Chd9 MGI Mouse Gene Detail - MGI:1924001 - chromodomain helicase DNA binding protein 9

Symbol

Chd9
Name

chromodomain helicase DNA binding protein 9
Synonyms

1810014J18Rik, 9030205D12Rik, A330063D19Rik, AD013, mKIAA0308

Feature Type

protein coding gene
IDs

MGI:1924001
NCBI Gene: 109151
Alliance

gene page
Transcription Start Sites

16 TSS

Sequence Map

Chr8:91554980-91781144 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 8, 44.25 cM
Mapping Data

1 experiment

SNPs within 2kb

5434 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1924001	protein coding gene	Chr8:91554930-91781144 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0033927	protein coding gene	Chr8:92034283-92269967 (+)
A/J	MGP_AJ_G0033910	protein coding gene	Chr8:88417620-88644000 (+)
AKR/J	MGP_AKRJ_G0033836	protein coding gene	Chr8:90919273-91151552 (+)
BALB/cJ	MGP_BALBcJ_G0033902	protein coding gene	Chr8:88582692-88809096 (+)
C3H/HeJ	MGP_C3HHeJ_G0033612	protein coding gene	Chr8:91607016-91850941 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0034423	protein coding gene	Chr8:95464787-95696863 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0031364	protein coding gene	Chr8:82365407-82586785 (+)
CAST/EiJ	MGP_CASTEiJ_G0032944	protein coding gene	Chr8:91099942-91336482 (+)
CBA/J	MGP_CBAJ_G0033588	protein coding gene	Chr8:98679697-98926540 (+)
DBA/2J	MGP_DBA2J_G0033742	protein coding gene	Chr8:87986783-88212832 (+)
FVB/NJ	MGP_FVBNJ_G0033689	protein coding gene	Chr8:86921260-87145539 (+)
LP/J	MGP_LPJ_G0033834	protein coding gene	Chr8:92152887-92390283 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0033732	protein coding gene	Chr8:101101421-101342525 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0034441	protein coding gene	Chr8:91014032-91253809 (+)
PWK/PhJ	MGP_PWKPhJ_G0032646	protein coding gene	Chr8:87293310-87519096 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0032483	protein coding gene	Chr8:89885326-90119086 (+)
WSB/EiJ	MGP_WSBEiJ_G0033056	protein coding gene	Chr8:91483344-91714257 (+)

Human Ortholog

CHD9, chromodomain helicase DNA binding protein 9

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

CHD9, chromodomain helicase DNA binding protein 9
Synonyms

AD013, CHD-9, CReMM, KISH2, PRIC320
Links

HGNC:25701

NCBI Gene ID: 80205

neXtProt AC: NX_Q3L8U1

UniProt: Q3L8U1
Chr Location

16q12.2; chr16:53054991-53329150 (+) GRCh38

MGI Vertebrate Homology

Chd9 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: CHD9
Gene Tree

Chd9

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Phenotype Summary

6 phenotypes from 3 alleles in 3 genetic backgrounds
14 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	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

132
Endonuclease-mediated

3
Gene trapped

125
Targeted

4
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

250 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for null mutations are viable and fertile, although growing oocytes exhibit a less loosened chromatin structure.

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All GO Annotations

10
GO References

6

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	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	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

724
Tissues

14
cDNA Data

83
Literature Summary

1

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase chd9

ZFIN chd9

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All Sequences

109
RefSeq

40
UniProt

8
CCDS

CCDS22517.1, CCDS80912.1

Ensembl

ENSMUSG00000056608 (Evidence)
NCBI Gene

109151

			Length	Strain/Species	Flank
genomic	ENSMUSG00000056608	Ensembl Gene Model \| MGI Sequence Detail	226165	C57BL/6J	± kb
transcript	ENSMUST00000109614	Ensembl \| MGI Sequence Detail	11565	Not Applicable
polypeptide	ENSMUSP00000105243	Ensembl \| MGI Sequence Detail	2885	Not Applicable

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UniProt

8 Sequences
Protein Ontology

PR:000005415 chromodomain-helicase-DNA-binding protein 9

(term hierarchy)
EC

3.6.4.12
InterPro Domains

IPR006576 BRK domain

IPR037259 BRK domain superfamily

IPR000953 Chromo/chromo shadow domain

IPR023780 Chromo domain

IPR051493 Chromodomain-helicase-DNA-binding

IPR016197 Chromo-like domain superfamily

IPR001650 Helicase, C-terminal domain-like

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

IPR049730 SNF2/RAD5-like, C-terminal helicase domain
GlyGen

Q8BYH8 1 site, 1 O-linked glycan (1 site)

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All nucleic 84

cDNA 83

Primer pair 1

Microarray probesets 2

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MGI:1924942, MGI:2444510

Summaries

All 42

Developmental Gene Expression 1

Gene Ontology 6

Phenotypes 14
Earliest

J:65060 Kawai J, et al., Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90
Latest

J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Chd9:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr78687	Chr8:91554933-91554964 (+)	-31 bp
Tssr78688	Chr8:91555448-91555470 (+)	479 bp
Tssr78689	Chr8:91555476-91555523 (+)	520 bp
Tssr78690	Chr8:91584708-91584714 (+)	29,731 bp
Tssr78691	Chr8:91588582-91588585 (+)	33,604 bp
Tssr78697	Chr8:91610684-91610712 (+)	55,718 bp
Tssr78698	Chr8:91622919-91622925 (+)	67,942 bp
Tssr78699	Chr8:91626748-91626751 (+)	71,770 bp
Tssr78700	Chr8:91635193-91635225 (+)	80,229 bp
Tssr78701	Chr8:91635227-91635247 (+)	80,257 bp
Tssr78702	Chr8:91661867-91661873 (+)	106,890 bp
Tssr78703	Chr8:91681551-91681687 (+)	126,639 bp
Tssr78704	Chr8:91681707-91681724 (+)	126,736 bp
Tssr78705	Chr8:91682026-91682043 (+)	127,055 bp
Tssr78706	Chr8:91682046-91682116 (+)	127,101 bp
Tssr78707	Chr8:91682137-91682147 (+)	127,162 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)
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