Clock Gene in Animal Update: 2009.3.13 Site Map
Clock Gene Homolog
PERIOD CLOCK, NPAS2 ARNTL [BMAL] DEC, (cwo) Id1-4 NF1L3 [E4BP4] (vri)
DBP, (pdp1) NR1D1 [REV-ERB] RORA-C SIRT1-7 CRY, PHR TIM, (timeless)
GSK3 (sgg) CSNK1 CSNK2 BTRC (slmb) FBXL3 FBXL15 (jet)

CRY, Photolyase

→ Outlineeng→JPNJPN; → Mutant list

Scientific name Gene GeneID Homologene Blink Protein
Homo sapiens CRY1 1407 7042 hs_CRY1 NP_004066
CRY2 1408 56466 hs_CRY2 NP_066940
Mus musculus Cry1 12952 7042 mm_CRY1 NP_031797
Cry2 12953 56466 mm_CRY2 NP_034093
Gallus gallus CRY1 374093 7042 gg_CRY1 NP_989576
CRY2 4001811 56466 gg_CRY2 NP_989575
CRY4(PHR) 395100 100994 gg_CRY4 NP_001034685
LOC424919(CPD-PHR) 424919 17893 gg_PHR XP_422729
Xenopus tropicalis cry1 550065 - xt_CRY1 NP_001017311
LOC100170456(cry4) 100170456 - xt_CRY4 NP_001123706
LOC100144974 (cry5) 100144974 - xt_6-4PHR NP_001120012
JGI:365106 (cry-dash) 365106 - - 365106.txt
JGI:173754 (CPD-PHR) 173754 - - 173754.txt
Xenopus laevis cry1-A(Sup) 394398 - xl_CRY1-A NP_001081129
Cry1(PHR) 496373 - xl_PHR NP_001088990
Xl64phr (6-4phr) 397827 - xl_6-4PHR NP_001081421
xlcry-dash 403387 - xl_CRY-DASH NP_001084438
LOC733427 733427 - xl_CPD_PHR NP_001089127
Danio rerio cry1a 100003956 117460 dr_CRY1A NP_001070765
  cry1b 554836 117460 dr_CRY1B NP_571865
cry2a 573209 - dr_CRY2A NP_571866
cry2b 83780 - dr_CRY2B NP_571867
cry3 83774 56466 dr_CRY3 NP_571861
cry4(PHR) 83775 100994 dr_CRY4 NP_571862
cry5(z6-4phr) 83776 101154 dr_CRY5 NP_571863
cry-dash 402986 101347 dr_CRY-DASH NP_991249
zgc:66475 (PHR) 394039 17893 dr_PHR NP_957358
Ciona intestinalis 235623 (bacterial PHR) 235623  - - Cioin_235623.txt
Branchiostoma floridae BF_96662(CRY Sup)= BF_230263 7249379 - bf_CRYsup XP_002234099
BF_60127(PHR) 7206346 - bf_PHRa XP_002227682
BF_232039(PHR) 7250214 - bf_PHRb XP_002234098
Strongylocentrotus purpuratus LOC580742(Sup) 580742 - sp_CRY1A XP_785873
LOC581225(Photo) 581225 - sp_CRY XP_786331
cry5(PHR) 583959 - sp_CRY5 XP_788938
cry-dash 578347 - sp_CRY-DASH XP_783613
Apis mellifera cry2  410197 - am_CRY2 NP_001077099
Anopheles gambiae AGAP004261 1274104 7042 ag_CRY2 XP_313179
AGAP001958 1281165 65214 ag_CRY1 XP_321104
AGAP008651 1275500 101154 ag_PHR6-4 XP_314748
AGAP005052 1274733 17893 ag_PHR XP_313925
Drosophila melanogaster cry 42305 65214 dm_CRY NP_732407
phr6-4 35322 101154 dm_PHR6-4 NP_477188
phr 35735 17893 dm_PHR NP_523653
Caenorhabditis elegans Not found - - - -
Nematostella vectensis v1g194898 =v1g230851 5501898 - nv_CRY1 XP_001623146
v1g203127 (6-4phr) 5516268  - nv_6-4PHR XP_001636303
v1g106211 5512527 - nv_v1g106211 XP_001632850
v1g106062 5512526 - nv_v1g106062 XP_001632849
v1g168581 5510586 - nv_v1g168581 XP_001631029
v1g219650(cry-dash) 5502007 - nv_CRY-DASH XP_001623243
v1g106104 5512563 - nv_v1g106104 *P XP_001632847
Trichoplax adhaerens TA_18352(bacterial PHR) 6748974 - ta_PHR1 XP_002107759
TA_51590(bacterial PHR) 6749774 - ta_PHR2 XP_002108560
Plasmodium falciparum PFE0675c 812950 17893 PlFa_PHR XP_001351693
Saccharomyces cerevisiae PHR1 854568 22339 SaCe_PHR1 NP_015031
Kluyveromyces lactis KLLA0D00462g 2893203 22339 KlLa_PHR XP_453092
Magnaporthe grisea MGG_06836 2685009 22339 MaGr_PHR XP_370339
Neurospora crassa NCU08626 3880994 22339 NeCr_PHR XP_964834
NCU00582 3881951 - NeCr_CRY-DASH XP_965722
Arabidopsis thaliana CRY1 826470 22339 ArTh_CRY1 NP_567341
CRY2 839529 - ArTh_CRY2 NP_171935
CRY3(CRY-DASH) 832554 101347 ArTh_CRY3 NP_568461
UVR3(6-4PHR) 820804 101154 ArTh_UVR3 NP_001030703
PHR1 837792 17893 ArTh_PHR1 NP_849651
PHR2 819372 94099 ArTh_PHR2 NP_182281
Oryza sativa Os04g0452100 4336008 22339 OrSa_CRY1B NP_001052950
Os02g0573200 4329738 - OrSa_CRY1A NP_001047200
CRY2 (discontinued) 3062990 - OrSa_CRY2 BAD23780
Os06g0661800(CRY-DASH) 4341749 101347 OrSa_CRY3 NP_001058278
Os10g0167600(PHR1) 4348178 17893 OrSa_PHR1 NP_001064225
Os03g0343400 4332801 94099 OrSa_PHR2 NP_001050077
Os02g0204400 4328669 101154 OrSa_6-4PHR NP_001046243
Plant and Fungi genes (green cells) were shown in this site, if the gene was listed in Homologene of animal gene.
Mammalian CRY acts as a negative regulators of the circadian clock.
Drosophila and plant cry are not essential to maintain rhythm, but have a crucial role in light input to circadian oscillators (Stanewsky1998).
Photolyases (PHR and cry-DASH) were added for reference.

Cladogram of CRY, PHR

Phylogram of CRY, PHR

List of CRY, PHR sequences for ClustalW2 DND file of CRY, PHR for TreeView
Note: Cladogram using raw data of ClustalW2 was different from previous reports (Zhu2005, Rubin2008)
Bacterial PHR were included: Stenotrophomonas maltophilia (Gram negative bacterium), Smlt1825; Xanthomonas campestris, XCC1435; Rhodospirillum centenum (photosynthetic bacterium), RC1_2026; Labrenzia alexandrii, SADFL11_4534.


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