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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

CLOCK Gene

protein-coding   GIFtS: 70
GCID: GC04M056294

Clock Circadian Regulator

(Previous names: clock (mouse) homolog, clock homolog (mouse))
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Clock Circadian Regulator1 2     Circadian Locomoter Output Cycles Kaput Protein2
Class E Basic Helix-Loop-Helix Protein 82 3     Circadian Locomoter Output Cycles Protein Kaput2
bHLHe82 3     Clock Homolog2
EC 2.3.1.483 8     BHLHE83
Clock (Mouse) Homolog1     KIAA03343
Clock Homolog (Mouse)1     hCLOCK3
KAT13D2     

External Ids:    HGNC: 20821   Entrez Gene: 95752   Ensembl: ENSG000001348527   OMIM: 6018515   UniProtKB: O155163   

Export aliases for CLOCK gene to outside databases

Previous GC identifers: GC04M056102 GC04M056260 GC04M056214 GC04M056139 GC04M055988 GC04M052247


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for CLOCK Gene:
This gene product regulates circadian rhythm and metabolism. The protein encodes a transcription factor of the
basic helix-loop-helix (bHLH) family and a DNA binding histone acetyltransferase. Polymorphisms in this gene may
be associated with behavioral changes in certain populations and with obesity and metabolic syndrome. Alternative
splicing results in multiple transcript variants. (provided by RefSeq, Jun 2012)

GeneCards Summary for CLOCK Gene: 
CLOCK (clock circadian regulator) is a protein-coding gene. Diseases associated with CLOCK include delayed sleep phase syndrome, and advanced sleep phase syndrome, and among its related super-pathways are Circadian Clock and Circadian entrainment. GO annotations related to this gene include protein dimerization activity and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is ARNT2.

UniProtKB/Swiss-Prot: CLOCK_HUMAN, O15516
Function: ARNTL/2-CLOCK heterodimers activate E-box element (5'-CACGTG-3') transcription of a number of proteins
of the circadian clock. Activates transcription of PER1 and PER2. This transcription is inhibited in a feedback
loop by PER and CRY proteins. Has intrinsic histone acetyltransferase activity and this enzymatic function
contributes to chromatin-remodeling events implicated in circadian control of gene expression (By similarity).
Acetylates primarily histones H3 and H4 (By similarity). Acetylates also a non-histone substrate: ARNTL (By
similarity). Plays a role in DNA damage response (DDR) signaling during the S phase

Gene Wiki entry for CLOCK Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000004.11  NT_022853.15  NC_018915.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CLOCK gene promoter:
         Pax-5   Sp1   Bach2   CUTL1   PPAR-alpha   CREB   deltaCREB   PPAR-gamma2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCLOCK promoter sequence
   Search SABiosciences Chromatin IP Primers for CLOCK

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CLOCK


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 4q12   Ensembl cytogenetic band:  4q12   HGNC cytogenetic band: 4q12

CLOCK Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLOCK gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04M056294:  view genomic region     (about GC identifiers)

Start:
56,294,070 bp from pter      End:
56,413,305 bp from pter
Size:
119,236 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: CLOCK_HUMAN, O15516 (See protein sequence)
Recommended Name: Circadian locomoter output cycles protein kaput  
Size: 846 amino acids; 95304 Da
Subunit: Component of the circadian clock oscillator which includes the CRY proteins, CLOCK or NPAS2, ARNTL or
ARNTL2, CSNK1D and/or CSNK1E, TIMELESS and the PER proteins. Efficient DNA binding requires dimerization with
another bHLH protein. Heterodimerization with ARNTL is required for E-box-dependent transactivation, for CLOCK
nuclear translocation and degradation, and, for phosphorylation of both CLOCK and ARNTL. Interaction with PER and
CRY proteins requires translocation to the nucleus. Interaction of the CLOCK-ARNTL heterodimer with PER or CRY
inhibits transcription activation. Binds weakly ARNTL and ARNTL2 to form heterodimers which bind poorly to the
E-box motif (By similarity)
Subcellular location: Nucleus. Chromosome. Cytoplasm (By similarity). Nucleus (By similarity). Note=Shuffling
between the cytoplasm and the nucleus is under circadian regulation and is ARNTL-dependent. Phosphorylated form
located in the nucleus (By similarity). Localizes to sites of DNA damage in a H2AX-independent manner
Miscellaneous: CLOCK-ARNTL double mutations within the PAS domains result in syngernistic desensitization to high
levels of CRY on repression of CLOCK-ARNTL transcriptional activity of PER1 and disrupt circadian rhythmicity
Sequence caution: Sequence=BAA20792.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;
1 PDB 3D structure from and Proteopedia for CLOCK:
4H10 (3D)    
Secondary accessions: A0AV01 A2I2N9 O14516 Q9UIT8

