Chd4 MGI Mouse Gene Detail - MGI:1344380 - chromodomain helicase DNA binding protein 4

Symbol

Chd4
Name

chromodomain helicase DNA binding protein 4
Synonyms

9530019N15Rik, D6Ertd380e, MGC:11769, Mi-2beta

Feature Type

protein coding gene
IDs

MGI:1344380
NCBI Gene: 107932
Alliance

gene page
Transcription Start Sites

11 TSS

Sequence Map

Chr6:125072944-125107554 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 6, 59.28 cM
Mapping Data

4 experiments

SNPs within 2kb

256 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1344380	protein coding gene	Chr6:125072943-125107554 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0031285	protein coding gene	Chr6:128422183-128460379 (+)
A/J	MGP_AJ_G0031255	protein coding gene	Chr6:123579594-123615038 (+)
AKR/J	MGP_AKRJ_G0031183	protein coding gene	Chr6:126955731-126990935 (+)
BALB/cJ	MGP_BALBcJ_G0031263	protein coding gene	Chr6:123175298-123211098 (+)
C3H/HeJ	MGP_C3HHeJ_G0030986	protein coding gene	Chr6:127010644-127052480 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0031719	protein coding gene	Chr6:131803053-131838375 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0028869	protein coding gene	Chr6:120783469-120817619 (+)
CAST/EiJ	MGP_CASTEiJ_G0030367	protein coding gene	Chr6:127222729-127259959 (+)
CBA/J	MGP_CBAJ_G0030947	protein coding gene	Chr6:136856215-136899375 (+)
DBA/2J	MGP_DBA2J_G0031103	protein coding gene	Chr6:122510642-122546164 (+)
FVB/NJ	MGP_FVBNJ_G0031053	protein coding gene	Chr6:121420878-121455455 (+)
LP/J	MGP_LPJ_G0031183	protein coding gene	Chr6:128587596-128626364 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0031091	protein coding gene	Chr6:140897023-140933415 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0031754	protein coding gene	Chr6:126852139-126892781 (+)
PWK/PhJ	MGP_PWKPhJ_G0030082	protein coding gene	Chr6:120750902-120788922 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0029911	protein coding gene	Chr6:124934644-124968331 (+)
WSB/EiJ	MGP_WSBEiJ_G0030452	protein coding gene	Chr6:127220111-127257791 (+)

Human Ortholog

CHD4, chromodomain helicase DNA binding protein 4

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

CHD4, chromodomain helicase DNA binding protein 4
Synonyms

CHD-4, Mi-2b, Mi2-BETA, SIHIWES
Links

HGNC:1919

NCBI Gene ID: 1108

neXtProt AC: NX_Q14839

UniProt: Q14839
Chr Location

12p13.31; chr12:6570082-6607439 (-) GRCh38.p7

Alliance of Genome Resources

Chd4 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: CHD4
Gene Tree

Chd4

Diseases

6 with human CHD4 associations

				Human Disease	Mouse Models
				colon adenocarcinoma IDs colon adenocarcinoma DOID:234 MESH:D003110 NCI:C4349 UMLS_CUI:C0338106
				colorectal cancer IDs colorectal cancer DOID:9256 ICD10CM:C18.9 KEGG:05210 MESH:D015179 NCI:C2956 NCI:C4978 OMIM:114500 UMLS_CUI:C0009404 UMLS_CUI:C0346629
				lung adenocarcinoma IDs lung adenocarcinoma DOID:3910 DOID:4826 EFO:0000571 MESH:D000077192 NCI:C27745 NCI:C3512 UMLS_CUI:C0152013 UMLS_CUI:C1335060
				lung cancer IDs lung cancer DOID:1324 DOID:13075 DOID:1322 DOID:9881 ICD10CM:C34.1 ICD10CM:C34.2 ICD10CM:C34.3 ICD9CM:162.3 ICD9CM:162.4 ICD9CM:162.5 ICD9CM:162.8 OMIM:211980 OMIM:608935 OMIM:612571 OMIM:612593 OMIM:614210 UMLS_CUI:C0024624 UMLS_CUI:C0153491 UMLS_CUI:C0153492 UMLS_CUI:C0153493
				lymphoma IDs lymphoma DOID:0060058 DOID:1033 DOID:353 ICD10CM:C85.9 MESH:D008223 NCI:C3208 NCI:C7065 UMLS_CUI:C0024299 UMLS_CUI:C0598798
				rectum cancer IDs rectum cancer DOID:1993 DOID:1989 ICD10CM:C20 ICD9CM:154.1 MESH:D012004 NCI:C7418 NCI:C9382 UMLS_CUI:C0007113 UMLS_CUI:C0949022

Click on a disease name to see all genes associated with that disease.

