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CHD4 Gene

protein-coding   GIFtS: 68
GCID: GC12M006679

Chromodomain Helicase DNA Binding Protein 4

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Chromodomain Helicase DNA Binding Protein 41 2     Mi2-BETA2
CHD-42 3     Chromodomain-Helicase-DNA-Binding Protein 42
ATP-Dependent Helicase CHD42 3     EC 3.6.4.123
Mi-2 Autoantigen 218 KDa Protein2 3     Mi2-beta3
Mi-2b2     EC 3.6.18

External Ids:    HGNC: 19191   Entrez Gene: 11082   Ensembl: ENSG000001116427   OMIM: 6032775   UniProtKB: Q148393   

Export aliases for CHD4 gene to outside databases

Previous GC identifers: GC12M006534 GC12M006653 GC12M006558 GC12M006549 GC12M006533


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for CHD4 Gene:
The product of this gene belongs to the SNF2/RAD54 helicase family. It represents the main component of the
nucleosome remodeling and deacetylase complex and plays an important role in epigenetic transcriptional
repression. Patients with dermatomyositis develop antibodies against this protein. (provided by RefSeq, Jul 2008)

GeneCards Summary for CHD4 Gene:
CHD4 (chromodomain helicase DNA binding protein 4) is a protein-coding gene. Diseases associated with CHD4 include right bundle branch block, and dermatomyositis. GO annotations related to this gene include RNA polymerase II repressing transcription factor binding and ATP-dependent DNA helicase activity. An important paralog of this gene is CHD6.

UniProtKB/Swiss-Prot: CHD4_HUMAN, Q14839
Function: Component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by
deacetylating histones

Gene Wiki entry for CHD4 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000012.12  NT_009759.17  NC_018923.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the CHD4 gene promoter:
         E2F-3a   E2F-4   E2F-5   E2F-2   GATA-2   Max   E2F-1   E2F   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCHD4 promoter sequence
   Search Chromatin IP Primers for CHD4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CHD4


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

Entrez Gene cytogenetic band: 12p13   Ensembl cytogenetic band:  12p13.31   HGNC cytogenetic band: 12p13

CHD4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CHD4 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12M006679:  view genomic region     (about GC identifiers)

Start:
6,679,248 bp from pter      End:
6,716,642 bp from pter
Size:
37,395 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: CHD4_HUMAN, Q14839 (See protein sequence)
Recommended Name: Chromodomain-helicase-DNA-binding protein 4  
Size: 1912 amino acids; 218005 Da
Subunit: Central component of the nucleosome remodeling and histone deacetylase (NuRD) repressor complex.
Interacts directly with IKFZ1 in the NuRD complex. Interacts with TRIM27. Part of a complex containing ATR and
HDAC2. Interacts with KLF1; the interaction depends on sumoylation of KLF1, and leads to its transcriptional
repression. Interacts with ZGPAT; the interaction is direct. Interacts with BCL6, BRD4 and PCNT
Miscellaneous: One of the main antigens reacting with anti-MI-2 positive sera of dermatomyositis
5 PDB 3D structures from and Proteopedia for CHD4:
1MM2 (3D)        1MM3 (3D)        2EE1 (3D)        2L5U (3D)        2L75 (3D)    
Secondary accessions: Q8IXZ5
Alternative splicing: 2 isoforms:  Q14839-1   Q14839-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for CHD4: NX_Q14839

Explore proteomics data for CHD4 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys504, Lys987, Lys1057, Lys1092, Lys1837, Lys1852, Lys1855, Lys1865
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for CHD4 (Q14839) (see all 21)
     DEAHRLK  TGTPLQN  NQSKFFR  FLLSTRA 


    See CHD4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001264.2  
    ENSEMBL proteins: 
     ENSP00000440392   ENSP00000440542   ENSP00000437506   ENSP00000444614   ENSP00000312419  
     ENSP00000349508  
    Reactome Protein details: Q14839

    CHD4 Human Recombinant Protein Products:

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    Browse OriGene Protein Over-expression Lysates
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    Novus Biologicals CHD4 Protein
    Novus Biologicals CHD4 Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    ProSpec Recombinant Protein for CHD4
    Cloud-Clone Corp. Proteins for CHD4

