Ctcf MGI Mouse Gene Detail - MGI:109447

Symbol

Ctcf
Name

CCCTC-binding factor

Feature Type

protein coding gene
IDs

MGI:109447
NCBI Gene: 13018
Alliance

genome feature page
Transcription Start Sites

8 TSS

Sequence Map

Chr8:106363200-106409554 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 8, 53.04 cM
Mapping Data

1 experiment

SNPs within 2kb

771 from dbSNP Build 142
Strain Annotations

19

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_109447	protein coding gene	Chr8:106351135-106409554 (+)
129S1/SvImJ	ENSMUSG00200013512	protein coding gene	Chr8:100642634-100690480 (+)
A/J	ENSMUSG00195015881	protein coding gene	Chr8:100965090-101012932 (+)
AKR/J	ENSMUSG00220014712	protein coding gene	Chr8:101107755-101155601 (+)
BALB/cJ	ENSMUSG00180020809	protein coding gene	Chr8:100970929-101018770 (+)
C3H/HeJ	ENSMUSG00175024550	protein coding gene	Chr8:101027610-101075446 (+)
C57BL/6NJ	ENSMUSG00215015981	protein coding gene	Chr8:100641995-100689830 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0031488	protein coding gene	Chr8:96757910-96806634 (+)
CAST/EiJ	ENSTCUG00005021374	protein coding gene	Chr8:100406538-100454170 (+)
CBA/J	ENSMUSG00210029536	protein coding gene	Chr8:100955324-101003162 (+)
DBA/2J	ENSMUSG00185005521	protein coding gene	Chr8:107064104-107111936 (+)
FVB/NJ	ENSMUSG00205013116	protein coding gene	Chr8:99939631-99987475 (+)
JF1/MsJ	ENSUMUG00000007117	protein coding gene	Chr8:109397307-109445145 (+)
LP/J	ENSMUSG00230034349	protein coding gene	Chr8:110744502-110792336 (+)
NOD/ShiLtJ	ENSMUSG00190026377	protein coding gene	Chr8:101094539-101142381 (+)
NZO/HlLtJ	ENSMUSG00225019876	protein coding gene	Chr8:114095033-114142869 (+)
PWK/PhJ	ENSLUMG00010003908	protein coding gene	Chr8:100878320-100926349 (+)
SPRET/EiJ	ENSMSPG00010034508	protein coding gene	Chr8:102956174-103003673 (+)
WSB/EiJ	ENSIUOG00005030426	protein coding gene	Chr8:101766709-101814579 (+)

Human Ortholog

CTCF, CCCTC-binding factor

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

CTCF, CCCTC-binding factor
Synonyms

CFAP108, FAP108, MRD21
Links

HGNC:13723

NCBI Gene ID: 10664

UniProt: P49711
Chr Location

16q22.1; chr16:67561831-67639189 (+) GRCh38

MGI Vertebrate Homology

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

vertebrate homology predictions: CTCF
Gene Tree

Ctcf

Diseases

5 with human CTCF associations

				Human Disease	Mouse Models
				autosomal dominant intellectual developmental disorder 21 IDs autosomal dominant intellectual developmental disorder 21 DOID:0070051 OMIM:615502
				basal cell carcinoma IDs basal cell carcinoma DOID:2513 DOID:4275 DOID:4276 EFO:0004193 KEGG:05217 MESH:D018295 NCI:C156767 NCI:C3784 UMLS_CUI:C0007117 UMLS_CUI:C0206710 UMLS_CUI:C1368295
				female breast cancer IDs female breast cancer DOID:0050671
				skin melanoma IDs skin melanoma DOID:8923 DOID:0050609 DOID:10043 DOID:10046 DOID:10051 DOID:10052 DOID:10055 DOID:8922 ICD10CM:C43.9 ICD9CM:172 ICD9CM:172.0 ICD9CM:172.2 ICD9CM:172.4 ICD9CM:172.5 ICD9CM:172.9 MESH:D000096142 NCI:C3510 UMLS_CUI:C0151779
				skin squamous cell carcinoma IDs skin squamous cell carcinoma DOID:3151 MESH:D000099314 NCI:C4819 UMLS_CUI:C0553723

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

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Phenotype Summary

31 phenotypes from 4 alleles in 3 genetic backgrounds
7 phenotypes from multigenic genotypes
1 images
70 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

153
Endonuclease-mediated

6
Gene trapped

135
Targeted

11
Transgenic

1
Genomic Mutations

1 involving Ctcf
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

78 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a null allele die prior to implantation. Mice homozygous for a conditional allele activated in T cells exhibit a defect in the transition from immature single positive T cells to double positive T cells. Heterozygosity for the p.R567W mutation leads to thin body, while homozygosity affects heart, lung and neuronal development, leading to death shortly after birth.

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All GO Annotations

92
GO References

29

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

942
Tissues

235
cDNA Data

165
Literature Summary

25

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA CTCF

Xenbase ctcf

ZFIN ctcf

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All Sequences

88
RefSeq

38
UniProt

5
CCDS

CCDS22606.1

Ensembl

ENSMUSG00000005698 (Evidence)
NCBI Gene

13018

			Length	Strain/Species	Flank
genomic	ENSMUSG00000005698	Ensembl Gene Model \| MGI Sequence Detail	46355	C57BL/6J	± kb
transcript	ENSMUST00000005841	Ensembl \| MGI Sequence Detail	3782	Not Applicable
polypeptide	ENSMUSP00000005841	Ensembl \| MGI Sequence Detail	736	Not Applicable

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UniProt

5 Sequences
Protein Ontology

PR:000005997 transcriptional repressor CTCF

(term hierarchy)
InterPro Domains

IPR056438 CTCF-like, C2H2 zinc finger

IPR036236 Zinc finger C2H2 superfamily

IPR013087 Zinc finger C2H2-type

IPR050331 Zinc finger PRDM4/PRDM1/PRDM14-like
GlyGen

Q61164 1 site, 1 O-linked glycan (1 site)

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All nucleic 172

cDNA 166

Primer pair 6

Antibodies 7

Microarray probesets 4

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MGD-MRK-38492, MGI:2142760

Summaries

All 306

Developmental Gene Expression 25

Gene Ontology 29

Phenotypes 70
Earliest

J:33964 Filippova GN, et al., An exceptionally conserved transcriptional repressor, CTCF, employs different combinations of zinc fingers to bind diverged promoter sequences of avian and mammalian c-myc oncogenes. Mol Cell Biol. 1996 Jun;16(6):2802-13
Latest

J:382969 Huang TC, et al., Global reorganization of genome architecture at the transition to gametogenesis. Nat Struct Mol Biol. 2026 Mar;33(3):433-447

TSS for Ctcf:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr79169	Chr8:106362413-106362434 (+)	-776 bp
Tssr79170	Chr8:106363120-106363131 (+)	-74 bp
Tssr79171	Chr8:106363141-106363221 (+)	-19 bp
Tssr79172	Chr8:106363222-106363244 (+)	33 bp
Tssr79173	Chr8:106363558-106363611 (+)	385 bp
Tssr79174	Chr8:106375951-106375955 (+)	12,753 bp
Tssr79175	Chr8:106390799-106390811 (+)	27,605 bp
Tssr2677	Chr8:106390929-106390944 (+)	27,737 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 09/01/2026 MGI 6.24