Explore the universe of human proteins at neXtProt for CLOCK: NX_O15516

Explore proteomics data for CLOCK at MOPED 

Post-translational modifications:

  • UniProtKB: Phosphorylation is dependent on CLOCK-ARNTL heterodimer formation (By similarity)
  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_O15516

  • 4/13 DME Specific Peptides for CLOCK (O15516) (see all 13)
     KSQDSGS  LQSTSTQ  SYEDRVC  LEALDGFF 

    CLOCK Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    CLOCK Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_001254772.1  NP_004889.1  

    ENSEMBL proteins: 
     ENSP00000308741   ENSP00000370723   ENSP00000426983   ENSP00000396649  
    Reactome Protein details: O15516
    Human Recombinant Protein Products for CLOCK: 
    Browse Purified and Recombinant Proteins at EMD Millipore
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Browse OriGene full length recombinant human proteins expressed in human HEK293 cells
    OriGene Protein Over-expression Lysate for CLOCK
    OriGene Custom MassSpec 
    OriGene Custom Protein Services for CLOCK
    GenScript Custom Purified and Recombinant Proteins Services for CLOCK
    Novus Biologicals CLOCK Proteins
    Novus Biologicals CLOCK Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for CLOCK 

    Gene Ontology (GO): 5/7 cellular component terms (GO ID links to tree view) (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005667transcription factor complex IPI9576906
    GO:0005694chromosome IDA--
    GO:0005730NOT nucleolus IDA--
    GO:0005737cytoplasm ----

    CLOCK for ontologies           About GeneDecksing



    CLOCK Antibody Products: 
    EMD Millipore Mono- and Polyclonal Antibodies for the study of CLOCK
    R&D Systems Antibodies for CLOCK
    Cell Signaling Technology (CST) Antibodies for CLOCK 
    OriGene Antibodies for CLOCK
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    GenScript Custom Superior Antibodies Services for CLOCK
    Novus Biologicals CLOCK Antibodies
    Abcam antibodies for CLOCK
    Cloud-Clone Corp. Antibodies for CLOCK 
    ThermoFisher Antibodies for CLOCK
    LSBio Antibodies in human, mouse, rat for CLOCK 

    Assay Products for CLOCK: 
    Browse Kits and Assays available from EMD Millipore
    OriGene Custom Assay Services for CLOCK
    Browse R&D Systems for biochemical assays
    GenScript Custom Assay Services for CLOCK
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for CLOCK 
    Cloud-Clone Corp. CLIAs for CLOCK


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    KAT: Chromatin-modifying enzymes / K-acetyltransferases
    bHLH: Basic helix-loop-helix proteins

    5/6 InterPro protein domains (see all 6):
     IPR013655 PAS_fold_3
     IPR001610 PAC
     IPR013767 PAS_fold
     IPR000014 PAS
     IPR011598 bHLH_dom

    Graphical View of Domain Structure for InterPro Entry O15516

    ProtoNet protein and cluster: O15516

    5 Blocks protein domains:
    IPB000014 PAS domain
    IPB001067 Nuclear translocator signature
    IPB001092 Basic helix-loop-helix dimerization domain bHLH
    IPB001610 PAC motif
    IPB013655 PAS fold-3


    UniProtKB/Swiss-Prot: CLOCK_HUMAN, O15516
    Similarity: Contains 1 bHLH (basic helix-loop-helix) domain
    Similarity: Contains 1 PAC (PAS-associated C-terminal) domain
    Similarity: Contains 2 PAS (PER-ARNT-SIM) domains


    CLOCK for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CLOCK_HUMAN, O15516
    Function: ARNTL/2-CLOCK heterodimers activate E-box element (5'-CACGTG-3') transcription of a number of proteins
    of the circadian clock. Activates transcription of PER1 and PER2. This transcription is inhibited in a feedback
    loop by PER and CRY proteins. Has intrinsic histone acetyltransferase activity and this enzymatic function
    contributes to chromatin-remodeling events implicated in circadian control of gene expression (By similarity).
    Acetylates primarily histones H3 and H4 (By similarity). Acetylates also a non-histone substrate: ARNTL (By
    similarity). Plays a role in DNA damage response (DDR) signaling during the S phase
    Catalytic activity: Acetyl-CoA + [histone] = CoA + acetyl-[histone]