    CHD4 Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of CHD4
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    Cell Signaling Technology (CST) Antibodies for CHD4  (CHD-4)
    OriGene Antibodies for CHD4
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    Abcam antibodies for CHD4
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    ThermoFisher Antibody for CHD4
    LSBio Antibodies in human, mouse, rat for CHD4

    CHD4 Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    GenScript Custom Assay Services for CHD4
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for CHD4
    Cloud-Clone Corp. CLIAs for CHD4


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    PHF: Zinc fingers, PHD-type

    Selected InterPro protein domains (see all 19):
     IPR009463 DUF1087
     IPR001841 Znf_RING
     IPR001965 Znf_PHD
     IPR000953 Chromo_domain/shadow
     IPR000330 SNF2_N

    Graphical View of Domain Structure for InterPro Entry Q14839

    ProtoNet protein and cluster: Q14839

    Selected Blocks protein domains (see all 7):
    IPB000330 SNF2 related domain
    IPB000953 Chromo domain
    IPB001841 Zn-finger
    IPB001965 Zn-finger-like
    IPB002464 ATP-dependent helicase


    UniProtKB/Swiss-Prot: CHD4_HUMAN, Q14839
    Similarity: Belongs to the SNF2/RAD54 helicase family
    Similarity: Contains 2 chromo domains
    Similarity: Contains 1 helicase ATP-binding domain
    Similarity: Contains 1 helicase C-terminal domain
    Similarity: Contains 2 PHD-type zinc fingers


    CHD4 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,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CHD4_HUMAN, Q14839
    Function: Component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by
    deacetylating histones
    Catalytic activity: ATP + H(2)O = ADP + phosphate

         Genatlas biochemistry entry for CHD4:
    DNA binding protein with two chromatin organization (chromo) domains,and a helicase domain,4,component of the
    chromatin remodeling complex

         Enzyme Numbers (IUBMB): EC 3.6.12 EC 3.6.4.121

         Gene Ontology (GO): Selected molecular function terms (see all 12):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001103RNA polymerase II repressing transcription factor binding IPI--
    GO:0003676nucleic acid binding ----
    GO:0003677DNA binding IEA--
    GO:0004003ATP-dependent DNA helicase activity TAS9326634
    GO:0004386helicase activity ----
         
    CHD4 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for CHD4:
     Decreased viability  Increased cell death in HCT116 

         4 MGI mutant phenotypes (inferred from 3 alleles(MGI details for Chd4):
     cellular  hematopoietic system  immune system  no phenotypic analysis 

    CHD4 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Chd4tm1.2Kge for CHD4

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CHD4
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for CHD4

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for CHD4
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for CHD4

    miRNA
    Products:
        
    miRTarBase miRNAs that target CHD4:
    hsa-mir-15a-5p (MIRT051330), hsa-mir-615-3p (MIRT039684), hsa-mir-98-5p (MIRT027771), hsa-mir-193b-3p (MIRT016455), hsa-mir-491-5p (MIRT004656), hsa-mir-17-5p (MIRT050859), hsa-let-7b-5p (MIRT032436), hsa-mir-877-3p (MIRT036982), hsa-mir-484 (MIRT041696), hsa-mir-197-3p (MIRT048143)

    Block miRNA regulation of human, mouse, rat CHD4 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate CHD4 (see all 16):
    hsa-miR-98 hsa-miR-3140-3p hsa-miR-300 hsa-let-7d hsa-miR-381 hsa-let-7c hsa-let-7i hsa-miR-548aa
    SwitchGear 3'UTR luciferase reporter plasmidCHD4 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for CHD4
    Predesigned siRNA for gene silencing in human, mouse, rat CHD4

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for CHD4

    Clone
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    OriGene clones in human, mouse for CHD4 (see all 5)
    OriGene ORF clones in mouse, rat for CHD4
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: CHD4 (NM_001273)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CHD4
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CHD4

    Cell Line
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    Browse ESI BIO Cell Lines and PureStem Progenitors for CHD4 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CHD4


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    CHD4_HUMAN, Q14839: Nucleus. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Note=Associates
    with centrosomes in interphase
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytoskeleton5
    nucleus5

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005737cytoplasm IDA17626165
    GO:0005813centrosome IDA17626165
    GO:0016581NuRD complex IDA19644445
    GO:0043234protein complex ----

    CHD4 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    SuperPaths for CHD4 About   (see all 8)  
    See pathways by source

