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

Summary

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 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
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

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_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Submit: New GeneRIF Correction

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

D6Ertd380e (e-PCR), detects polymorphism
- UniSTS:167483

RH143540 (e-PCR)
- UniSTS:232786

AA963793 (e-PCR)
- UniSTS:243386

RH64827 (e-PCR)
- UniSTS:78038

MARC_34374-34375:1062687298:1 (e-PCR)
- UniSTS:466943

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
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

Go to the top of the page Help

Preferred Names: chromodomain-helicase-DNA-binding protein 4

Names: Mi-2 autoantigen

NP_001414103.1

EC 3.6.4.12

XP_006237458.1

EC 3.6.4.12

XP_006237459.1

EC 3.6.4.12

XP_006237460.1

EC 3.6.4.12

XP_006237461.1

EC 3.6.4.12

XP_006237462.1

EC 3.6.4.12

XP_006237463.1

EC 3.6.4.12

XP_063141495.1

EC 3.6.4.12

XP_063141496.1

EC 3.6.4.12

XP_063141497.1

EC 3.6.4.12

XP_063141498.1

EC 3.6.4.12

XP_063141499.1

EC 3.6.4.12

XP_063141500.1

EC 3.6.4.12

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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)

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

NC_086022.1 Reference GRCr8

Range

159584623..159617867

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
XM_063285429.1 → XP_063141499.1 chromodomain-helicase-DNA-binding protein 4 isoform X11
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
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
XM_063285425.1 → XP_063141495.1 chromodomain-helicase-DNA-binding protein 4 isoform X5
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
XM_063285427.1 → XP_063141497.1 chromodomain-helicase-DNA-binding protein 4 isoform X9
XM_063285428.1 → XP_063141498.1 chromodomain-helicase-DNA-binding protein 4 isoform X10
XM_063285426.1 → XP_063141496.1 chromodomain-helicase-DNA-binding protein 4 isoform X7
XM_063285430.1 → XP_063141500.1 chromodomain-helicase-DNA-binding protein 4 isoform X12