         Genatlas biochemistry entry for CLOCK:
    CLOCK gene,homolog to murine Clock,regulator of circadian rhythms,with two major transcripts 8 and
    10kb,predominantly expressed in the suprachiasmatic nuclei and cerebellum

         Enzyme Number (IUBMB): EC 2.3.1.481 2

         Gene Ontology (GO): 5/10 molecular function terms (GO ID links to tree view) (see all 10):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000978RNA polymerase II core promoter proximal region sequence-specific DNA binding IDA18411297
    GO:0000982RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity ISS--
    GO:0001190RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription ISS--
    GO:0003677DNA binding ----
    GO:0003700sequence-specific DNA binding transcription factor activity ISS--
         
    CLOCK for ontologies           About GeneDecksing


    Phenotypes:
         11 MGI mutant phenotypes (inferred from 3 alleles(MGI details for Clock):
     adipose tissue  behavior/neurological  cardiovascular system  digestive/alimentary  growth/size 
     homeostasis/metabolism  integument  liver/biliary system  nervous system  no phenotypic analysis 
     reproductive system 

    CLOCK for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Clocktm1.1Rep for CLOCK

       inGenious Targeting Laboratory - Custom generated mouse model solutions for CLOCK 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for CLOCK

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for CLOCK 
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for CLOCK 

    miRNA
    Products:
        
    miRTarBase miRNAs that target CLOCK:
    hsa-mir-141 (MIRT002951), hsa-mir-182 (MIRT005358)

    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat CLOCK
    8/86 QIAGEN miScript miRNA Assays for microRNAs that regulate CLOCK (see all 86):
    hsa-miR-607 hsa-miR-106a hsa-miR-15a hsa-miR-200a hsa-miR-30d hsa-miR-30a hsa-miR-3622b-3p hsa-miR-93
    SwitchGear 3'UTR luciferase reporter plasmidCLOCK 3' UTR sequence
    Inhib. RNA
    Products:
        
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for CLOCK
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat CLOCK

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for CLOCK
    Sirion Biotech Customized adenovirus for overexpression of CLOCK

    Clone
    Products:
         
    Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
    OriGene clones in human, mouse for CLOCK (see all 7)
    OriGene ORF clones in mouse, rat for CLOCK
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: CLOCK (NM_004898)
    Sino Biological Human cDNA Clone for CLOCK
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CLOCK
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CLOCK
    Sirion Biotech Customized lentivirus for stable overexpression of CLOCK 
                         Customized lentivirus expression plasmids for stable overexpression of CLOCK 

    Cell Line
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    GenScript Custom overexpressing Cell Line Services for CLOCK
    Search LifeMap BioReagents cell lines for CLOCK
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLOCK


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for CLOCK About   (see all 8)                                                                                              See pathways by source

    SuperPathContained pathways About
    1Circadian Clock
    Circadian Clock0.40
    Circadian Clock in Mammals0.30
    Circadian rhythm0.35
    2Circadian entrainment
    Dopaminergic synapse0.37
    3Influenza A
    Herpes simplex infection0.33
    4Metabolic States and Circadian Oscillators
    Metabolic States and Circadian Oscillators
    5Diurnally regulated genes with circadian orthologs
    Diurnally regulated genes with circadian orthologs

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    2 Downloadable PowerPoint Slides of QIAGEN Pathway Central Maps for CLOCK
        Metabolic States and Circadian Oscillators
    Circadian Clock in Mammals

    1 Cell Signaling Technology (CST) Pathway for CLOCK
        Chromatin Regulation / Acetylation

    2 BioSystems Pathways for CLOCK
        Diurnally regulated genes with circadian orthologs
    Circadian rhythm pathway


    2        Reactome Pathways for CLOCK
        Circadian Clock
    Circadian Repression of Expression by REV-ERBA


    3         Kegg Pathways  (Kegg details for CLOCK):
        Circadian rhythm
    Dopaminergic synapse
    Herpes simplex infection


    CLOCK for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for CLOCK

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/50 Interacting proteins for CLOCK (O155163 ENSP000003087414) via UniProtKB, MINT, STRING, and/or I2D (see all 50)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ARNTL2Q8WYA13, ENSP000002665034I2D: score=3 STRING: ENSP00000266503
    DBPQ105863, ENSP000002221224I2D: score=2 STRING: ENSP00000222122
    PER2O150553, ENSP000002546574I2D: score=2 STRING: ENSP00000254657
    SIRT1Q96EB63, ENSP000002120154I2D: score=2 STRING: ENSP00000212015
    CRY2Q49AN03, ENSP000004067514I2D: score=1 STRING: ENSP00000406751
    About this table

