Nomenclature issues

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Gene Names and Gene Products

Gene Name

See the full Nomenclature Guidelines here:

Below are examples where human ortholgs 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 of how to deal with this situation. We are also in constant discussion with SwissProt who in turn are in contact with HGNC to resolve such naming issues over the longterm.

  • DDB_G0286759 | keratinocytes-associated protein 2 homolog

Description: similar to the mammalian KRTCAP2 (keratinocytes-associated protein 2); contains 4 putative transmembrane domains

  • DDB_G0291374 | 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

  • DDB_G0284959 | optic atrophy 3-like family 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

  • DDB_G0278819 | HAT repeat-containing protein

Description: ortholog of human CRNKL1 (crooked neck-like 1) involved in pre-mRNA splicing; contains 11 HAT (Half A TPR) repeats

  • 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
Comment: This is OK because (1) it does not refer to a 'body part', (2) it's published as such and (3) the NPC1 name has been changed to npcA, which (to me at least) indicates that there's a difference.

  • 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

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