Clock Gene in Animal Update: 2009.5.8 Site Map

ClockBase: Notes


About "Clock Gene"

The “clock gene” in animal was not clearly defined.
Generally, the "clock genes" are essential components of a circadian rhythm of behavior.

In the table, we listed homologous genes for known "clock gene" with following features.
1.  Circadian rhythm of behavior was abolished by loss-of-function mutation of the gene in animal.
ex.  per (period), tim (timeless) (fly)
If rhythmic behavior is spoiled in mutant animal, but circadian rhythm itself was intact (ex. rhythmic expression of clock genes and clock controlled genes), the gene cannot be regarded as clock gene.
The gene was defined as a "output gene". Output gene was not listed in the table.
ex. Fmr1, lark (fly)
2. Period length (tau) of behavioral rhythm is changed by mutation of the gene in animal.
ex. CSNK1E, double-time (hamster, mouse, fly)
3. Phase shift of circadian rhythm by light pulse was spoiled by mutation of the gene in animal, the gene was regarded as a "input gene". We listed cell-autonomous clocks controlling genes in the table.
ex. cry (cryptochrome)jet (fly)
Mouse Per1, Bhlhe40(Dec1) and Bhlhe41(Dec2) can be classified to input gene.

Note, rhythmic expression is one feature of most of "clock gene", but is not essential nor sufficient. There are hundreds of rhythmic transcribed "clock-controlled genes (cgg)".
Sirt1 was included to the table temporarily. Circadian function of SIRT1was shown in culture cells, but not in animal mutant.

Gene name

Gene name of human, mouse, frog and fly was shown according guidelines for gene nomenclature.
Gene name was italicized except Xenopus according guideline: "Gene names should be in lower case and not in italics" (Suggested Xenopus Gene Name Guidelines).
Human gene name was shown in upper case according guideline: ex., CLOCK.
Mouse gene name was capitalized according guideline: ex., Clock.
Fly gene was shown in a full name or in a common name, if it was simple: ex., clk = clock
Branchiostoma, Anopheles, Nematostella and Trichoplax. Gene Symbols were abbreviated: ex., BRAFLDRAFT_63636 = BF_63636.
GB number was used for Apis mellifera instead of symbol, if the gene was not named.
Gene name was painted as follows.
Red: clock function was reported in animal model. Mutation was found in human sleep disorder.
Yellow: clock function was reported in cultured cell.
Non clock family genes were listed in table for reference.

Protein (deduced gene product) name in BLINK, Cladogram and Phylogram

Animal selection

Animal species was selected as follows,
For Chordata, one species was selected from each taxonomic Class.
For Class Insecta, well characterized three species were listed.


Genes belong to same Homologene was shown in arbitrary color.
If unknown gene has certain similarity to known gene, Homologene field was paint with same color to the known gene.
Homolog in fungi and plant were listed, if it was listed in Homologene. While listed in Homologene, mammalian species (chimpanzee, Pan troglodytes; dog, Canis lupus; cattle, Bos taurus; Rat, Rattus norvegicus) were omitted.

Homology search

Definition of Homolog
Homolog(1) was identified using NCBI Blast using Refseq protein sequence for human or Drosophila gene products as a query.
We also used BLAST service listed in "Tools".

The gene product with highest similarity to query was examined by Blast search against human and Drosophila database.
If the candidate shows the highest similarity to the human or Drosophila query, then the candidate was regarded as the homolog of human or Drosophila gene.

For family genes, the candidate was examined by phylogenetic analysis using ClustalW2.

Homolog in fungi and plant were listed without similarity search, if it was listed in Homologene.

Tools for the homology search

  1. Homolog (Homologue) is a relationship of genes with originated from a common ancestral gene in genetics. Homolog includes ortholog and paralog.

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