Cldn13 (claudin 13) - Rat Genome Database

Name: Cldn13
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Cldn13 (claudin 13) Mus musculus

Analyze

No known orthologs.

Symbol:

Cldn13

Name:

claudin 13

RGD ID:

1624020

MGI Page

MGI

Description:

Predicted to enable structural molecule activity. Predicted to be involved in several processes, including bicellular tight junction assembly; establishment of skin barrier; and positive regulation of wound healing. Located in lateral plasma membrane. Is expressed in several structures, including brain; genitourinary system; gut; hemolymphoid system gland; and skeleton. Human ortholog(s) of this gene implicated in ovarian cancer and pancreatic cancer. Orthologous to human CLDN4 (claudin 4).

Type:

protein-coding

RefSeq Status:

REVIEWED

Previously known as:

2500004B14Rik; claudin-13; MGC144291; MGC144292

RGD Orthologs

Alliance Orthologs

More Info

homologs ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Other homologs ²				less info ...
Homo sapiens (human):	CLDN4 (claudin 4)	HGNC	Ensembl, Panther, PhylomeDB
Homo sapiens (human):	CLDN17 (claudin 17)	HGNC	Treefam
Homo sapiens (human):	CLDN8 (claudin 8)	HGNC	Treefam
Alliance orthologs ³
Homo sapiens (human):	CLDN4 (claudin 4)	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	cldnb (claudin b)	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)
Danio rerio (zebrafish):	cldna (claudin a)	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	cldn4	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)

Latest Assembly:

GRCm39 - Mouse Genome Assembly GRCm39

Position:

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	134,943,104 - 134,944,384 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	5	134,943,103 - 134,944,380 (-)	Ensembl		GRCm39 Ensembl
GRCm38	5	134,914,250 - 134,915,530 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	134,914,249 - 134,915,526 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	135,390,120 - 135,391,396 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	5	135,198,877 - 135,200,153 (-)	NCBI		MGSCv36	mm8
Celera	5	131,925,073 - 131,926,349 (-)	NCBI		Celera
Cytogenetic Map	5	G2	NCBI
cM Map	5	74.88	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (EXP)

benzo[a]pyrene (EXP)

cyclosporin A (EXP)

paracetamol (EXP)

Tributyltin oxide (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

bicellular tight junction assembly (IBA)

cell adhesion (IBA)

establishment of skin barrier (ISO)

positive regulation of cell migration (ISO)

positive regulation of wound healing (ISO)

regulation of cell morphogenesis (ISO)

Cellular Component

anchoring junction (IEA)

bicellular tight junction (IBA,ISO)

cell-cell junction (ISO)

lateral plasma membrane (IDA)

membrane (IEA)

plasma membrane (IBA,ISO)

tight junction (ISO)

Molecular Function

structural molecule activity (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

hepatitis C pathway (IEA)

Phenotype Annotations Click to see Annotation Detail View

Mammalian Phenotype

decreased blood urea nitrogen level (IEA)

decreased fasting circulating glucose level (IEA)

decreased grip strength (IEA)

decreased mean corpuscular volume (IEA)

increased circulating alanine transaminase level (IEA)

increased circulating potassium level (IEA)

increased circulating sodium level (IEA)

increased erythrocyte cell number (IEA)

increased hemoglobin content (IEA)

persistence of hyaloid vascular system (IEA)

References

References - curated

#	Reference Title	Reference Citation
1.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
2.	Mouse MP Annotation Import Pipeline	RGD automated import pipeline
3.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:10225958	PMID:10349636	PMID:11042159	PMID:11076861	PMID:11217851	PMID:11585919	PMID:11779826	PMID:12466851	PMID:12477932	PMID:14610273	PMID:16141072	PMID:16141073
PMID:16651389	PMID:16774906	PMID:17383680	PMID:18036336	PMID:18480174	PMID:18554416	PMID:20844758	PMID:21267068	PMID:21677750	PMID:21873635	PMID:22155109	PMID:22275141
PMID:24194600	PMID:24825397	PMID:27626380	PMID:34737342	PMID:38355793

