{"id":582,"date":"2017-04-14T12:28:27","date_gmt":"2017-04-14T12:28:27","guid":{"rendered":"https:\/\/bipaa.genouest.org\/is\/?page_id=582"},"modified":"2017-04-14T12:30:16","modified_gmt":"2017-04-14T12:30:16","slug":"gene-nomenclature","status":"publish","type":"page","link":"https:\/\/bipaa.genouest.org\/is\/gene-nomenclature\/","title":{"rendered":"Gene nomenclature"},"content":{"rendered":"

This page lists rules to assign gene names and symbols for different gene families. These rules are intended to be followed (at least) for all genomes hosted on BIPAA.<\/p>\n

Write to bipaa@inra.fr<\/a> if you would like to modify rules or add your own rules for a new gene family.<\/p>\n

Cuticle and chitin related proteins<\/h3>\n
Note: we found that Drosophila rules for symbols were the best, after comparison with Anopheles, Tribolium or any other well-annotated insect, see this gene for example (Cuticular protein 67Fa1<\/b>):\u00a0htt,<\/b>p:\/\/flybase.org\/reports\/FBgn0036108.html<\/a><\/div>\n
We may comment on the numbering they used (linked to cytogenetic coordinates, that we do not have in our and most genomes)<\/div>\n
<\/div>\n
\n
\n
M&M: Cuticular proteins were named and described following that adopted for\u00a0<\/span>Drososphila melanogaster<\/i>\u00a0annotation (Fly Base\u00a0version\u00a0nn).<\/span><\/span><\/div>\n
Names were given as “<\/span><\/span>Cuticular protein nnn<\/b>” (no padding zeros) as soon that they were identified by CPFP (Reference).<\/span><\/span><\/div>\n
Descriptions<\/span><\/span>\u00a0added the protein family as predicted by\u00a0CPFP\u00a0<\/b><\/span><\/span>(Reference)<\/span>, dated of March 2017.<\/span><\/div>\n
\u00a0<\/span><\/span><\/div>\n
Symbols<\/b>\u00a0were chosen as\u00a0CPRnnn<\/b>\u00a0(including padding<\/span> zeros), and following\u00a0Flybase rule<\/u><\/b>, not other insects annotations.<\/span><\/span><\/div>\n<\/div>\n<\/div>\n
\u00a0<\/span><\/span><\/div>\n
\n
Name<\/b>:<\/span><\/span><\/div>\n
\n
\n
Cuticular protein nnn (we do not include padding 0<\/u>)<\/span><\/div>\n<\/div>\n<\/div>\n
Desc<\/b>:<\/span><\/span><\/div>\n
\n
Cuticular protein nnn, Family bla-bla (Here we report exactely t<\/b>he terminology\u00a0of an automated classifier of cuticular proteins, CPFP =\u00a0CutProtFamPred<\/a>)<\/span><\/div>\n<\/div>\n
Symbol<\/b>:<\/span><\/div>\n
CPRnnn (here we do include the zeros<\/u>)<\/span><\/div>\n
<\/div>\n
Example:<\/span><\/u><\/i><\/b><\/span><\/div>\n
<\/div>\n
\n
Name<\/b>:<\/span><\/span><\/div>\n
Cuticular protein 1<\/span><\/div>\n
Desc<\/b>:<\/span><\/span><\/div>\n
Cuticular protein 1, Family\u00a0CPR_RR-1\u00a0<\/span><\/span><\/div>\n
Symbol<\/b>:<\/span><\/div>\n
CPR001<\/span><\/div>\n<\/div>\n
<\/div>\n
<\/div>\n<\/div>\n
So, when you are speaking with a Phylloxera researcher, you will cite this protein as CPR001 (symbol) or CPR 1 cuticular protein (name),<\/div>\n
and when speaking with any other people, you will label it as DviCPR001 (of course not precluding of any other isoform = splice variant, if present, which would DviCPR001-A, B, C\u2026)<\/div>\n","protected":false},"excerpt":{"rendered":"

This page lists rules to assign gene names and symbols for different gene families. These rules are intended to be followed (at least) for all genomes hosted on BIPAA. Write to bipaa@inra.fr if you would like to modify rules or add your own rules for a new gene family. Cuticle and chitin related proteins Note: … Continue reading Gene nomenclature<\/span> →<\/span><\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-582","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/bipaa.genouest.org\/is\/wp-json\/wp\/v2\/pages\/582","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/bipaa.genouest.org\/is\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/bipaa.genouest.org\/is\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/bipaa.genouest.org\/is\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/bipaa.genouest.org\/is\/wp-json\/wp\/v2\/comments?post=582"}],"version-history":[{"count":4,"href":"https:\/\/bipaa.genouest.org\/is\/wp-json\/wp\/v2\/pages\/582\/revisions"}],"predecessor-version":[{"id":586,"href":"https:\/\/bipaa.genouest.org\/is\/wp-json\/wp\/v2\/pages\/582\/revisions\/586"}],"wp:attachment":[{"href":"https:\/\/bipaa.genouest.org\/is\/wp-json\/wp\/v2\/media?parent=582"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}