled vocabulary.<\/p>\n<p><span class=\"Apple-style-span\" style=\"white-space: pre;\"><strong>Qualifier<\/strong>: \/pseudogene=<\/span><\/p>\n<p><span class=\"Apple-style-span\" style=\"white-space: pre;\"><strong>Definition<\/strong>: indicates that this feature is a pseudogene of the <\/span><span class=\"Apple-style-span\" style=\"white-space: pre;\">element named by the feature key<\/span><\/p>\n<p><span class=\"Apple-style-span\" style=\"white-space: pre;\"><strong>Value format<\/strong>: “TYPE”<\/span><\/p>\n<p><span class=\"Apple-style-span\" style=\"white-space: pre;\">where TYPE is one of the following: <\/span><span class=\"Apple-style-span\" style=\"white-space: pre;\">processed, unprocessed, unitary, allelic, unknown<\/span><\/p>\n<p><span class=\"Apple-style-span\" style=\"white-space: pre;\"><strong>Examples<\/strong>:<\/span><\/p>\n<p><span class=\"Apple-style-span\" style=\"white-space: pre;\">\/pseudogene=”processed”<\/span><\/p>\n<p><span class=\"Apple-style-span\" style=\"white-space: pre;\">\/pseudogene=”unprocessed”<\/span><\/p>\n<p><span class=\"Apple-style-span\" style=\"white-space: pre;\">\/pseudogene=”unitary”<\/span><\/p>\n<p><span class=\"Apple-style-span\" style=\"white-space: pre;\">\/pseudogene=”allelic”<\/span><\/p>\n<p><span class=\"Apple-style-span\" style=\"white-space: pre;\">\/pseudogene=”unknown”<\/span><\/p>\n<p><strong>Comment<\/strong>: TYPE is a term taken from the INSDC controlled vocabulary for pseudogenes:<\/p>\n<p><strong>processed<\/strong>: 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.<\/p>\n<p><strong>unprocessed<\/strong>: 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.<\/p>\n<p><strong>unitary<\/strong>: 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.<\/p>\n<p><strong>allelic<\/strong>: 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.<\/p>\n<p><strong>unknown<\/strong>: the submitter does not know the method of pseudogenisation.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>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…<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":233,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"acf":[],"_links":{"self":[{"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/pages\/56"}],"collection":[{"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/comments?post=56"}],"version-history":[{"count":1,"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/pages\/56\/revisions"}],"predecessor-version":[{"id":57,"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/pages\/56\/revisions\/57"}],"up":[{"embeddable":true,"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/pages\/233"}],"wp:attachment":[{"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/media?parent=56"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}