    SuperPathContained pathways About
    1RNA Polymerase I Promoter Opening
    RNA Polymerase I Transcription0.78
    RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription0.73
    RNA Polymerase I Promoter Clearance0.78
    2RNA Polymerase I Promoter Escape
    RNA Polymerase I Transcription Initiation0.55
    3Gene Expression
    Gene Expression0.40
    4Development NOTCH1 mediated pathway for NF KB activity modulation
    Transcription Sin3 and NuRD in transcription regulation0.35
    5Macrophage Differentiation and Growth Inhibition by METS
    DNA Methylation and Transcriptional Repression0.30

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for CHD4
        DNA Methylation and Transcriptional Repression

    1 Cell Signaling Technology (CST) Pathway for CHD4
        Chromatin Regulation / Acetylation

    1 GeneGo (Thomson Reuters) Pathway for CHD4
        Transcription Sin3 and NuRD in transcription regulation

    1 BioSystems Pathway for CHD4
        Signaling events mediated by HDAC Class I

    1 Reactome Pathway for CHD4
        RNA Polymerase I Transcription Initiation


    1 Kegg Pathway  (Kegg details for CHD4):
        Viral carcinogenesis


    CHD4 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Arrays including CHD4: 
              Tumor Metastasis in human mouse rat
              Epigenetic Chromatin Remodeling Factors in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for CHD4

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

    Selected Interacting proteins for CHD4 (Q148391, 2, 3 ENSP000003495084) via UniProtKB, MINT, STRING, and/or I2D (see all 806)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H3AP684313, ENSP000003502754I2D: score=1 STRING: ENSP00000350275
    HIST1H3BP684313I2D: score=1 
    HIST1H3CP684313I2D: score=1 
    HIST1H3DP684313I2D: score=1 
    HIST1H3EP684313I2D: score=1 
    About this table

    Gene Ontology (GO): 5 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-templated IEA--
    GO:0006355regulation of transcription, DNA-templated ----
    GO:0006357regulation of transcription from RNA polymerase II promoter TAS9326634
    GO:0016568chromatin modification IEA--
    GO:0032508DNA duplex unwinding TAS9326634

    CHD4 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for CHD4



    (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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for CHD4 gene: 
    NM_001273.2  

    Unigene Cluster for CHD4:

    Chromodomain helicase DNA binding protein 4
    Hs.162233  [show with all ESTs]
    Unigene Representative Sequence: BC038596
    15 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000544484 ENST00000544040 ENST00000535717 ENST00000542717 ENST00000536301
    ENST00000540960 ENST00000537634 ENST00000545083 ENST00000536999 ENST00000535810
    ENST00000545942 ENST00000430771 ENST00000545584 ENST00000309577(uc001qpp.3)
    ENST00000357008(uc001qpn.3 uc001qpo.3)
    miRNA
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    Block miRNA regulation of human, mouse, rat CHD4 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate CHD4 (see all 16):
    hsa-miR-98 hsa-miR-3140-3p hsa-miR-300 hsa-let-7d hsa-miR-381 hsa-let-7c hsa-let-7i hsa-miR-548aa
    SwitchGear 3'UTR luciferase reporter plasmidCHD4 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat CHD4
    Clone
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    OriGene clones in human, mouse for CHD4 (see all 5)
    OriGene ORF clones in mouse, rat for CHD4
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: CHD4 (NM_001273)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CHD4
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CHD4
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for CHD4
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat CHD4
      QuantiTect SYBR Green Assays in human, mouse, rat CHD4
      QuantiFast Probe-based Assays in human, mouse, rat CHD4

    Additional mRNA sequence: 

    AK128741.1 BC014964.1 BC025962.1 BC038596.1 CR936680.1 X86691.1 

    Selected DOTS entries (see all 37):

    DT.450173  DT.91770737  DT.92066676  DT.101965737  DT.100039470  DT.121195024  DT.100831846  DT.95122233 
    DT.121194989  DT.121195105  DT.100831848  DT.95122343  DT.100831851  DT.121195138  DT.97814519  DT.100039469 
    DT.100831843  DT.75111364  DT.92040119  DT.95122287  DT.100032934  DT.100039471  DT.100831845  DT.102835948 

    Selected AceView cDNA sequences (see all 213):

