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Xenopus gene nomenclature

Working guidelines for naming Xenopus transgenics and mutant lines

These working nomenclature guidelines were developed in consultation with the Xenopus stock centers, following best practices used by all other model organisms. Using standard nomenclature is critical to make your research accessible to the broad scientific community and to ensure consistency and provenance.
  • Transgenic Constructs: Overview

      Tg(enhancer or promoter:ORF or gene symbol)#Lab code
      Example: Tg(cryga:GFP)2Grngr A gamma crystallin GFP construct from the Grainger Lab Example: Tg(Rno.elas:DNthra-GFP)1Ryff Construct with Rat elastase promoter driving dominant negative thyroid hormone receptor from the Ryfell Lab
    • Brevity and clarity in the transgenic construct name are encouraged.
    • Tg indicates transgene, and the entire construct name is italicized.
    • The most salient features of the transgene should be described within parentheses, no spaces.
    • List regulatory sequences to the left of colon ( : ) and coding sequences to right.
    • Use the official gene symbol for Xenopus genes (e.g., tubb2b not NBT).
    • Fluorescent proteins are capitalized or start with a capital letter (e.g., GFP, Katushka, Tomato)
    • Fluorescent protein prefixes are in lower case (e.g., eGFP, mCherry) (do not underline).
    • Hyphens ( – ) indicate fusion proteins (do not use equals sign = or double colons ::).
    • Modified functionality (e.g., CA = constitutively active, DN = dominant negative) is indicated as prefix to gene symbol, (e.g., DNthra).
    • If gene sequence(s) are from another species, precede gene symbol with 3-letter species code, and a period (eg., Dre.ins ; Hsa=human, Rno=rat, Dre=zebrafish, Mmu=mouse, Ssa=salmon, etc).
    • Multiple cassettes are separated by a comma ( , ) (e.g, Tg(tubb2b:GFP,NBTtau:GFP)1Amaya.
    • Where one regulatory sequence drives more than one coding sequence, state regulatory sequence once and separate coding sequences with a comma (e.g, Tg(CMV:GFP,RFP)2Senk).
    • Origin/source is identified with a serial number and ILAR lab code, in superscript, at end of name.
    • Do not indicate the method used for transgenesis (e.g., sperm-mediated, pTrangenesis, REMI).
    • Engineered sequences (e.g., GFP, Cre, rtTA, tetO) do not need foreign/bacterial species prefixes.
    • Do not include the size of the promoter/enhancer cis-regulatory sequence in the Tg name, rather report this in the full description of the transgene in the publication and in stock center record.
    • The full transgenic construct or line name should be included in the methods section. Once fully defined, it is acceptable to use an abbreviated name in the body of a manuscript. Example: Tg(Rno.elas.DNthra-GFP)1Ryff could be simplified to Tg(elas:DNthra-GFP).
  • Transgenic Xenopus Lines: Overview

      Species.Tg(enhancer or promoter:ORF or gene symbol)#Lab code
      Example: Xtr.Tg(cryga:GFP)3NXR A X. tropicalis Tg line carrying a gamma crystallin GFP construct, the third line made by the NXR Example: Tg(Rno.elas:DNthra-GFP)1Ryff Construct with Rat elastase promoter driving dominant negative thyroid hormone receptor from the Ryfell Lab
    • Each maintained Tg Xenopus line is given an official, stable name that is based on the Tg construct(s) used, with the following additions:
      • Species is indicated using a 3-letter code, followed by a period ( . ).
      • Xla is the abbreviation for X. laevis
        Xtr is the abbreviation for X. tropicalis
      • Each line should be fully described, including background strain, and generation number if known.
      • When a sequence of the alternate Xenopus species is used i.e., a X. laevis line that carries a construct made with X. tropicalis sequence, indicate this within the cassette/construct name using the 3-letter abbreviation, as is done for other foreign genes.
      • Example:    Xla.Tg(Xtr.shh:eGFP)2NXR
        This Tg X. laevis line carries a X. tropicalis sequence for the sonic hedgehog gene cis-regulatory elements, driving enhanced GFP. The second line with this transgene established by the NXR.
  • Mutant Xenopus Lines: Overview

      Species.gene symbol or phenotypemutation#Lab code
      Example: Xla.apctm5Vlemx The 5th mutant X. laevis line generated by TALEN targeted mutation of the adenomateous polyposis coli (apc) gene, from the Vleminckx lab.
    • Each maintained mutant Xenopus line is given an official, stable name.
    • Species is indicated using a 3-letter code, Xla or Xtr, followed by a period.
    • The line is named after the location of the mutation, whether it is known (use a gene symbol) or unknown (use a described phenotype), in italics, with no spaces.
    • The mutation type is indicated in superscript (e.g., tm=targeted mutation, ins=insertion, m=mutation, del=deletion), followed by a serial number and ILAR lab code.

Coming Soon: the extended "Working Guidelines for Xenopus Transgenic Nomenclature".

The Working Xenopus Transgenic & Mutant Nomenclature Guidelines will be available on Xenbase. These working guidelines are under constant review. Please address all comments or questions to Xenbase.

Last Updated: 11/4/2015

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