Nomenclature Issues

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Gene Names and Gene Products

Gene Name

Problem: human ortholgs that have a name that does not make sense for Dicty. We curate many human orthologs, and the basic rule is to use the human approved (HGNC) gene name in lower case. However, when the human gene name and protein product are krtcap2 and keratinocytes-associated protein 2, however, these are unsuitable for Dicty. Here are examples ( how to deal with this situation. We need to agree on common guidelines.

  • geneDDB0266488 | keratinocytes-associated protein 2 homolog

Description: similar to the mammalian KRTCAP2 (keratinocytes-associated protein 2); contains 4 putative transmembrane domains
http://www.dictybase.org/db/cgi-bin/gene_page.pl?primary_id=DDB0266488

  • geneDDB0266491 | conserved eukaryotic transmembrane protein

Description: ortholog of the H. sapiens TEX261 (testis expressed 261); contains a putative N-terminal signal sequence and 3 to 4 additional transmembrane domains
http://www.dictybase.org/db/cgi-bin/gene_page.pl?primary_id=DDB0266491

  • opa3 | optic atrophy 3-like protein

Description: ortholog of the conserved OPA3; in H. sapiens, defects in OPA3 cause type III 3-methylglutaconic aciduria (MGA type III), also known as optic atrophy plus syndrome
http://www.dictybase.org/db/cgi-bin/gene_page.pl?feature_id=198810

  • CRNKL1 | Synonym Crn | HAT repeat-containing protein | crooked neck-like protein

Description: ortholog of human CRNKL1 involved in pre-mRNA splicing; contains 11 HAT (Half A TPR) repeats
http://www.dictybase.org/db/cgi-bin/gene_page.pl?feature_id=183399

  • xpr1 | SPX domain-containing protein | EXS domain-containing protein | putative xenotropic and polytropic retrovirus receptor

Description: ortholog of XPR1, which in mammals confers susceptibility to infection with murine leukaemia viruses; also similar to yeast SYG1, a G-protein associated signal transduction protein
http://www.dictybase.org/db/cgi-bin/gene_page.pl?feature_id=201127

  • npcA | Niemann-Pick C type protein
    • Description: ortholog of NPC1, a Patch family protein, mutated in Niemann-Pick disease, a form of lipidosis characterized by the accumulation of unestrified cholesterol in the lysosomes' contains a signal peptide and 14 predicted transmembrane domains
    • I dont mind that one so much because (1) it's published as such and (2) the NPC1 name has been changed to npcA, which (to me at least) indicates that there's a difference. -Pascale

http://www.dictybase.org/db/cgi-bin/gene_page.pl?feature_id=159773

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