Cnot9 MGI Mouse Gene Detail - MGI:1928902 - CCR4-NOT transcription complex, subunit 9

Symbol

Cnot9
Name

CCR4-NOT transcription complex, subunit 9
Synonyms

2610007F23Rik, FL10, Rqcd1

Feature Type

protein coding gene
IDs

MGI:1928902
NCBI Gene: 58184
Alliance

genome feature page
Transcription Start Sites

8 TSS

Sequence Map

Chr1:74545217-74570001 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 1, 38.54 cM
Mapping Data

2 experiments

SNPs within 2kb

526 from dbSNP Build 142
Strain Annotations

19

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1928902	protein coding gene	Chr1:74545192-74570001 (+)
129S1/SvImJ	ENSMUSG00200032103	protein coding gene	Chr1:72208282-72233035 (+)
A/J	ENSMUSG00195008281	protein coding gene	Chr1:71633142-71657922 (+)
AKR/J	ENSMUSG00220010286	protein coding gene	Chr1:71778963-71803727 (+)
BALB/cJ	ENSMUSG00180016962	protein coding gene	Chr1:71891901-71916695 (+)
C3H/HeJ	ENSMUSG00175015239	protein coding gene	Chr1:72033521-72058295 (+)
C57BL/6NJ	ENSMUSG00215010242	protein coding gene	Chr1:71937229-71962020 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0014265	protein coding gene	Chr1:68065640-68088631 (+)
CAST/EiJ	ENSTCUG00005027222	protein coding gene	Chr1:71662006-71686770 (+)
CBA/J	ENSMUSG00210033273	protein coding gene	Chr1:71717748-71742507 (+)
DBA/2J	ENSMUSG00185029740	protein coding gene	Chr1:72811583-72836314 (+)
FVB/NJ	ENSMUSG00205032890	protein coding gene	Chr1:71386831-71411618 (+)
JF1/MsJ	ENSUMUG00000004665	protein coding gene	Chr1:71711901-71736246 (+)
LP/J	ENSMUSG00230009719	protein coding gene	Chr1:72801451-72826205 (+)
NOD/ShiLtJ	ENSMUSG00190033145	protein coding gene	Chr1:71943503-71968277 (+)
NZO/HlLtJ	ENSMUSG00225038652	protein coding gene	Chr1:76016559-76041312 (+)
PWK/PhJ	ENSLUMG00010013029	protein coding gene	Chr1:71288426-71320210 (+)
SPRET/EiJ	ENSMSPG00010017802	protein coding gene	Chr1:73388801-73413306 (+)
WSB/EiJ	ENSIUOG00005012237	protein coding gene	Chr1:71565282-71590033 (+)

Human Ortholog

CNOT9, CCR4-NOT transcription complex subunit 9

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

CNOT9, CCR4-NOT transcription complex subunit 9
Synonyms

CAF40, CT129, RCD-1, RCD1, RQCD1
Links

HGNC:10445

NCBI Gene ID: 9125

UniProt: Q92600
Chr Location

2q35; chr2:218568580-218597080 (+) GRCh38

MGI Vertebrate Homology

Cnot9 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: CNOT9
Gene Tree

Cnot9

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Phenotype Summary

4 phenotypes from 1 allele in 1 genetic background
21 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

66
Chemically induced (ENU)

1
Chemically induced (other)

1
Gene trapped

58
Radiation induced

2
Targeted

4
Genomic Mutations

3 involving Cnot9
Incidental Mutations

APF
Find Mice (IMSR)

43 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Embryos homozygous for an ENU-induced allele exhibit abnormal nervous system and brain morphology, cranioedema, and caudal body truncation. Mice carrying a targeted allele exhibit embryonic lethality.

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All GO Annotations

35
GO References

12

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	membraneless 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

730
Tissues

75
cDNA Data

9
Literature Summary

7

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase cnot9

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All Sequences

42
RefSeq

4
UniProt

1
CCDS

CCDS35615.1

Ensembl

ENSMUSG00000026174 (Evidence)
NCBI Gene

58184

			Length	Strain/Species	Flank
genomic	ENSMUSG00000026174	Ensembl Gene Model \| MGI Sequence Detail	24785	C57BL/6J	± kb
transcript	ENSMUST00000087215	Ensembl \| MGI Sequence Detail	3268	Not Applicable
polypeptide	ENSMUSP00000084466	Ensembl \| MGI Sequence Detail	299	Not Applicable

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UniProt

1 Sequence
Protein Ontology

PR:000014295 CCR4-NOT transcription complex subunit 9

(term hierarchy)
InterPro Domains

IPR011989 Armadillo-like helical

IPR016024 Armadillo-type fold

IPR007216 CCR4-NOT transcription complex subunit 9

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All nucleic 10

cDNA 10

Antibodies 2

Microarray probesets 4

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MGI:1913825, MGI:2138295

Summaries

All 58

Developmental Gene Expression 7

Gene Ontology 12

Phenotypes 21
Earliest

J:134667 Roderick TH, et al., Two radiation-induced chromosomal inversions in mice (Mus musculus). Proc Natl Acad Sci U S A. 1970 Oct;67(2):961-7
Latest

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

TSS for Cnot9:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr7425	Chr1:74545182-74545197 (+)	-27 bp
Tssr7426	Chr1:74545203-74545264 (+)	17 bp
Tssr7427	Chr1:74545270-74545279 (+)	58 bp
Tssr7428	Chr1:74545468-74545533 (+)	284 bp
Tssr7429	Chr1:74545537-74545546 (+)	325 bp
Tssr7430	Chr1:74545861-74545877 (+)	652 bp
Tssr7431	Chr1:74550566-74550575 (+)	5,354 bp
Tssr7432	Chr1:74568407-74568411 (+)	23,192 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, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 09/08/2026 MGI 6.24