PER3 (period circadian regulator 3)

symbol
PER3
locus group
protein-coding gene
location
1p36.23
gene_family
-
alias symbol
-
alias name
None
entrez id
8863
ensembl gene id
ENSG00000049246
ucsc gene id
uc057bxs.1
refseq accession
NM_016831
hgnc_id
HGNC:8847
approved reserved
1999-06-11
1p36.23
ChineseEnglish

PER3 (Period Circadian Regulator 3) is a core component of the Period (Per) gene family, which, alongside PER1 and PER2, plays a pivotal role in orchestrating the mammalian circadian rhythm, the approximately 24-hour cycle governing physiological and behavioral processes. The PER3 protein, characterized by the presence of PAS domains that facilitate protein-protein interactions and a nuclear localization signal, forms a critical inhibitory complex with CRY (Cryptochrome) proteins. This complex acts to suppress the transcriptional activity of the CLOCK/BMAL1 heterodimer, thereby establishing a negative feedback loop that maintains the stability and precision of the circadian oscillation. Expression of PER3 is prominent in the suprachiasmatic nucleus (SCN), the master pacemaker of the brain, as well as in peripheral tissues, where its levels exhibit robust circadian oscillations. The stability and function of PER3, like other PER family members, are tightly regulated by phosphorylation events, particularly those mediated by casein kinase 1 epsilon and delta (CK1ε/δ), which target the protein for degradation. Genetic variations in PER3 have significant clinical and physiological implications; for instance, the rs57875989 polymorphism is associated with a "morningness" phenotype, while specific rare mutations can lead to Familial Advanced Sleep Phase Syndrome (FASPS). Furthermore, altered PER3 expression is linked to an increased risk of sleep disorders, depression, and bipolar disorder, and circadian disruptions involving PER3 may contribute to metabolic abnormalities such as impaired glucose metabolism. Experimental manipulations highlight the gene's nuanced role: overexpression can enhance circadian stability but potentially reduce sensitivity to light-induced phase resetting, whereas knockdown leads to attenuated circadian amplitude, disrupted sleep architecture characterized by reduced REM sleep, and cognitive decline. Notably, PER3 length polymorphisms, such as the 5-repeat allele, are strongly correlated with individual differences in resilience to sleep deprivation. Beyond its primary role in timekeeping, PER3 is implicated in tumorigenesis, with aberrant methylation patterns observed in certain cancers, underscoring the broader biological significance of the PER family in maintaining homeostasis through shared structural motifs and regulatory mechanisms, despite functional redundancies and tissue-specific expression differences.

Nucleotide sequence of PER3:[NCBI]
Loading Gene Browser...
Protein Sequence
1MPRGEAPGPG RRGAKDEALG EESGERWSPE FHLQRKLADS
41SHSEQQDRNR VSEELIMVVQ EMKKYFPSER RNKPSTLDAL
81 NYALRCVHS VQANSEFFQI LSQNGAPQAD VSMYSLEELA
121TIASEHTSKN TDTFVAVFSF LSGRLVHISE QAALILNRKK
161D VLASSHFV DLLAPQDMRV FYAHTARAQL PFWNNWTQRA
201ARYECAPVKP FFCRIRGGED RKQEKCHSPF RIIPYLIHVH
241HP AQPELES EPCCLTVVEK IHSGYEAPRI PVNKRIFTTT
281HTPGCVFLEV DEKAVPLLGY LPQDLIGTSI LSYLHPEDRS
321LMV AIHQKV LKYAGHPPFE HSPIRFCTQN GDYIILDSSW
361SSFVNPWSRK ISFIIGRHKV RTSPLNEDVF ATKIKKMNDN
401DKDI TELQE QIYKLLLQPV HVSVSSGYGS LGSSGSQEQL
441VSIASSSEAS GHRVEETKAE QMTLQQVYAS VNKIKNLGQQ
481LYIES MTKS SFKPVTGTRT EPNGGGECKT FTSFHQTLKN
521NSVYTEPCED LRNDEHSPSY QQINCIDSVI RYLKSYNIPA
561LKRKCI SCT NTTSSSSEED KQNHKADDVQ ALQAGLQIPA
601IPKSEMPTNG RSIDTGGGAP QILSTAMLSL GSGISQCGYS
641STIVHVP PP ETARDATLFC EPWTLNMQPA PLTSEEFKHV
681GLTAAVLSAH TQKEEQNYVD KFREKILSSP YSSYLQQESR
721SKAKYSYF Q GDSTSKQTRS AGCRKGKHKR KKLPEPPDSS
761SSNTGSGPRR GAHQNAQPCC PSAASSPHTS SPTFPPAAMV
801PSQAPYLVP AFPLPAATSP GREYAAPGTA PEGLHGLPLS
841EGLQPYPAFP FPYLDTFMTV FLPDPPVCPL LSPSFLPCPF
881LGATASSAIS PSMSSAMSP TLDPPPSVTS QRREEEKWEA
921QSEGHPFITS RSSSPLQLNL LQEEMPRPSE SPDQMRRNTC
961PQTEYCVTGN N GSESSPAT TGALSTGSPP RENPSHPTAS
1001ALSTGSPPMK NPSHPTASAL STGSPPMKNP SHPTASTLSM
1041GLPPSRTPSH PT ATVLSTG SPPSESPSRT GSAASGSSDS
1081SIYLTSSVYS SKISQNGQQS QDVQKKETFP NVAEEPIWRM
1121IRQTPERILM TYQ VPERVK EVVLKEDLEK LESMRQQQPQ
1161FSHGQKEELA KVYNWIQSQT VTQEIDIQAC VTCENEDSAD
1201GAATSCGQVL VEDS C
Structure predicted by AlphaFold DB(UniProt: P56645). Color indicates pLDDT confidence (dark blue = high, yellow/orange = low).
SNP variants of PER3:           Showing partial SNPs
rs172933       rs228730       rs228731       rs228732       rs571577       rs571578       rs697682       rs2794664       rs2797687       rs3753502       rs41278956       rs58073588       rs58675180       rs61772144       rs78018177       rs78495981       rs112027086      