    Gene Ontology (GO): 5/9 biological process terms (GO ID links to tree view) (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000077DNA damage checkpoint IMP--
    GO:0006355regulation of transcription, DNA-dependent ISS--
    GO:0006357regulation of transcription from RNA polymerase II promoter TAS10198158
    GO:0007165signal transduction TAS10198158
    GO:0007623circadian rhythm TAS10198158

    CLOCK for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    CLOCK for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for CLOCK

    2 HMDB Compounds for CLOCK    About this table
    CompoundSynonyms CAS #PubMed Ids
    Acetyl-CoAS-Acetyl coenzyme A (see all 13)72-89-9--
    Coenzyme AAcetoacetyl coenzyme A sodium salt (see all 21)85-61-0--

    6 Novoseek inferred chemical compound relationships for CLOCK gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    arylalkylamine 54.8 1 17645697 (1)
    melatonin 46 1 17645697 (1)
    fluvoxamine 41.3 3 19347611 (3)
    dopamine 3.55 3 20002961 (1), 17116390 (1)
    oxygen 0 1 11726537 (1)
    nadph 0 1 11441146 (1)

    1 PharmGKB related drug/compound annotation for CLOCK gene    About this table
    Drug/compound PharmGKB Annotation
    lithiumCA  

    Search CenterWatch for drugs/clinical trials and news about CLOCK

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for CLOCK gene (2 alternative transcripts): 
    NM_001267843.1  NM_004898.3  

    Unigene Clusters for CLOCK:

    Clock circadian regulator
    Hs.436975  [show with all ESTs], Hs.689578
    Unigene Representative Sequences: NM_001267843, AK124437
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000309964(uc010igu.1 uc003haz.1 uc003hba.1) ENST00000511124
    ENST00000381322 ENST00000513440 ENST00000479384 ENST00000506747 ENST00000435527
    ENST00000508049 ENST00000506923 ENST00000509151 ENST00000513033

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat CLOCK
    8/86 QIAGEN miScript miRNA Assays for microRNAs that regulate CLOCK (see all 86):
    hsa-miR-607 hsa-miR-106a hsa-miR-15a hsa-miR-200a hsa-miR-30d hsa-miR-30a hsa-miR-3622b-3p hsa-miR-93
    SwitchGear 3'UTR luciferase reporter plasmidCLOCK 3' UTR sequence
    Inhib. RNA
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    Clone
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    OriGene clones in human, mouse for CLOCK (see all 7)
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    GenScript: all cDNA clones in your preferred vector: CLOCK (NM_004898)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CLOCK
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CLOCK
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    OriGene qSTAR qPCR primer pairs in human, mouse for CLOCK
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CLOCK

    Additional mRNA sequence: AK124437.1 

    14 DOTS entries:

    DT.441675  DT.314439  DT.99945732  DT.40214180  DT.101970560  DT.216306  DT.101955682  DT.75158934 
    DT.75193604  DT.95366244  DT.121222253  DT.75102725  DT.91717144  DT.91651650 

    24/76 AceView cDNA sequences (see all 76):

    BP379100 BC041878 AI288889 AI636144 BP337839 AI272643 AA629229 AW170657 
    AA856550 AB002332 AA425089 NM_004898 AA588008 BX097215 AA883954 AA856549 
    CA454629 BE540895 AW069711 BG623849 CD359988 BP346357 AK124437 BQ436907 

    GeneLoc Exon Structure

    5/6 Alternative Splicing Database (ASD) splice patterns (SP) for CLOCK (see all 6)    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b · 7c ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b · 12c ^ 13a · 13b ^ 14a · 14b · 14c ^ 15
    SP1:                                                                                                              -     -                     
    SP2:        -                                   -                                                                                             
    SP3:                                                                                                                                          
    SP4:                                                                                                              -                           
    SP5:                                                                                                                                          


    ECgene alternative splicing isoforms for CLOCK

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    CLOCK expression in normal human tissues (normalized intensities)      CLOCK embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AAACTTGAGC
    CLOCK Expression
    About this image


    CLOCK expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/32 selected tissues (see all 32) fully expand
     
     Skeletal Muscle (Muscoskeletal System)    fully expand to see all 15 entries
             Multinuclear Myocytes Lumbar Back Muscles
             skeletal muscle ; myocytes   
     
