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

Gene ID: 117535, updated on 13-Apr-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
Ensembl: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 RNA polymerase II-specific DNA-binding transcription factor binding activity; histone deacetylase binding activity; and transcription coregulator binding activity. Involved in negative regulation of transcription by RNA polymerase II and terminal button organization. Predicted to be located in centrosome; cytoplasm; and nucleoplasm. Predicted to be part of NuRD complex; RNA polymerase II transcription regulator complex; and protein-DNA complex. Orthologous to human CHD4 (chromodomain helicase DNA binding protein 4). [provided by Alliance of Genome Resources, Apr 2022]
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. 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
  2. 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
  3. 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
  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 mediates proliferation and migration of non-small cell lung cancer via the RhoA/ROCK pathway by regulating PHF5A. Xu N, et al. BMC Cancer, 2020 Mar 30. PMID 32228507, Free PMC Article

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 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 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 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 
part_of 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

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
    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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