Tissue expression of PER3:    [UniProt]

Gene expression across tissues
Forward Primer
Forward Tm
Reverse Primer
Reverse Tm
Score
CGTTCAAGCAAACAGTGAG
57
TCAAGACTGTACATGCTCAC
57
ATCGACATTCAAGCCTGTG
58
TACCAGAACCTGACCACAG
58
AAGTTCGAACCCAGTTCAC
58
ATGTGACATAAGCCCATGC
58
CTGCTTTGATCCTGAATCGT
58
AGCAGGTCAACAAAGTGAG
58
TAAAGTTCGAACCCAGTTCAC
58
GTGACATAAGCCCATGCAC
59
GACATTCAAGCCTGTGTCAC
59
TTCTACCAGAACCTGACCAC
59
AGAGACGCAATAAACCAAGC
59
ACTCACTGTTTGCTTGAACG
59
CGTTGATGACGAGAACACC
59
CACATAACTTCTCTGCAAACTG
58
TGCTTTGATCCTGAATCGT
57
AAGCAGGTCAACAAAGTGAG
58
AAAGTTCGAACCCAGTTCAC
58
GTGACATAAGCCCATGCAC
59
Transcription Factors
Target Gene
Interaction Type
PubMed References
ARNTL
PER3
Activation
CLOCK
PER3
Activation

Subcellular localization of PER3 (and its protein):

[UniProt]     [GenomeNet]

" d="M482.414,245.296c3.539,4.293,4.455,10.009,0.202,11 c-4.244,0.996-4.983-10.983-8.293-8.438c-5.271,4.08,9.834,12.271,5.144,17.287c-3.717,3.607-6.172-5.75-10.839-1.976 c-4.673,3.776,6.781,7.299,2.831,11.326c-4.354,4.045-6.979-1.449-9.837-5.517c-1.193-1.742-2.059-3.851-3.595-2.748 c-1.516,1.078-1.854,1.795-0.938,3.666c2.374,4.854,9.235,10.119,5.156,12.535c-5.636,3.346-5.044-8.871-9.426-7.574 c-4.388,1.291,2.557,10.66-1.245,11.141c-4.089,0.545-3.483-10.239-6.979-8.575c-2.522,1.206-0.929,3.071-0.938,4.899 c0.004,1.32-0.964,3.6-2.372,4.062c-3.593,1.171-8.544-1.065-10.251-3.59c-6.04-8.93,0.396-15.997,4.639-7.015 c3.023,4.642,5.182,0.834,2.839-2.219c-1.032-1.354-4.309-5.901-0.781-7.252c2.904-1.113,4.271,1.941,5.985,4.592 c2.61,4.016,5.485,0.117,3.031-3.414c-1.828-2.633-2.74-3.803,3.156-7.42c6.405-4.369,6.52,3.869,10.077,0.646 c2.309-1.832-4.783-5.149,0.06-8.995c2.896-2.293,5.18,6.207,7.961,3.516c3.523-2.737-7.717-7.369,0.117-11.736 C473.413,240.77,480.519,242.891,482.414,245.296z"/> Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
  • plasma membrane
  • cytoplasm
  • extracellular
  • golgi
  • vesicle
  • cytoskeleton
  • endoplasmic reticulum
  • nucleus
  • endosome
  • lysosome
  • mitochondrion

