PER3 period circadian regulator 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PER3provided by HGNC
Official Full Name: period circadian regulator 3provided by HGNC
Primary source: HGNC:HGNC:8847
See related: Ensembl:ENSG00000049246 MIM:603427; Vega:OTTHUMG00000001216
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: GIG13; FASPS3
Summary: This gene is a member of the Period family of genes and is expressed in a circadian pattern in the suprachiasmatic nucleus, the primary circadian pacemaker in the mammalian brain. Genes in this family encode components of the circadian rhythms of locomotor activity, metabolism, and behavior. This gene is upregulated by CLOCK/ARNTL heterodimers but then represses this upregulation in a feedback loop using PER/CRY heterodimers to interact with CLOCK/ARNTL. Polymorphisms in this gene have been linked to sleep disorders. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2014]
Expression: Ubiquitous expression in thyroid (RPKM 14.6), fat (RPKM 11.2) and 24 other tissues See more
Orthologs: mouse all

Genomic context

Location:: 1p36.23

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
109	current	GRCh38.p12 (GCF_000001405.38)	1	NC_000001.11 (7784285..7845181)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (7844413..7905241)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

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GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Study identified several CpG sites and specifically several CpGs in the PTPRS and PER3 genes differentially methylated between obese and non-obese children, suggesting a role for DNA methylation concerning development of childhood obesity.
Title: PTPRS and PER3 methylation levels are associated with childhood obesity: results from a genome-wide methylation analysis.
these findings suggest that rhythmic expression of the circadian clock gene PER3 is associated with the amount of daily physical activity and physical fitness in older adults
Title: Positive association between physical activity and PER3 expression in older adults.
PER3 polymorphisms links with chronotype and affective dimensions
Title: ARNTL, CLOCK and PER3 polymorphisms - links with chronotype and affective dimensions.
data suggest that, PER3(4/4) genotype may accelerate the course of disease in multiple sclerosis susceptible individuals especially in women
Title: PER3 VNTR polymorphism in Multiple Sclerosis: A new insight to impact of sleep disturbances in MS.
The impact of PER3 polymorphisms on sleep cycle and insomnia in older adults is reported.
Title: Associations between period 3 gene polymorphisms and sleep- /chronotype-related variables in patients with late-life insomnia.
there is a significant association between the PER3 polymorphism and the extraversion personality trait
Title: Higher scores in the extraversion personality trait are associated with a functional polymorphism in the PER3 gene in healthy subjects.
PER34/4 genotype may accelerate the course of disease in multiple sclerosis susceptible individuals.
Title: Is there a change of paradigm towards more effective treatment early in the course of apparent high-risk MS?
CLOCK rs1801260*C and PER3(4/4) influence myelination processes by regulating sleep quality and quantity.
Title: Clock genes associate with white matter integrity in depressed bipolar patients.
4 and 5 variable-number tandem-repeat polymorphisms appear to influence sensitivity to the effects of stressful urban environments on sleep
Title: Period 3 gene polymorphism and sleep adaptation to stressful urban environments.
TFEB regulates PER3 expression via glucose-dependent effects on CLOCK/BMAL1
Title: TFEB regulates PER3 expression via glucose-dependent effects on CLOCK/BMAL1.

Submit: New GeneRIF Correction See all GeneRIFs (102)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Advanced sleep phase syndrome, familial, 3 MedGen: C4225169 OMIM: 616882 GeneReviews: Not available	not available

NHGRI GWAS Catalog

Description
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. NHGRI GWA Catalog NHGRI GWA CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of period homolog 3 (Drosophila, PER3) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

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Circadian entrainment, organism-specific biosystem (from KEGG)
Circadian entrainment, organism-specific biosystemCircadian entrainment is a fundamental property by which the period of the internal biological clock is entrained by recurring exogenous signals, such that the organism's endocrine and behavioral rhy...
Circadian entrainment, conserved biosystem (from KEGG)
Circadian entrainment, conserved biosystemCircadian entrainment is a fundamental property by which the period of the internal biological clock is entrained by recurring exogenous signals, such that the organism's endocrine and behavioral rhy...
Circadian rhythm, organism-specific biosystem (from KEGG)
Circadian rhythm, organism-specific biosystemCircadian rhythm is an internal biological clock, which enables to sustain an approximately 24-hour rhythm in the absence of environmental cues. In mammals, the circadian clock mechanism consists of ...
Circadian rhythm, conserved biosystem (from KEGG)
Circadian rhythm, conserved biosystemCircadian rhythm is an internal biological clock, which enables to sustain an approximately 24-hour rhythm in the absence of environmental cues. In mammals, the circadian clock mechanism consists of ...
Circadian rythm related genes, organism-specific biosystem (from WikiPathways)
Circadian rythm related genes, organism-specific biosystemThis is currently not a pathway but a list of circadian rhythm related genes and proteins. The source for this information is the gene ontology. The genes and proteins were filtered for "circadian rh...
Herpes simplex infection, organism-specific biosystem (from KEGG)
Herpes simplex infection, organism-specific biosystemHerpes simplex virus (HSV) infections are very common worldwide, with the prevalence of HSV-1 reaching up to 80%-90%. Primary infection with HSV takes place in the mucosa, followed by the establishme...
Herpes simplex infection, conserved biosystem (from KEGG)
Herpes simplex infection, conserved biosystemHerpes simplex virus (HSV) infections are very common worldwide, with the prevalence of HSV-1 reaching up to 80%-90%. Primary infection with HSV takes place in the mucosa, followed by the establishme...
Melatonin metabolism and effects, organism-specific biosystem (from WikiPathways)
Melatonin metabolism and effects, organism-specific biosystemMelatonin is an important regulator of circadian rythmus and influences also insulin secretion, immune function, retinal function and neuroprotection. The synthesis starts with the amino acid tryptop...

