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    PER3 period circadian clock 3 [ Homo sapiens (human) ]

    Gene ID: 8863, updated on 20-Apr-2017
    Official Symbol
    PER3provided by HGNC
    Official Full Name
    period circadian clock 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]
    Orthologs
    Location:
    1p36.23
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 1 NC_000001.11 (7784285..7845181)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (7844413..7905241)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene calmodulin binding transcription activator 1 Neighboring gene uncharacterized LOC105376689 Neighboring gene vesicle associated membrane protein 3 Neighboring gene urotensin 2 Neighboring gene TNF receptor superfamily member 9

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Advanced sleep phase syndrome, familial, 3
    MedGen: CN235882 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

    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

    • 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...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    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 
    ubiquitin protein ligase binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    circadian regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of transcription from RNA polymerase II promoter 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 
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    period circadian protein homolog 3
    Names
    cell growth-inhibiting gene 13 protein
    circadian clock protein PERIOD 3
    hPER3
    period circadian protein 3

    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

    1. NG_046850.1 RefSeqGene

      Range
      5050..65802
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001289861.1NP_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:285377
      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:285373
      PAS_3; PAS fold
      pfam12114
      Location:10641179
      Period_C; Period protein 2/3C-terminal region
    2. NM_001289862.1NP_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:285377
      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:285373
      PAS_3; PAS fold
      pfam12114
      Location:10831198
      Period_C; Period protein 2/3C-terminal region
    3. NM_001289863.1NP_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:285377
      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:285373
      PAS_3; PAS fold
      pfam12114
      Location:10571172
      Period_C; Period protein 2/3C-terminal region
    4. NM_001289864.1NP_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:763878
      Period_C; Period protein 2/3C-terminal region
    5. NM_016831.2NP_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:284376
      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:284372
      PAS_3; PAS fold
      pfam12114
      Location:10741189
      Period_C; Period protein 2/3C-terminal region

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p7 Primary Assembly

      Range
      7784285..7845181
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017002735.1XP_016858224.1  period circadian protein homolog 3 isoform X15

    2. XM_017002730.1XP_016858219.1  period circadian protein homolog 3 isoform X11

    3. XM_017002731.1XP_016858220.1  period circadian protein homolog 3 isoform X12

    4. XM_017002734.1XP_016858223.1  period circadian protein homolog 3 isoform X14

    5. XM_017002736.1XP_016858225.1  period circadian protein homolog 3 isoform X16

    6. XM_017002727.1XP_016858216.1  period circadian protein homolog 3 isoform X8

    7. XM_017002733.1XP_016858222.1  period circadian protein homolog 3 isoform X14

    8. XM_017002728.1XP_016858217.1  period circadian protein homolog 3 isoform X9

    9. XM_017002732.1XP_016858221.1  period circadian protein homolog 3 isoform X13

    10. XM_005263524.3XP_005263581.1  period circadian protein homolog 3 isoform X5

      Conserved Domains (3) summary
      cd00130
      Location:285377
      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:285373
      PAS_3; PAS fold
      pfam12114
      Location:10831192
      Period_C; Period protein 2/3C-terminal region
    11. XM_011542385.2XP_011540687.1  period circadian protein homolog 3 isoform X1

      Conserved Domains (3) summary
      cd00130
      Location:285377
      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:285373
      PAS_3; PAS fold
      pfam12114
      Location:10821197
      Period_C; Period protein 2/3C-terminal region
    12. XM_011542390.2XP_011540692.1  period circadian protein homolog 3 isoform X6

      Conserved Domains (3) summary
      cd00130
      Location:285377
      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:285373
      PAS_3; PAS fold
      pfam12114
      Location:10751190
      Period_C; Period protein 2/3C-terminal region
    13. XM_017002724.1XP_016858213.1  period circadian protein homolog 3 isoform X3

    14. XM_017002725.1XP_016858214.1  period circadian protein homolog 3 isoform X4

    15. XM_017002723.1XP_016858212.1  period circadian protein homolog 3 isoform X2

    16. XM_017002726.1XP_016858215.1  period circadian protein homolog 3 isoform X7

    17. XM_017002738.1XP_016858227.1  period circadian protein homolog 3 isoform X18

    18. XM_017002737.1XP_016858226.1  period circadian protein homolog 3 isoform X17

    19. XM_017002729.1XP_016858218.1  period circadian protein homolog 3 isoform X10

    Alternate CHM1_1.1

    Genomic

    1. NC_018912.2 Alternate CHM1_1.1

      Range
      7832226..7892978
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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