Genomics

Variants

Variants in Cldn13
47 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	154
Count of miRNA genes:	145
Interacting mature miRNAs:	149
Transcripts:	ENSMUST00000008987
Prediction methods:	Miranda, Rnahybrid
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (GRCm39)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
13464243	Ahl20_m	age related hearing loss, early onset 20 (mouse)					5	107906299	141906412	Mouse
1300913	Bwefm_m	body weight females and males day 10 (mouse)			Not determined		5	109439348	143439459	Mouse
11528552	Scram1_m	spinal cord resistance to astrocytoma modifier 1 (mouse)					5	121455402	151758149	Mouse
1301363	Pbwg13_m	postnatal body weight growth 13 (mouse)			Not determined		5	125133457	151758149	Mouse
1300827	Cora1_m	correlation in cytokine production 1 (mouse)			Not determined		5	115156883	149157015	Mouse
13464251	Ahl21_m	age related hearing loss, early onset 21 (mouse)					5	109167240	143167381	Mouse
1301226	Bbaa2_m	B.burgdorferi-associated arthritis 2 (mouse)			Not determined		5	115156883	149157015	Mouse
12880406	Jcdq2_m	joint cartilage degeneration QTL 2 (mouse)					5	129787831	151758149	Mouse
13464143	Bbaa2b_m	B.burgdorferi-associated arthritis 2b (mouse)					5	133052969	140709801	Mouse
11049557	Lmr26_m	leishmaniasis resistance 26 (mouse)					5	133925558	151758149	Mouse
14746986	Manh58_m	mandible shape 58 (mouse)					5	102446283	136446283	Mouse
10412239	Alpq7_m	alcohol preference QTL 7 (mouse)			Not determined		5	104705939	138705939	Mouse
10412191	Bbaa24_m	B.burgdorferi-associated arthritis 24 (mouse)			Not determined		5	119945037	141700466	Mouse
11341716	Rvfs3_m	Rift Valley fever susceptibility 3 (mouse)					5	26441234	138455402	Mouse
10412202	Bbaa26_m	B.burgdorferi-associated arthritis 26 (mouse)			Not determined		5	104583688	138555455	Mouse
1301362	Prnr1_m	prion resistance 1 (mouse)			Not determined		5	89418876	146787935	Mouse
11532736	Sluc33b_m	susceptibility to lung cancer 33b (mouse)					5	102945037	136945196	Mouse
10043890	Trigq4_m	triglyceride QTL 4 (mouse)			Not determined		5	107906299	141906412	Mouse
27226719	Tibw6_m	tibia width 6, proximal, 16 week (mouse)					5	72857343	139985755	Mouse
1301543	Hypch_m	hypercholesterolemia (mouse)			Not determined		5	109238624	139118905	Mouse
4141081	Nidd7k_m	Nidd7 on KK-A (mouse)			Not determined			119945037	149347326	Mouse
1301986	Bpq4_m	blood pressure QTL 4 (mouse)			Not determined		5	121555236	151758149	Mouse
4142473	Chlq11_m	circulating hormone level QTL 11 (mouse)			Not determined		5	107906299	141906412	Mouse
4141218	Ath24_m	atherosclerosis 24 (mouse)			Not determined			129520084	151758149	Mouse
1301102	Cia14_m	collagen induced arthritis 14 (mouse)			Not determined		5	113320385	138555455	Mouse
1301857	Bglq14_m	body growth late QTL 14 (mouse)			Not determined		5	118948964	151758149	Mouse
10412197	Bbaa25_m	B.burgdorferi-associated arthritis 25 (mouse)			Not determined		5	109167240	143167381	Mouse
1302079	Lbw3_m	lupus NZB x NZW 3 (mouse)			Not determined		5	124700335	151758149	Mouse
1301715	Elmaz2_m	elevated maze behavior 2 (mouse)			Not determined		5	125178229	141700466	Mouse
12859290	Criq2_m	Citrobacter rodentium infection QTL 2 (mouse)					5	101332579	135332579	Mouse
1301624	Aevm2_m	autoimmune extremity vasculitis in MRL mice 2 (mouse)			Not determined		5	101863832	135864028	Mouse