     Limb (Muscoskeletal System)    fully expand to see all 6 entries
             Multinuclear Myocytes Forelimb Dorsal Muscles
             limb/hindlimb   
     
     Epithelium
             vagina ; squamous epithelial cells   
     
     Colon (Gastrointestinal Tract)    fully expand to see all 4 entries
             colon ; endothelial cells   
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Hippocampus

    See CLOCK Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CLOCK

    SOURCE GeneReport for Unigene clusters: Hs.436975 Hs.689578

    UniProtKB/Swiss-Prot: CLOCK_HUMAN, O15516
    Tissue specificity: Expressed in all tissues examined including spleen, thymus, prostate, testis, ovary, small
    intestine, colon, leukocytes, heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas. Highest
    levels in testis and skeletal muscle. Low levels in thymus, lung and liver. Expressed in all brain regions with
    highest levels in cerebellum. Highly expressed in the suprachiasmatic nucleus (SCN)

        SABiosciences Expression via Pathway-Focused PCR Arrays including CLOCK: 
              Notch Signaling Targets in human mouse rat
              Circadian Rhythms in human mouse rat

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for CLOCK gene from 6/14 species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Clock1 , 5 circadian locomotor output cycles kaput1, 5 91.04(n)1
    96.67(a)1
      5 (40.63 cM)5
    127531  NM_007715.51  NP_031741.11 
     762121775 
    chicken
    (Gallus gallus)
    Aves CLOCK1 clock homolog (mouse) 82.03(n)
    87.44(a)
      373991  NM_204174.2  NP_989505.2 
    lizard
    (Anolis carolinensis)
    Reptilia CLOCK6
    clock circadian regulator
    82(a)
    1 ↔ 1
    5(104767119-104794656)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.5662 Xenopus laevis circadian rhythmicity protein CLOCK more 74.93(n)    AF227985.1 
    zebrafish
    (Danio rerio)
    Actinopterygii clock2 clock 73.51(n)   30140  AF133306.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Clk1 , 3 positive regulation of transcription,
    DNA-dependent more3
    Clock1
    50(a)3
    46.68(n)1
    38.62(a)1
      3 66A123
    388721  NM_001014576.11  NP_001014576.11 


    ENSEMBL Gene Tree for CLOCK (if available)
    TreeFam Gene Tree for CLOCK (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CLOCK gene
    ARNT22  NPAS22  ARNT2  EPAS12  NPAS32  HIF1A2  SIM22  SIM12  
    HIF3A2  ARNTL2  NPAS12  ARNTL22  
    7 SIMAP similar genes for CLOCK using alignment to 3 protein entries:     CLOCK_HUMAN (see all proteins):
    clock    NPAS2    ARNTL2    ARNTL    ARNT    NCOA2
    HIF3A

    CLOCK for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/2689 SNPs in CLOCK are shown (see all 2689)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs360466241,2
    C--52326121(+) TTTTA-/AA    
       
    /T/TA
    AAAAA
    2 -- int10--------
    rs1392083731,2
    C--56293570(+) AGTGGC/TGCAAT 2 -- ds50010--------
    rs1864937531,2
    --56293620(+) TTCTCA/CTGCCT 2 -- ds50010--------
    rs623036861,2
    C,F--56293659(+) TGCCCG/ACCACC 2 -- ds50012Minor allele frequency- A:0.50NA CSA 4
    rs716642931,2
    C--56293696(+) AGTAGAGAC/-  
            
    AGACA
    2 -- ds50011Minor allele frequency- -:0.50NA 2
    rs801130921,2
    C,F--56293812(+) CAACCG/ATTTTT 2 -- ds50011Minor allele frequency- A:0.02NA 120
    rs1412010301,2
    C--56293815(+) CCGTTC/TTTTCT 2 -- ds50010--------
    rs1506783471,2
    C--56293920(+) TATGCA/GAATAA 2 -- ds50010--------
    rs1155322031,2
    F--56294022(+) AAAATC/GGCTAC 2 -- ds50011Minor allele frequency- G:0.02NA 120
    rs37494721,2
    C,F--56294032(+) CTGCAG/ATAGGC 2 -- ds500111Minor allele frequency- A:0.26EA NA WA 2034

    HapMap Linkage Disequilibrium report for CLOCK (56294070 - 56413305 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for CLOCK:    About this table     
    Variant IDTypeSubtypePubMed ID
    dgv888e201CNV Deletion23290073
    esv2661534CNV Deletion23128226
    esv2727633CNV Deletion23290073
    esv1694176CNV Insertion17803354
    esv269816CNV Insertion20981092
    esv273628CNV Insertion20981092
    nsv10496CNV Loss18304495
    esv5988CNV Gain19470904


