CLDN3 (claudin 3) - Rat Genome Database

Name: CLDN3
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: CLDN3 (claudin 3) Sus scrofa

Analyze

Symbol:

CLDN3

Name:

claudin 3

RGD ID:

13921538

Description:

ENCODES a protein that exhibits identical protein binding (inferred); structural molecule activity (inferred); INVOLVED IN positive regulation of cell junction assembly (ortholog); response to ethanol (ortholog); ASSOCIATED WITH autism spectrum disorder (ortholog); autistic disorder (ortholog); Intestinal Reperfusion Injury (ortholog); FOUND IN apical junction complex (ortholog); cell-cell junction (ortholog); cytoplasm (ortholog); INTERACTS WITH amino acid; deoxynivalenol; diquat

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

claudin-3

RGD Orthologs

Human

Mouse

Rat

Bonobo

Dog

Squirrel

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	CLDN3 (claudin 3)	HGNC	Ensembl
Mus musculus (house mouse):	Cldn3 (claudin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Cldn3 (claudin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CLDN3 (claudin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CLDN3 (claudin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Cldn3 (claudin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	CLDN3 (claudin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Cldn3 (claudin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

Sscrofa11.1 - Pig Sscrofa11.1 Assembly

Position:

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	3	11,019,295 - 11,019,960 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	11,019,073 - 11,020,102 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	3	10,715,404 - 10,716,250 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autism spectrum disorder (ISO)

autistic disorder (ISO)

Intestinal Reperfusion Injury (ISO)

intestinal volvulus (ISO)

Neurodevelopmental Disorders (ISO)

peptic esophagitis (ISO)

pleomorphic xanthoastrocytoma (ISO)

Prostatic Neoplasms (ISO)

schizophrenia (ISO)

Stomach Neoplasms (ISO)

Volvulus Of Midgut (ISO)

Williams-Beuren syndrome (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

amino acid (EXP)

deoxynivalenol (EXP)

diquat (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

actin cytoskeleton reorganization (IEA)

bicellular tight junction assembly (IEA)

calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules (IEA)

cell junction maintenance (IEA)

epithelial cell morphogenesis (IEA)

establishment of endothelial blood-brain barrier (IEA)

negative regulation of cell migration (IEA)

negative regulation of cell population proliferation (IEA)

negative regulation of gene expression (IEA)

negative regulation of wound healing (IEA)

positive regulation of bicellular tight junction assembly (IEA)

positive regulation of cell junction assembly (ISO)

positive regulation of cell migration (IEA)

positive regulation of gene expression (IEA)

positive regulation of metallopeptidase activity (IEA)

positive regulation of protein phosphorylation (IEA)

positive regulation of wound healing (IEA)

regulation of cell morphogenesis (IEA)

regulation of membrane permeability (IEA)

regulation of transepithelial transport (IEA)

response to ethanol (ISO)

response to hypoxia (IEA)

Cellular Component

apical junction complex (ISO)

apicolateral plasma membrane (IEA)

bicellular tight junction (IEA)

cell-cell junction (ISO)

cytoplasm (ISO)

integral component of membrane (IEA)

lateral plasma membrane (IEA)

protein-containing complex (IEA)

tight junction (ISO)

Molecular Function

identical protein binding (IEA)

protein binding (ISO)

structural molecule activity (IEA)

References

Genomics

Comparative Map Data

CLDN3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	3	11,019,295 - 11,019,960 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	11,019,073 - 11,020,102 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	3	10,715,404 - 10,716,250 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CLDN3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	7	73,768,997 - 73,770,270 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	7	73,768,997 - 73,770,270 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	7	73,183,327 - 73,184,600 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	7	72,821,263 - 72,822,512 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	7	72,627,978 - 72,629,227	NCBI
Celera	7	68,661,514 - 68,662,787 (-)	NCBI
Cytogenetic Map	7	q11.23	NCBI
HuRef	7	69,065,982 - 69,067,255 (-)	NCBI		HuRef
CHM1_1	7	73,329,029 - 73,330,302 (-)	NCBI		CHM1_1
CRA_TCAGchr7v2	7	72,516,399 - 72,517,672 (-)	NCBI

Cldn3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	135,015,068 - 135,016,330 (+)	NCBI	GRCm39		mm39
GRCm38	5	134,986,214 - 134,987,476 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	134,986,214 - 134,987,472 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	135,462,084 - 135,463,342 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	5	135,270,841 - 135,272,099 (+)	NCBI			mm8
Celera	5	131,997,044 - 131,998,302 (+)	NCBI		Celera
Cytogenetic Map	5	G2	NCBI
cM Map	5	74.93	NCBI

Cldn3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	12	21,831,341 - 21,832,813 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	12	21,831,342 - 21,832,813 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	12	23,849,259 - 23,850,731 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	12	23,471,431 - 23,472,903 (-)	NCBI		Celera
Cytogenetic Map	12	q12	NCBI

CLDN3
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	7	80,924,338 - 80,925,761 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	7	80,924,731 - 80,925,393 (-)	Ensembl	panpan1.1		panPan2