    BM785630 BQ687173 CB112094 BE503137 AU130723 BU184696 AA380377 BE080730 
    BQ221803 CN482904 BQ437443 BM475669 T11014 BQ684399 BU855947 BU182542 
    BP377961 BQ774777 BQ877361 BQ937692 AI806023 BM469915 BM818068 BQ720569 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for CHD4 (see all 33)    About this scheme

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

    ExUns: 14b · 14c ^ 15 ^ 16 ^ 17a · 17b · 17c ^ 18 ^ 19a · 19b ^ 20a · 20b ^ 21a · 21b ^ 22 ^ 23a · 23b ^ 24a · 24b ^ 25 ^ 26a · 26b · 26c · 26d ^ 27 ^ 28a ·
    SP1:                                                                                                                                                            
    SP2:                                                                                                                                                            
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                                            

    ExUns: 28b ^ 29a · 29b · 29c ^ 30a · 30b · 30c ^ 31a · 31b ^ 32a · 32b · 32c ^ 33a · 33b · 33c · 33d ^ 34a · 34b ^ 35a · 35b ^ 36a · 36b ^ 37 ^ 38a · 38b · 38c ^
    SP1:                                                                                                                                                            
    SP2:                          -                                                                                                                                 
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                                            

    ExUns: 39a · 39b ^ 40 ^ 41 ^ 42a · 42b ^ 43 ^ 44a ·
    SP1:                                                
    SP2:                                                
    SP3:                                                
    SP4:                                                
    SP5:                                                


    ECgene alternative splicing isoforms for CHD4

    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    CHD4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CAGCAGTAGC
    CHD4 Expression
    About this image


    CHD4 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 10) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Ovarian Mesenchymal Stroma Cells Ovary Interstitium
             Oviduct
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
     
     Bone (Muscoskeletal System)
             Bone Marrow
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
    CHD4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CHD4 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.162233
        Pathway & Disease-focused RT2 Profiler PCR Arrays including CHD4: 
              Tumor Metastasis in human mouse rat
              Epigenetic Chromatin Remodeling Factors in human mouse rat

    Primer
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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)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for CHD4 gene from Selected species (see all 19)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Chd41 , 5 chromodomain helicase DNA binding protein 41, 5 91.27(n)1
    98.69(a)1
      6 (59.28 cM)5
    1079321  NM_145979.21  NP_666091.11 
     1250959815 
    chicken
    (Gallus gallus)
    Aves CHD41 chromodomain helicase DNA binding protein 4 78.84(n)
    91.25(a)
      418278  XM_003640441.2  XP_003640489.2 
    lizard
    (Anolis carolinensis)
    Reptilia CHD46
    chromodomain helicase DNA binding protein 4
    90(a)
    1 ↔ 1
    GL343381.1(733743-766721)
    African clawed frog
    (Xenopus laevis)
    Amphibia b230399n07-prov2 chromodomain helicase DNA binding protein 4 78.57(n)    BC046866.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.271882 Transcribed sequence with moderate similarity to protein more 79.65(n)    CA473451.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Mi-23 chromatin assembly/disassembly ATP
    dependent DNA more
    62(a)
    (best of 2)
        --
    worm
    (Caenorhabditis elegans)
    Secernentea let-4181 let-418 59.33(n)
    61(a)
      178970  NM_072122.4  NP_504523.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes CHD16
    Chromatin remodeler that regulates various aspects...
    25(a)
    1 → many
    V(505392-509798) YER164W
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons PKR21 PKR2 53.18(n)
    46.49(a)
      829320  NM_119341.2  NP_194918.2 
    rice
    (Oryza sativa)
    Liliopsida Os.109052 Oryza sativa (japonica cultivar-group) cDNA cloneJ more 70.83(n)    NM_187372.1 


    ENSEMBL Gene Tree for CHD4 (if available)
    TreeFam Gene Tree for CHD4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CHD4 gene
    CHD62  CHD52  CHD92  CHD12  CHD72  CHD82  CHD32  CHD22  
    13 SIMAP similar genes for CHD4 using alignment to 5 protein entries:     CHD4_HUMAN (see all proteins):
    DKFZp434P202    DKFZp434K213    AIRE    CHD5    CHD3    SHPRH
    SP110    PHF21A    SMARCA5    CHD1L    CHD8    HELLS
    SMARCA1