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-74176 (e-PCR)
- UniSTS:23043

AL033593 (e-PCR)
- UniSTS:93454

SHGC-74162 (e-PCR)
- UniSTS:67643

PER3_1734 (e-PCR)
- UniSTS:280907

SHGC-53173 (e-PCR)
- UniSTS:56656

SHGC-74175 (e-PCR)
- UniSTS:25940

SHGC-112332 (e-PCR)
- UniSTS:168534

RH93635 (e-PCR)
- UniSTS:91378

D1S1294 (e-PCR)
- UniSTS:149491

D1S3614 (e-PCR)
- UniSTS:83449

GDB:182522 (e-PCR)
- UniSTS:155385

SHGC-74167 (e-PCR)
- UniSTS:22524

Homology

Homologs of the PER3 gene: The PER3 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 204 organisms have orthologs with human gene PER3
The Hierarchical Catalog of Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
kinase binding	IEA Inferred from Electronic Annotation more info
protein binding	IPI Inferred from Physical Interaction more info	PubMed
transcription corepressor binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
transcription factor binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
ubiquitin protein ligase binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
circadian regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info	PubMed
entrainment of circadian clock by photoperiod	IBA Inferred from Biological aspect of Ancestor more info	PubMed
negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed
negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
protein stabilization	IMP Inferred from Mutant Phenotype more info	PubMed
regulation of circadian sleep/wake cycle, sleep	IMP Inferred from Mutant Phenotype more info	PubMed
response to light stimulus	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Component	Evidence Code	Pubs
cytoplasm	IBA Inferred from Biological aspect of Ancestor more info	PubMed
cytoplasm	IDA Inferred from Direct Assay more info	PubMed
nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: period circadian protein homolog 3

Names: cell growth-inhibiting gene 13 protein; circadian clock protein PERIOD 3; hPER3; period circadian clock 3; period circadian protein 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_046850.1 RefSeqGene

Range

5050..65802

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001289861.1 → NP_001276790.1 period circadian protein homolog 3 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame segment compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AK308303, AL157954, CN480408, Z98884

Consensus CDS

CCDS76097.1

UniProtKB/Swiss-Prot

P56645

UniProtKB/TrEMBL

A0A087WV69

Related

ENSP00000479223.1, ENST00000614998.4

Conserved Domains (3) summary

cd00130
Location:285 → 377

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam08447
Location:285 → 373

PAS_3; PAS fold

pfam12114
Location:1064 → 1179

Period_C; Period protein 2/3C-terminal region
NM_001289862.1 → NP_001276791.1 period circadian protein homolog 3 isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AB047686, AL157954, CN480408, HY151851, Z98884

Consensus CDS

CCDS72695.1

UniProtKB/Swiss-Prot

P56645

Related

ENSP00000482093.1, ENST00000613533.4

Conserved Domains (3) summary

cd00130
Location:285 → 377

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam12114
Location:1082 → 1195

Period_C; Period protein 2/3C-terminal region

cl25496
Location:756 → 1066

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
NM_001289863.1 → NP_001276792.1 period circadian protein homolog 3 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate in-frame splice junction at the 3' end of an exon and lacks an alternate in-frame segment compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AK307760, AL157954, CN480408, HY151851, Z98884

UniProtKB/Swiss-Prot

P56645

Conserved Domains (3) summary

cd00130
Location:285 → 377

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam08447
Location:285 → 373

PAS_3; PAS fold

pfam12114
Location:1057 → 1172

Period_C; Period protein 2/3C-terminal region
NM_001289864.1 → NP_001276793.1 period circadian protein homolog 3 isoform 5

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (5) is shorter at the N-terminus and lacks a single internal aa compared to isoform 1.

