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    Chd4 chromodomain helicase DNA binding protein 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 117535, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Chd4provided by RGD
    Official Full Name
    chromodomain helicase DNA binding protein 4provided by RGD
    Primary source
    RGD:620064
    See related
    EnsemblRapid:ENSRNOG00000018309 AllianceGenome:RGD:620064
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Mi-2
    Summary
    Predicted to enable several functions, including ATP hydrolysis activity; histone deacetylase binding activity; and transcription corepressor activity. Involved in negative regulation of transcription by RNA polymerase II; regulation of synapse assembly; and terminal button organization. Is active in cerebellar granule cell to Purkinje cell synapse. Human ortholog(s) of this gene implicated in Sifrim-Hitz-Weiss syndrome; colorectal cancer (multiple); lung cancer (multiple); and lymphoma. Orthologous to human CHD4 (chromodomain helicase DNA binding protein 4). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 415.0), Kidney (RPKM 398.2) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Chd4 in Genome Data Viewer
    Location:
    4q42
    Exon count:
    40
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (159584623..159617867)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (157898503..157931632)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (157612531..157645660)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene lysophosphatidic acid receptor 5 Neighboring gene transfer RNA proline (anticodon AGG) 37 Neighboring gene uncharacterized LOC120102389 Neighboring gene small Cajal body-specific RNA 11 Neighboring gene NOP2 nucleolar protein Neighboring gene intermediate filament family orphan 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Anisoosmotic regulation of the Mi-2 autoantigen mRNA in H4IIE rat hepatoma cells and primary hepatocytes. Hammermann R, et al. FEBS Lett, 1998 Sep 11. PMID 9755851
    2. Characteristics of genomic alterations of lung adenocarcinoma in young never-smokers. Luo W, et al. Int J Cancer, 2018 Oct 1. PMID 29667179, Free PMC Article
    3. Prognostic significance of Cytokeratin 20-positive lymph node vascular endothelial growth factor A mRNA and chromodomain helicase DNA binding protein 4 in pN0 colorectal cancer patients. Wong SCC, et al. Oncotarget, 2018 Jan 23. PMID 29467924, Free PMC Article
    4. Association of the chromodomain helicase DNA-binding protein 4 (CHD4) missense variation p.D140E with cancer: potential interaction with smoking. Yamada M, et al. Genes Chromosomes Cancer, 2015 Feb. PMID 25407497
    5. CHD4-mediated loss of E-cadherin determines metastatic ability in triple-negative breast cancer cells. Luo CW, et al. Exp Cell Res, 2018 Feb 1. PMID 29305962

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ATP hydrolysis activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ATP-dependent chromatin remodeler activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ATP-dependent chromatin remodeler activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II-specific DNA-binding transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables double-stranded DNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables forked DNA-dependent helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables four-way junction helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone deacetylase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables single-stranded 3'-5' DNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transcription coregulator binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription corepressor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA duplex unwinding IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in double-strand break repair via homologous recombination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of synapse assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of synapse assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in terminal button organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of NuRD complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of NuRD complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of RNA polymerase II transcription regulator complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in centrosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cerebellar granule cell to Purkinje cell synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cerebellar granule cell to Purkinje cell synapse IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in chromosome, telomeric region ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of protein-DNA complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in site of DNA damage ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    chromodomain-helicase-DNA-binding protein 4
    Names
    Mi-2 autoantigen
    NP_001414103.1
    XP_006237458.1
    XP_006237459.1
    XP_006237460.1
    XP_006237461.1
    XP_006237462.1
    XP_006237463.1
    XP_063141495.1
    XP_063141496.1
    XP_063141497.1
    XP_063141498.1
    XP_063141499.1
    XP_063141500.1

    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.

    mRNA and Protein(s)

    1. NM_001427174.1 → NP_001414103.1  chromodomain-helicase-DNA-binding protein 4

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000004
      Related
      ENSRNOP00000091626.2, ENSRNOT00000107359.2

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086022.1 Reference GRCr8

      Range
      159584623..159617867
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006237396.5 → XP_006237458.1  chromodomain-helicase-DNA-binding protein 4 isoform X1

      UniProtKB/TrEMBL
      A0A8I6ACF8
      Conserved Domains (11) summary
      smart00298
      Location:622 → 676
      CHROMO; Chromatin organization modifier domain
      cd00024
      Location:540 → 577
      CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...
      cd00046
      Location:746 → 904
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd15531
      Location:372 → 414
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:451 → 493
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam00176
      Location:729 → 1025
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1068 → 1164
      Helicase_C; Helicase conserved C-terminal domain
      pfam06461
      Location:1413 → 1549
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:1302 → 1352
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:164 → 216
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:1770 → 1940
      CHDCT2; CHDCT2 (NUC038) domain