    CHD4 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for CHD4 (see all 738)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs22679681,2
    C,F,A,H--6679743(+) CAGAAG/AGAAGG 1 -- ut31 ese3 trp315Minor allele frequency- A:0.20EA NS NA 3388
    rs1164607311,2
    C--6679876(+) GACCCG/AAGGAG 1 -- int12Minor allele frequency- A:0.00WA EU 1441
    rs1159273771,2
    C--6679898(+) GATGAT/CAGGAA 1 -- int11Minor allele frequency- C:0.01WA 118
    rs1511017441,2
    C--6680007(+) GAAGAA/GGTGGT 1 -- int10--------
    rs2020490231,2
    C--6680017(+) TGTCAA/GGAAGA 1 -- int11Minor allele frequency- G:0.00EU 1323
    rs1995399101,2
    --6680031(+) TGGTCC/GTACCT 1 -- int10--------
    rs2020190641,2
    --6680053(+) GGTTCA/GGGTGC 2 P syn10--------
    rs2011219361,2
    --6680087(+) TGTTAA/CGCTCT 2 R L mis10--------
    rs2003624761,2
    C--6680223(+) GGTGGT/CGAGCT 1 -- int11Minor allele frequency- C:0.00EU 685
    rs1842051091,2
    --6680499(+) CCCCAC/GCTCCA 1 -- int10--------

    HapMap Linkage Disequilibrium report for CHD4 (6679248 - 6716642 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for CHD4:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv1065323CNV Deletion17803354
    esv2027881CNV Deletion18987734
    esv2675369CNV Deletion23128226
    nsv509452CNV Insertion20534489
    nsv832322CNV Loss17160897
    nsv826210CNV Gain20364138
    nsv826211CNV Gain20364138

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing CHD4
    DNA2.0 Custom Variant and Variant Library Synthesis for CHD4

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 603277    OMIM disorders: --

    11 diseases for CHD4:    
    About MalaCards
    right bundle branch block    dermatomyositis    myopia    mental retardation
    tonsillitis    endotheliitis    hiv-1    thyroiditis
    breast cancer    cerebritis    malaria

    1 disease from the University of Copenhagen DISEASES database for CHD4:
    Right bundle branch block

    CHD4 for disorders           About GeneDecksing


    Export disorders for CHD4 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)
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    PubMed articles for CHD4 gene, integrated from 10 sources (see all 114):
    (articles sorted by number of sources associating them with CHD4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The major dermatomyositis specific Mi-2 autoantigen is a presumed helicase involved in transcriptional activation. (PubMed id 7575689)1, 2, 3 Seelig H.P.... Genth E. (Arthritis Rheum. 1995)
    2. Molecular association between ATR and two components of the nucleosome remodeling and deacetylating complex, HDAC2 and CHD4. (PubMed id 10545197)1, 2, 9 Schmidt D.R. and Schreiber S.L. (Biochemistry 1999)
    3. Mi-2 beta associates with BRG1 and RET finger protein at the distinct regions with transcriptional activating and repressing abilities. (PubMed id 14530259)1, 2, 9 Shimono Y....Takahashi M. (J. Biol. Chem. 2003)
    4. Chromatin deacetylation by an ATP-dependent nucleosome remodelling complex. (PubMed id 9804427)1, 2, 9 Tong J.K....Schreiber S.L. (Nature 1998)
    5. ZIP: a novel transcription repressor, represses EGFR oncogene and suppresses breast carcinogenesis. (PubMed id 19644445)1, 2 Li R.... Shang Y. (EMBO J. 2009)
    6. Chromatin remodeling proteins interact with pericentrin to regulate centrosome integrity. (PubMed id 17626165)1, 2 Sillibourne J.E.... Doxsey S.J. (Mol. Biol. Cell 2007)
    7. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (Cell 2006)
    8. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    9. Engineering a protein scaffold from a PHD finger. (PubMed id 12842043)1, 2 Kwan A.H.Y....Mackay J.P. (Structure 2003)
    10. Two forms of the major antigenic protein of the dermatomyositis-specific Mi-2 autoantigen. (PubMed id 8843877)1, 3 Seelig H.P....Frank M.B. (Arthritis Rheum. 1996)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    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)
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    Entrez Gene: 1108 HGNC: 1919 AceView: CHD4.1 Ensembl:ENSG00000111642 euGenes: HUgn1108
    ECgene: CHD4 Kegg: 1108 H-InvDB: CHD4

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for CHD4 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for CHD4 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for CHD4 gene:
    Search GeneIP for patents involving CHD4

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



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