Source sequence(s)

AL157954, BC144137, CN480408, HY151851, Z98884

UniProtKB/Swiss-Prot

P56645

Conserved Domains (1) summary

pfam12114
Location:763 → 878

Period_C; Period protein 2/3C-terminal region
NM_016831.2 → NP_058515.1 period circadian protein homolog 3 isoform 4

See identical proteins and their annotated locations for NP_058515.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses alternate in-frame splice junctions at three exons compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AL157954, CN480408, HY151851

Consensus CDS

CCDS89.1

UniProtKB/Swiss-Prot

P56645

UniProtKB/TrEMBL

A2I2N5

Related

ENSP00000355031.2, OTTHUMP00000001354, ENST00000361923.2, OTTHUMT00000003607

Conserved Domains (3) summary

cd00130
Location:284 → 376

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam12114
Location:1073 → 1186

Period_C; Period protein 2/3C-terminal region

cl25496
Location:748 → 1057

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p12 Primary Assembly

Range

7784285..7845181

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017002734.1 → XP_016858223.1 period circadian protein homolog 3 isoform X16
XM_017002727.1 → XP_016858216.1 period circadian protein homolog 3 isoform X10
XM_024450612.1 → XP_024306380.1 period circadian protein homolog 3 isoform X19

Conserved Domains (3) summary

cd00130
Location:110 → 202

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam12114
Location:899 → 1012

Period_C; Period protein 2/3C-terminal region

cl25496
Location:574 → 883

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
XM_017002728.1 → XP_016858217.1 period circadian protein homolog 3 isoform X11
XM_017002730.2 → XP_016858219.1 period circadian protein homolog 3 isoform X13
XM_017002731.2 → XP_016858220.1 period circadian protein homolog 3 isoform X14
XM_005263524.4 → XP_005263581.1 period circadian protein homolog 3 isoform X6

Conserved Domains (3) summary

cd00130
Location:285 → 377

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam08447
Location:285 → 373

PAS_3; PAS fold

pfam12114
Location:1083 → 1192

Period_C; Period protein 2/3C-terminal region
XM_024450585.1 → XP_024306353.1 period circadian protein homolog 3 isoform X1

Related

ENSP00000366755.3, ENST00000377532.7

Conserved Domains (3) summary

cd00130
Location:285 → 377

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam12114
Location:1082 → 1195

Period_C; Period protein 2/3C-terminal region

cl25496
Location:756 → 1066

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
XM_017002733.2 → XP_016858222.1 period circadian protein homolog 3 isoform X16
XM_017002735.2 → XP_016858224.1 period circadian protein homolog 3 isoform X17
XM_024450611.1 → XP_024306379.1 period circadian protein homolog 3 isoform X18

Conserved Domains (3) summary

cd00130
Location:110 → 202

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam12114
Location:900 → 1013

Period_C; Period protein 2/3C-terminal region

cl28033
Location:567 → 882

Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region
XM_024450586.1 → XP_024306354.1 period circadian protein homolog 3 isoform X2

Conserved Domains (3) summary

cd00130
Location:285 → 377

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam12114
Location:1081 → 1194

Period_C; Period protein 2/3C-terminal region

cl25496
Location:756 → 1065

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
XM_024450587.1 → XP_024306355.1 period circadian protein homolog 3 isoform X5

Conserved Domains (3) summary

cd00130
Location:285 → 377

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam12114
Location:1075 → 1188

Period_C; Period protein 2/3C-terminal region

cl25496
Location:749 → 1059

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
XM_024450588.1 → XP_024306356.1 period circadian protein homolog 3 isoform X7

Conserved Domains (3) summary

cd00130
Location:285 → 377

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam12114
Location:1074 → 1187

Period_C; Period protein 2/3C-terminal region

cl25496
Location:749 → 1058

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
XM_017002723.2 → XP_016858212.1 period circadian protein homolog 3 isoform X3
XM_017002724.2 → XP_016858213.1 period circadian protein homolog 3 isoform X4
XM_017002726.2 → XP_016858215.1 period circadian protein homolog 3 isoform X8
XM_024450590.1 → XP_024306358.1 period circadian protein homolog 3 isoform X9

Conserved Domains (3) summary

cd00130
Location:284 → 376

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam12114
Location:1073 → 1186

Period_C; Period protein 2/3C-terminal region

cl25496
Location:748 → 1057

Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
XM_017002732.1 → XP_016858221.1 period circadian protein homolog 3 isoform X15
XM_017002738.2 → XP_016858227.1 period circadian protein homolog 3 isoform X21
XM_017002737.1 → XP_016858226.1 period circadian protein homolog 3 isoform X20
XM_017002729.1 → XP_016858218.1 period circadian protein homolog 3 isoform X12