Gene Ontology (GO) terms for PER3:

GO ID
Protein
Source DB
GO:0032922
A0A087WV69 (UniProtKB)
IEA
GO:0000122
P56645 (UniProtKB)
IEA
GO:0005515
P56645 (UniProtKB)
IPI
GO:0005634
P56645 (UniProtKB)
IEA
GO:0005737
P56645 (UniProtKB)
IEA
GO:0006351
P56645 (UniProtKB)
IEA
GO:0019900
P56645 (UniProtKB)
IEA
GO:0031625
P56645 (UniProtKB)
IEA
GO:0032922
P56645 (UniProtKB)
IEA
GO:0045187
P56645 (UniProtKB)
IMP
GO:0045187
P56645 (UniProtKB)
IMP
GO:0045187
P56645 (UniProtKB)
IMP
GO:0045187
P56645 (UniProtKB)
IMP
GO:0032922
Q8TAR6 (UniProtKB)
IEA

microRNAs potentially regulating PER3:     

String
BioGrid
IntAct
mentha
MINT
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Interacting Gene Interaction Source/Score
Disease Score NofPmids NofSnps Source
Disease Score NofPmids NofSnps Source
Myeloid Leukemia, Chronic 0.122995792 1 0 BeFree_CTD_human_LHGDN
Crohn Disease 0.122367032 1 1 GAD_GWASCAT
Substance Withdrawal Syndrome 0.12 1 0 CTD_human
Mammary Neoplasms 0.12 1 0 CTD_human
Sleep Deprivation 0.01183516 5 0 GAD
Bipolar Disorder 0.010553895 6 0 BeFree_GAD
Sleep Disorders 0.005819831 6 0 BeFree_GAD
Malignant neoplasm of prostate 0.005005506 2 12 BeFree_GAD
Schizophrenia 0.005005506 2 0 BeFree_GAD
Liver carcinoma 0.003810118 5 1 BeFree_LHGDN
Circadian genotypes in PER3 and time of prostate cancer radiotherapy interact to affect risk of late side-effects.
Webb AJ, Harper E, Rattay T, Aguado-Barrera ME, Avuzzi B, Bultijnck R, Choudhury A, De Ruysscher DK, Fuentes-Ríos O, Gutiérrez-Enríquez S, Kerns SL, Lobato-Busto R, McWilliam A, Noris Chiorda B, Rancati T, Rosenstein BS, Seibold P, Sperk E, Vega A, Veldeman L, Ward TH, West CM, Symonds P, Talbot CJ Clin Cancer Res IF: 10.9 2026-07-13
Genetic markers of stress, resilience and success at an elite military selection course.
Petrovick M, Hendricks J, Farina EK, Thompson LA, Knapik JJ, Pasiakos SM, McClung JP, Lieberman HR Physiol Behav IF: 2.7 2026-02-00
Advances in the genetics of refractive errors: Contributions from the CREAM consortium.
Li SWR, He X, Terry L, Verhoeven VJM, Lee SS, Lingham G, Guggenheim JA, Mackey DA, Saw SM, Klaver CCW, Pang CP, CREAM Consortium Acta Ophthalmol IF: 3.0 2025-11-13
Effects of prednisolone administration on clock gene expression and indices of circadian rhythms in healthy human males.
Hansen SB, Frederiksen JSS, Lodberg A, Poulsen MF, Andersen CBF, Oster H, Jessen N, Jørgensen JOL J Clin Endocrinol Metab IF: 5.4 2025-10-15
Association between genetic polymorphisms in circadian cycle genes (PER2, PER3, and HCRTR2) and Attention Deficit Hyperactivity Disorder (ADHD).
Alves RB, da Cunha LVR, Albuquerque ALB, de Souza RP, de Miranda DM, Alvim-Soares AM, de Marco L, Bastos-Rodrigues L Chronobiol Int IF: 2.5 2026-06-00
Exercise training alters circadian clock dynamics in cancer-bearing male mice.
Silveira LS, de Lima Junior EA, Rosa Neto JC, de Souza Teixeira AA Physiol Rep IF: 2.1 2026-02-00

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