Markers in Region

UniSTS:235334

Mouse Assembly	Chr	Position (strand)	Source	JBrowse
GRCm38	5	134,914,704 - 134,914,857	UniSTS	GRCm38
MGSCv37	5	135,390,574 - 135,390,727	UniSTS	GRCm37
Celera	5	131,925,527 - 131,925,680	UniSTS
Cytogenetic Map	5	G2	UniSTS

PMC99911P5

Mouse Assembly	Chr	Position (strand)	Source	JBrowse
GRCm38	5	134,914,755 - 134,915,270	UniSTS	GRCm38
MGSCv37	5	135,390,625 - 135,391,140	UniSTS	GRCm37
Celera	5	131,925,578 - 131,926,093	UniSTS
Cytogenetic Map	5	G2	UniSTS

UniSTS:493127

Mouse Assembly	Chr	Position (strand)	Source	JBrowse
GRCm38	5	134,914,389 - 134,915,446	UniSTS	GRCm38
MGSCv37	5	135,390,259 - 135,391,316	UniSTS	GRCm37
Celera	5	131,925,212 - 131,926,269	UniSTS
Cytogenetic Map	5	G2	UniSTS

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_020504	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC079938	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF124428	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF516681	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK010869	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC115481	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC115482	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BY079003	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH466529	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSMUST00000008987 ⟹ ENSMUSP00000008987

Type:

CODING

Position:

Mouse Assembly	Chr	Position (strand)	Source
GRCm39 Ensembl	5	134,943,103 - 134,944,380 (-)	Ensembl
GRCm38.p6 Ensembl	5	134,914,249 - 134,915,526 (-)	Ensembl

RefSeq Acc Id:

NM_020504 ⟹ NP_065250

RefSeq Status:

REVIEWED

Type:

CODING

Position:

Mouse Assembly	Chr	Position (strand)	Source
GRCm39	5	134,943,104 - 134,944,384 (-)	NCBI
GRCm38	5	134,914,250 - 134,915,530 (-)	ENTREZGENE
MGSCv37	5	135,390,120 - 135,391,396 (-)	RGD
Celera	5	131,925,073 - 131,926,353 (-)	ENTREZGENE
cM Map	5		ENTREZGENE

Sequence:

show sequence

AGATAGGGTCCTGTGTCAACTGCTGTGCTCACACTTGCTGGAGCTCGACATTTGACTACCTAGA
TCATCATTGGTGACAGTGGCCTCTCATACGTGCTGGCCCCCGATACTTTAAAATTCCATCCTCG
GCTCTTGGAATCCTGCATCTCTACAGCTGGACCCCTGACTCGTCCTGGTCCTGCCATTAGCAGA
CTCTGAGCCATGGTCGTCAGCAAACAAGAGGCCATCAGCTTCTCTGTGACTTCACTGGGTTGGG
TGGGTGCCATTGTGAGCTGCGTGCTGCCCGTTTGGAGGGTGACCTTTCCAGATGATGAGACAGA
CCCAGATGCCACCATTTGGGAGGGTCTGTGGCACATATGCCAGGTTCGGGAAAACAGGTGGATA
CAGTGTACACTGTATGACACCCGGATACTGGTAGCACAGGACATAAAAGTGTCTCGAGTCTTTA
TGGTCATCTGTACCATTGGAACCTGGCTGGGATTGCTGCTCTGTGTGCTTGGGGATTGGCGCAT
CAATTGTTTCATGAATTTTACTATTGAAGAGAACCTCTTGAAAGTAGCCGGTGGGATGTTTCTT
AGTGTTGGCCTTCTGATGCTGGTACCCCTGTCCTGGGTAACACACAACATCATCCATGGCTTCT
TTAACCCATTGCTTGGCTTCTCGAAGAAAGTACAGATGGGCTCTTCACTCTCCCTGGCCTGGAC
CAGCTCCCTGCTGCTGTTGCTGGGAGGCATCCTGCTCTGTGTCAACATCCCAGTATGCAGAGAC
TTTCCCCGTTGCATTGAGACCCCTAGTGCTAGACCTTCAGGAGCCAACAACGATACCTTAGATG
TTTGATGGCCAGCACACTCACGTCTGGAGGGGAAAACTTCCTCAAGAGGCCTCTCTCCAGGTTC
TAGAATCATTGAACTGGAGGGAGGAAAGACAGGTCTACGGAGCTGCCCACAAGCTGTGTAGTGG
ACTCTGGATGCGGCTAGCTGTGTCAGCACCATGCTGAGGTGGGCTTCTTGGTGCTGAAGCTGCC
CGAGTCTCCTATCTAAGGGACCCCAATAAAGTCATTGTTCCCCTAG

hide sequence

Protein Sequences


Protein RefSeqs	NP_065250	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAD17322	(Get FASTA)	NCBI Sequence Viewer
	AAI15482	(Get FASTA)	NCBI Sequence Viewer
	AAI15483	(Get FASTA)	NCBI Sequence Viewer
	AAN03863	(Get FASTA)	NCBI Sequence Viewer
	BAB27234	(Get FASTA)	NCBI Sequence Viewer
	EDL19410	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSMUSP00000008987
	ENSMUSP00000008987.5
GenBank Protein	Q9Z0S4	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_065250 ⟸ NM_020504

- UniProtKB:

Q9Z0S4 (UniProtKB/Swiss-Prot), Q547B2 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MVVSKQEAISFSVTSLGWVGAIVSCVLPVWRVTFPDDETDPDATIWEGLWHICQVRENRWIQCT
LYDTRILVAQDIKVSRVFMVICTIGTWLGLLLCVLGDWRINCFMNFTIEENLLKVAGGMFLSVG
LLMLVPLSWVTHNIIHGFFNPLLGFSKKVQMGSSLSLAWTSSLLLLLGGILLCVNIPVCRDFPR
CIETPSARPSGANNDTLDV

hide sequence

RefSeq Acc Id:

ENSMUSP00000008987 ⟸ ENSMUST00000008987

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q9Z0S4-F1-model_v2	AlphaFold	Q9Z0S4	1-211	view protein structure

Promoters

RGD ID:

6888276

Promoter ID:

EPDNEW_M7589

Type:

initiation region

Name:

Cldn13_1

Description:

Mus musculus claudin 13 , mRNA.

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Mouse Assembly	Chr	Position (strand)	Source
GRCm38	5	134,915,526 - 134,915,586	EPDNEW

RGD ID:

6837259

Promoter ID:

MM_KWN:44318

Type:

Non-CpG

SO ACC ID:

SO:0000170

Source:

MPROMDB

Tissues & Cell Lines:

Spleen

Transcripts:

OTTMUST00000064084

Position:

Mouse Assembly	Chr	Position (strand)	Source
MGSCv36	5	135,391,011 - 135,391,511 (-)	MPROMDB

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	MGI:1913102	AgrOrtholog
Ensembl Genes	ENSMUSG00000008843	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSMUST00000008987	ENTREZGENE
	ENSMUST00000008987.5	UniProtKB/Swiss-Prot
Gene3D-CATH	1.20.140.150	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro	Claudin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Claudin_CS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PMP22/EMP/MP20/Claudin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	mmu:57255	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD	MGI:1913102	ENTREZGENE
NCBI Gene	57255	ENTREZGENE
PANTHER	CLAUDIN-4	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PTHR12002	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	PMP22_Claudin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Cldn13	PhenoGen
PRINTS	CLAUDIN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	CLAUDIN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PROKAR_LIPOPROTEIN	UniProtKB/TrEMBL
UniProt	CLD13_MOUSE	UniProtKB/Swiss-Prot
	Q547B2	ENTREZGENE, UniProtKB/TrEMBL
	Q9Z0S4	ENTREZGENE

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)

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Imported Annotations - KEGG (archival)

Mammalian Phenotype