    2. XM_006237397.5 → XP_006237459.1  chromodomain-helicase-DNA-binding protein 4 isoform X2

      UniProtKB/TrEMBL
      A0A8I6ACF8
      Conserved Domains (11) summary
      smart00298
      Location:622 → 676
      CHROMO; Chromatin organization modifier domain
      cd00024
      Location:540 → 577
      CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...
      cd00046
      Location:746 → 904
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd15531
      Location:372 → 414
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:451 → 493
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam00176
      Location:729 → 1025
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1068 → 1164
      Helicase_C; Helicase conserved C-terminal domain
      pfam06461
      Location:1385 → 1521
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:1302 → 1352
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:164 → 216
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:1742 → 1913
      CHDCT2; CHDCT2 (NUC038) domain

    3. XM_006237399.5 → XP_006237461.1  chromodomain-helicase-DNA-binding protein 4 isoform X6

      UniProtKB/TrEMBL
      A0A8I6ACF8
      Conserved Domains (11) summary
      smart00298
      Location:615 → 669
      CHROMO; Chromatin organization modifier domain
      cd00024
      Location:533 → 570
      CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...
      cd00046
      Location:739 → 897
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd15531
      Location:365 → 407
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:444 → 486
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam00176
      Location:722 → 1018
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1061 → 1157
      Helicase_C; Helicase conserved C-terminal domain
      pfam06461
      Location:1378 → 1514
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:1295 → 1345
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:157 → 209
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:1735 → 1906
      CHDCT2; CHDCT2 (NUC038) domain

    4. XM_063285429.1 → XP_063141499.1  chromodomain-helicase-DNA-binding protein 4 isoform X11

    5. XM_006237401.5 → XP_006237463.1  chromodomain-helicase-DNA-binding protein 4 isoform X3

      UniProtKB/TrEMBL
      A0A8I6ACF8, E9PU01
      Related
      ENSRNOP00000052823.5, ENSRNOT00000055970.6
      Conserved Domains (11) summary
      smart00298
      Location:622 → 676
      CHROMO; Chromatin organization modifier domain
      cd00024
      Location:540 → 577
      CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...
      cd00046
      Location:746 → 904
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd15531
      Location:372 → 414
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:451 → 493
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam00176
      Location:729 → 1025
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1068 → 1164
      Helicase_C; Helicase conserved C-terminal domain
      pfam06461
      Location:1385 → 1521
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:1302 → 1352
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:164 → 216
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:1742 → 1912
      CHDCT2; CHDCT2 (NUC038) domain

    6. XM_006237398.5 → XP_006237460.1  chromodomain-helicase-DNA-binding protein 4 isoform X4

      UniProtKB/TrEMBL
      A0A8I6ACF8
      Conserved Domains (11) summary
      smart00298
      Location:622 → 676
      CHROMO; Chromatin organization modifier domain
      cd00024
      Location:540 → 577
      CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...
      cd00046
      Location:746 → 904
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd15531
      Location:372 → 414
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:451 → 493
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam00176
      Location:729 → 1025
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1068 → 1164
      Helicase_C; Helicase conserved C-terminal domain
      pfam06461
      Location:1384 → 1520
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:1301 → 1351
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:164 → 216
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:1741 → 1912
      CHDCT2; CHDCT2 (NUC038) domain

    7. XM_063285425.1 → XP_063141495.1  chromodomain-helicase-DNA-binding protein 4 isoform X5

    8. XM_006237400.5 → XP_006237462.1  chromodomain-helicase-DNA-binding protein 4 isoform X8

      UniProtKB/TrEMBL
      A0A8I6ACF8
      Conserved Domains (11) summary
      smart00298
      Location:609 → 663
      CHROMO; Chromatin organization modifier domain
      cd00024
      Location:527 → 564
      CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...
      cd00046
      Location:733 → 891
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd15531
      Location:359 → 401
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:438 → 480
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam00176
      Location:716 → 1012
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1055 → 1151
      Helicase_C; Helicase conserved C-terminal domain
      pfam06461
      Location:1372 → 1508
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:1289 → 1339
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:164 → 216
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:1729 → 1900
      CHDCT2; CHDCT2 (NUC038) domain

    9. XM_063285427.1 → XP_063141497.1  chromodomain-helicase-DNA-binding protein 4 isoform X9

    10. XM_063285428.1 → XP_063141498.1  chromodomain-helicase-DNA-binding protein 4 isoform X10

    11. XM_063285426.1 → XP_063141496.1  chromodomain-helicase-DNA-binding protein 4 isoform X7

    12. XM_063285430.1 → XP_063141500.1  chromodomain-helicase-DNA-binding protein 4 isoform X12

    Nucleotide Protein Strain
    Heading Accession and Version

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