CLDN3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	6	6,534,229 - 6,535,237 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Cldn3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936543	2,952,054 - 2,953,313 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CLDN3
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	28	9,301,312 - 9,303,496 (+)	NCBI
ChlSab1.1 Ensembl	28	9,302,446 - 9,303,108 (+)	Ensembl

Cldn3
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624740	14,065,172 - 14,066,432 (+)	NCBI

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	endocrine system	hemolymphoid system	nervous system	renal system	reproductive system	respiratory system
High
Medium	3
Low	5	3	3	3	2	3	1
Below cutoff							1

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001160075	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AEMK02000015	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY625258	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CU915481	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FJ887980	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FJ887981	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GFLN01036254	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSSSCT00000027640 ⟹ ENSSSCP00000064612

RefSeq Status:

Type:

CODING

Position:

Pig Assembly	Chr	Position (strand)	Source
Sscrofa11.1 Ensembl	3	11,019,295 - 11,019,960 (-)	Ensembl

RefSeq Acc Id:

NM_001160075 ⟹ NP_001153547

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Pig Assembly	Chr	Position (strand)	Source
Sscrofa11.1	3	11,019,073 - 11,020,102 (-)	NCBI

Sequence:

show sequence

TCCTCGTGTCCGTCTATCCGTCCGTCCGTCGGGGCGTCCATCCAGCGGCGCAGAGCCGTTCGCA
ACCAGGCCCCAGCGGCCCCGGCCCCTCGTCGTCCCGCACCCGGAGCTGCCCGGCCGAGCCGGCT
TTGGAGCAGCAGCCATGTCCATGGGCCTGGAGATCGCGGGCACCTCGCTAGCCGTCATGGGCTG
GCTGAGCACCATCGTGTGCTGCGCGCTGCCCATGTGGCGCGTCACGGCCTTCATCGGCAGCAGC
ATTATCACAGCGCGGATCACCTGGGAGGGCCTGTGGATGAACTGCGTGGTGCAGAGCACGGGCC
AGATGCAGTGCAAAGTGTACGACTCTCTGCTGGCGCTGCCGCAGGACCTGCAGGCGGCCCGCGC
CCTCATCGTCGTCGCCATCCTGCTGGCCGCCTTTGGGCTCCTTGTGGCGCTTGTGGGCGCCCAG
TGCACCAACTGCGTGCAGGACGACACGGCCAAAGCCAAGATCCTCTACTCCGCGCCGCGCTCCA
CCGTCGGGCCGGGCACCGGCACCGGCACGGCCTACGACCGCAAGGACTACGTATGAGGGGGCAG
CCGCGGAGAGTCCCCACCACCCCCACGAGCTCGTGCGCCCACCAGTCCTCCGTGCGGCCTTGCA
TCCGAGACCAGTCCACCCAGATGCTAGGCAGCTCTCTCGCCGGACTGGGAGGGGCCCGCCCGGT
GTCACCCTCCCCAGCTGCCACCCCTCCTCGGGCCGGGGAGCGGGATTGCGGAGCCCAGAGACCA
GTCAGCACGGACCATGAAACCT

hide sequence

Protein Sequences


Protein RefSeqs	NP_001153547	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAT42132	(Get FASTA)	NCBI Sequence Viewer
	ACP19336	(Get FASTA)	NCBI Sequence Viewer
	ACP19337	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_001153547 ⟸ NM_001160075
- UniProtKB:	C3VPJ6 (UniProtKB/TrEMBL)
- Sequence:	show sequence MSMGLEIAGTSLAVMGWLSTIVCCALPMWRVTAFIGSSIITARITWEGLWMNCVVQSTGQMQCK VYDSLLALPQDLQAARALIVVAILLAAFGLLVALVGAQCTNCVQDDTAKAKILYSAPRSTVGPG TGTGTAYDRKDYV hide sequence

RefSeq Acc Id:

ENSSSCP00000064612 ⟸ ENSSSCT00000027640

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSSCG00000035928	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSSSCP00000064612	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSSSCT00000027640	ENTREZGENE, UniProtKB/TrEMBL
InterPro	Claudin	UniProtKB/TrEMBL
	Claudin3	UniProtKB/TrEMBL
	Claudin_CS	UniProtKB/TrEMBL
	PMP22/EMP/MP20/Claudin	UniProtKB/TrEMBL
KEGG Report	ssc:431781	UniProtKB/TrEMBL
NCBI Gene	CLDN3	ENTREZGENE
PANTHER	PTHR12002	UniProtKB/TrEMBL
Pfam	PMP22_Claudin	UniProtKB/TrEMBL
PRINTS	CLAUDIN3	UniProtKB/TrEMBL
PROSITE	CLAUDIN	UniProtKB/TrEMBL
UniGene	Ssc.9102	ENTREZGENE
	Ssc.93114	ENTREZGENE
UniProt	A0A5G2QJG3_PIG	UniProtKB/TrEMBL
	C3VPJ5_PIG	UniProtKB/TrEMBL
	C3VPJ6	ENTREZGENE, UniProtKB/TrEMBL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD