Cldn1 MGI Mouse Gene Detail - MGI:1276109

Symbol

Cldn1
Name

claudin 1

Feature Type

protein coding gene
IDs

MGI:1276109
NCBI Gene: 12737
Alliance

gene page
Transcription Start Sites

7 TSS

Sequence Map

Chr16:26175395-26190589 bp, - strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 16, 18.00 cM
Mapping Data

2 experiments

SNPs within 2kb

520 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1276109	protein coding gene	Chr16:26175392-26190591 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0022693	protein coding gene	Chr16:24073836-24089804 (-)
A/J	MGP_AJ_G0022655	protein coding gene	Chr16:22944046-22959215 (-)
AKR/J	MGP_AKRJ_G0022629	protein coding gene	Chr16:23883701-23901006 (-)
BALB/cJ	MGP_BALBcJ_G0022660	protein coding gene	Chr16:23154266-23169391 (-)
C3H/HeJ	MGP_C3HHeJ_G0022424	protein coding gene	Chr16:23984640-24000527 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0023109	protein coding gene	Chr16:24625117-24640227 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0020627	protein coding gene	Chr16:23514197-23529636 (-)
CAST/EiJ	MGP_CASTEiJ_G0021953	protein coding gene	Chr16:24020757-24036652 (-)
CBA/J	MGP_CBAJ_G0022395	protein coding gene	Chr16:25656455-25671935 (-)
DBA/2J	MGP_DBA2J_G0022527	protein coding gene	Chr16:22897443-22912767 (-)
FVB/NJ	MGP_FVBNJ_G0022503	protein coding gene	Chr16:22882016-22897412 (-)
LP/J	MGP_LPJ_G0022595	protein coding gene	Chr16:23857845-23873858 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0022522	protein coding gene	Chr16:25078557-25093688 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0023121	protein coding gene	Chr16:23847244-23863073 (-)
PWK/PhJ	MGP_PWKPhJ_G0021692	protein coding gene	Chr16:23178551-23194258 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0021523	protein coding gene	Chr16:23594173-23612093 (-)
WSB/EiJ	MGP_WSBEiJ_G0021997	protein coding gene	Chr16:23767322-23783439 (-)

Human Ortholog

CLDN1, claudin 1

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

CLDN1, claudin 1
Synonyms

CLD1, ILVASC, SEMP1
Links

HGNC:2032

NCBI Gene ID: 9076

neXtProt AC: NX_O95832

UniProt: O95832
Chr Location

3q28; chr3:190305707-190322446 (-) GRCh38

MGI Vertebrate Homology

Cldn1 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: CLDN1
Gene Tree

Cldn1

Diseases

2 with human CLDN1 associations

				Human Disease	Mouse Models
				atopic dermatitis IDs atopic dermatitis DOID:3310 EFO:0000274 ICD10CM:L20 MESH:D003876 OMIM:603165 OMIM:PS603165 UMLS_CUI:C0011615
				Crohn's disease IDs Crohn's disease DOID:8778 DOID:8784 DOID:8855 DOID:8942 EFO:0000384 ICD10CM:K50.1 ICD9CM:555.1 MESH:D003424 NCI:C37262 UMLS_CUI:C0156147

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

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Phenotype Summary

9 phenotypes from 2 alleles in 2 genetic backgrounds
4 images
16 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

12
Endonuclease-mediated

5
Targeted

7
Incidental Mutations

APF
Find Mice (IMSR)

29 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Animals homozygous for a mutation in this gene have wrinkled skin and die within 1 day after birth.

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All GO Annotations

68
GO References

22

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

954
Tissues

114
cDNA Data

74
Literature Summary

58

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GENSAT

GEO

Expression Atlas
Other Vertebrate Links

GEISHA CLDN1

Xenbase cldn1

ZFIN cldn1

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All Sequences

44
RefSeq

2
UniProt

3
CCDS

CCDS28087.1

Ensembl

ENSMUSG00000022512 (Evidence)
NCBI Gene

12737

			Length	Strain/Species	Flank
genomic	12737	NCBI Gene Model \| MGI Sequence Detail	15195	C57BL/6J	± kb
transcript	NM_016674	RefSeq \| MGI Sequence Detail	3263	C57BL/6
polypeptide	O88551	UniProt \| EBI \| MGI Sequence Detail	211	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000005537 claudin-1

(term hierarchy)
InterPro Domains

IPR006187 Claudin

IPR003548 Claudin-1

IPR017974 Claudin, conserved site

IPR004031 PMP-22/EMP/MP20/Claudin

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All nucleic 80

cDNA 74

Primer pair 6

Microarray probesets 5

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MGI:2146462

Summaries

All 133

Developmental Gene Expression 58

Gene Ontology 22

Phenotypes 16
Earliest

J:48635 Furuse M, et al., Claudin-1 and -2: novel integral membrane proteins localizing at tight junctions with no sequence similarity to occludin. J Cell Biol. 1998 Jun 29;141(7):1539-50
Latest

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

TSS for Cldn1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr140635	Chr16:26190578-26190596 (-)	2 bp
Tssr140634	Chr16:26190554-26190571 (-)	26 bp
Tssr140633	Chr16:26190531-26190542 (-)	52 bp
Tssr140632	Chr16:26190405-26190431 (-)	171 bp
Tssr140631	Chr16:26177859-26177890 (-)	12,714 bp
Tssr140630	Chr16:26177539-26177542 (-)	13,048 bp
Tssr140629	Chr16:26176869-26176891 (-)	13,709 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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