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Phenotype Summary

19 phenotypes from 5 alleles in 5 genetic backgrounds
5 phenotypes from multigenic genotypes
39 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	immune system	integument	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	neoplasm	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	vision/eye

Click cells to view annotations.

All Mutations and Alleles

45
Endonuclease-mediated

2
Gene trapped

34
Targeted

9
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

51 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a gene trapped allele exhibit embryonic lethality between E3.5 and E4.5, absent blastocoele failure of trophectoderm function and increased apoptosis in blastocysts.

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All GO Annotations

57
GO References

18

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	establishment of localization	homeostatic process	immune system process	lipid metabolic process	nucleic acid-templated transcription	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	non-membrane-bounded organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

891
Tissues

102
cDNA Data

20
Literature Summary

24

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase chd4

ZFIN chd4a, chd4b

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Chd4 interacts with 187 markers (Mir7-1, Mir7-2, Mir7b, ...) View All

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All Sequences

103
RefSeq

32
UniProt

14
CCDS

CCDS20543.1

Ensembl

ENSMUSG00000063870 (Evidence)
NCBI Gene

107932

			Length	Strain/Species	Flank
genomic	ENSMUSG00000063870	Ensembl Gene Model \| MGI Sequence Detail	34611	C57BL/6J	± kb
transcript	ENSMUST00000112390	Ensembl \| MGI Sequence Detail	6537	Not Applicable
polypeptide	ENSMUSP00000108009	Ensembl \| MGI Sequence Detail	1922	Not Applicable

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UniProt

14 Sequences
Protein Ontology

PR:000005410 chromodomain-helicase-DNA-binding protein 4

(term hierarchy)
EC

3.6.4.12
InterPro Domains

IPR012957 CHD, C-terminal 2

IPR012958 CHD, N-terminal

IPR009462 CHD subfamily II, SANT-like domain

IPR000953 Chromo/chromo shadow domain

IPR023780 Chromo domain

IPR016197 Chromo-like domain superfamily

IPR002464 DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site

IPR009463 Domain of unknown function DUF1087

IPR001650 Helicase, C-terminal

IPR014001 Helicase superfamily 1/2, ATP-binding domain

IPR027417 P-loop containing nucleoside triphosphate hydrolase

IPR038718 SNF2-like, N-terminal domain superfamily

IPR000330 SNF2, N-terminal

IPR011011 Zinc finger, FYVE/PHD-type

IPR019787 Zinc finger, PHD-finger

IPR001965 Zinc finger, PHD-type

IPR019786 Zinc finger, PHD-type, conserved site

IPR013083 Zinc finger, RING/FYVE/PHD-type

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All nucleic 23

cDNA 21

Primer pair 1

Other 1

Microarray probesets 4

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MGI:1196402, MGI:1889374, MGI:1924653, MGI:2384852

Summaries

All 112

Developmental Gene Expression 24

Gene Ontology 18

Phenotypes 39
Earliest

J:54004 Kim J, et al., Ikaros DNA-binding proteins direct formation of chromatin remodeling complexes in lymphocytes. Immunity. 1999 Mar;10(3):345-55
Latest

J:328872 El Abdellaoui-Soussi F, et al., Interplay between the Chd4/NuRD Complex and the Transcription Factor Znf219 Controls Cardiac Cell Identity. Int J Mol Sci. 2022 Aug 24;23(17)

TSS for Chd4:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr2015	Chr6:125072973-125072999 (+)	42 bp
Tssr58906	Chr6:125073095-125073104 (+)	156 bp
Tssr58907	Chr6:125073108-125073121 (+)	171 bp
Tssr58908	Chr6:125073132-125073152 (+)	198 bp
Tssr58912	Chr6:125074040-125074072 (+)	1,112 bp
Tssr58913	Chr6:125077831-125077845 (+)	4,894 bp
Tssr58914	Chr6:125080393-125080401 (+)	7,453 bp
Tssr58915	Chr6:125090474-125090503 (+)	17,545 bp
Tssr58916	Chr6:125090858-125090875 (+)	17,923 bp
Tssr58917	Chr6:125099433-125099467 (+)	26,506 bp
Tssr58918	Chr6:125106826-125106835 (+)	33,887 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Copyright, and Privacy Statement Send questions and comments to User Support.	last database update 03/14/2023 MGI 6.22