    Human Gene Mutation Database (HGMD): CLOCK
    SABiosciences Cancer Mutation PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for CLOCK

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 601851    OMIM disorders: --

    20/41 diseases for CLOCK (see all 41):    About MalaCards
    delayed sleep phase syndrome    advanced sleep phase syndrome    narcolepsy    seasonal affective disorder
    cluster headache    mood disorder    headache    sleep disorder
    autistic disorder    mental disorders    cocaine dependence    bulimia nervosa
    bipolar disorder    bipolar i disorder    pandas    obesity
    eating disorder    schizoaffective disorder    major depressive disorder    smith magenis syndrome

    1 disease from the University of Copenhagen DISEASES database for CLOCK:
    Sleep disorder

    CLOCK for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:  
    Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015

    10 Novoseek inferred disease relationships for CLOCK gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    delayed sleep phase syndrome 75 1 11927136 (1)
    bipolar disorder 48.7 4 20072116 (2), 14582141 (1), 17428266 (1)
    narcolepsy 41.7 2 16125818 (2)
    major depression 39.4 5 10898925 (2), 19347611 (2), 20072116 (1)
    mood disorders 33.8 4 12898572 (1), 20072116 (1), 19708722 (1), 19224106 (1)
    colon carcinoma 22 2 16393700 (1)
    schizophrenia 0 7 17116390 (3), 19224106 (3)
    shock 0 2 17347670 (1)
    tumors 0 5 19148895 (2), 20124474 (1)
    obesity 0 1 20065968 (2), 18314271 (2), 18541547 (1), 19846548 (1) (see all 5)

    Genetic Association Database (GAD): CLOCK
    Human Genome Epidemiology (HuGE) Navigator: CLOCK (103 documents)

    Export disorders for CLOCK gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for CLOCK gene, integrated from 9 sources (see all 222):
    (articles sorted by number of sources associating them with CLOCK)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular cloning and characterization of the human CLOCK gene: expression in the suprachiasmatic nuclei. (PubMed id 10198158)1, 2, 3, 9 Steeves T.D.L.... Takahashi J.S. (1999)
    2. CLOCK gene T3111C polymorphism is associated with Japanese schizophrenics: a preliminary study. (PubMed id 17116390)1, 4, 9 Takao T....Asada T. (2007)
    3. CLOCK gene is implicated in weight reduction in obese patients participating in a dietary programme based on the Mediterranean diet. (PubMed id 20065968)1, 4, 9 Garaulet M....Ordovas J.M. (2010)
    4. CLOCK genetic variation and metabolic syndrome risk: modulation by monounsaturated fatty acids. (PubMed id 19846548)1, 4, 9 Garaulet M....Ordovas J.M. (2009)
    5. CLOCK may Predict the Response to Fluvoxamine Treatment in Japanese Major Depressive Disorder Patients. (PubMed id 19347611)1, 4, 9 Kishi T....Iwata N. (2009)
    6. CLOCK gene 3111C/T polymorphism is not associated with seasonal variations in mood and behavior in Korean college students. (PubMed id 17239050)1, 4, 9 Paik J.W....Kim L. (2007)
    7. Association study of clock gene (CLOCK) and schizophrenia and mood disorders in the Japanese population. (PubMed id 19224106)1, 4, 9 Kishi T....Iwata N. (2009)
    8. Clock genes may influence bipolar disorder susceptibility and dysfunctional circadian rhythm. (PubMed id 18228528)1, 4, 9 Shi J....Liu C. (2008)
    9. Insomnia improvement during antidepressant treatment and CLOCK gene polymorphism. (PubMed id 15952199)1, 4, 9 Serretti A....Smeraldi E. (2005)
    10. Genetic variants in human CLOCK associate with total energy intake and cytokine sleep factors in overweight subjects (GOLDN populati on). (PubMed id 19888304)1, 4, 9 Garaulet M....Ordovas J.M. (2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 9575 HGNC: 2082 AceView: CLOCK Ensembl:ENSG00000134852 euGenes: HUgn9575
    ECgene: CLOCK Kegg: 9575 H-InvDB: CLOCK

    (According to HUGE)
    About This Section
    HUGE: KIAA0334

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for CLOCK Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for CLOCK gene:
    Search GeneIP for patents involving CLOCK

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    About This Section

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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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