Cdh13 (cadherin 13) - Rat Genome Database

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Gene: Cdh13 (cadherin 13) Rattus norvegicus
Analyze
Symbol: Cdh13
Name: cadherin 13
RGD ID: 619745
Description: Predicted to enable several functions, including adiponectin binding activity; beta-catenin binding activity; and low-density lipoprotein particle binding activity. Involved in cellular response to toxic substance and cellular response to xenobiotic stimulus. Located in perinuclear region of cytoplasm. Is active in GABA-ergic synapse. Used to study substance-related disorder. Biomarker of coronary restenosis. Human ortholog(s) of this gene implicated in breast cancer (multiple); lung non-small cell carcinoma; reproductive organ cancer (multiple); and urinary bladder cancer. Orthologous to human CDH13 (cadherin 13); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 2-acetamidofluorene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: cadherin-13; Cdht; MGC93172; T-cadherin; Tcad
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: Cdh13em1Mcwi
Genetic Models: SS-Cdh13em1Mcwi
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81963,258,251 - 64,296,122 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1963,258,122 - 64,296,119 (+)EnsemblGRCr8
mRatBN7.21946,349,562 - 47,387,462 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1946,349,430 - 47,387,459 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1953,154,689 - 54,181,827 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01953,822,337 - 54,862,256 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01956,050,181 - 57,076,905 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01950,848,793 - 51,971,618 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1950,848,736 - 51,972,103 (+)Ensemblrn6Rnor6.0
Rnor_5.01962,345,236 - 62,720,155 (+)NCBIRnor_5.0Rnor_5.0rn5
Rnor_5.01961,621,434 - 62,245,798 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41948,507,173 - 49,575,123 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1945,613,369 - 46,646,704 (+)NCBICelera
RGSC_v3.11948,512,053 - 49,580,001 (+)NCBI
Cytogenetic Map19q12NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-nitropyrene  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2-acetamidofluorene  (EXP)
3-Chloro-4-(dichloromethyl)-5-hydroxy-2(5H)-furanone  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (EXP)
acrylamide  (EXP)
aflatoxin B1  (EXP,ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
alpha-naphthoflavone  (EXP)
ammonium chloride  (EXP)
anthracen-2-amine  (EXP)
atrazine  (EXP)
benzo[a]pyrene  (EXP,ISO)
beta-lapachone  (ISO)
beta-naphthoflavone  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol AF  (ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
Butylbenzyl phthalate  (ISO)
cadmium atom  (EXP)
cadmium dichloride  (EXP)
cantharidin  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
CGP 52608  (ISO)
chlordecone  (ISO)
chlorpyrifos  (EXP)
chrysene  (ISO)
clobetasol  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
daunorubicin  (ISO)
DDE  (ISO)
decabromodiphenyl ether  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (EXP,ISO)
dieldrin  (ISO)
dimethylarsinic acid  (EXP)
dioxygen  (ISO)
Domiphen bromide  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
fenvalerate  (EXP)
flutamide  (EXP)
folic acid  (ISO)
fulvestrant  (ISO)
furan  (EXP)
glycine betaine  (EXP)
glyphosate  (EXP)
graphite  (EXP)
hexadecanoic acid  (ISO)
indole-3-methanol  (EXP)
isoprenaline  (ISO)
kainic acid  (ISO)
L-ascorbic acid  (ISO)
lead diacetate  (EXP)
lipopolysaccharide  (ISO)
mercury dibromide  (ISO)
methamphetamine  (ISO)
methimazole  (EXP)
methoxychlor  (EXP)
methylmercury chloride  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-acetyl-L-cysteine  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
nitrofen  (EXP)
ozone  (ISO)
paracetamol  (ISO)
perfluorononanoic acid  (ISO)
permethrin  (EXP)
phenylmercury acetate  (ISO)
SB 431542  (ISO)
serpentine asbestos  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
temozolomide  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. Effect of DNA Methylation on Identification of Aggressive Prostate Cancer. Alumkal JJ, etal., Urology. 2008 Apr 1;.
2. Molecular analysis of a multistep lung cancer model induced by chronic inflammation reveals epigenetic regulation of p16 and activation of the DNA damage response pathway. Blanco D, etal., Neoplasia. 2007 Oct;9(10):840-52.
3. T-cadherin is a major glycophosphoinositol-anchored protein associated with noncaveolar detergent-insoluble domains of the cardiac sarcolemma. Doyle DD, etal., J Biol Chem. 1998 Mar 20;273(12):6937-43.
4. Promoter hypermethylation of tumor suppressor genes in urine from patients with cervical neoplasia. Feng Q, etal., Cancer Epidemiol Biomarkers Prev. 2007 Jun;16(6):1178-84.
5. Correlation between CpG methylation profiles and hormone receptor status in breast cancers. Feng W, etal., Breast Cancer Res. 2007;9(4):R57.
6. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
8. T-cadherin supports angiogenesis and adiponectin association with the vasculature in a mouse mammary tumor model. Hebbard LW, etal., Cancer Res. 2008 Mar 1;68(5):1407-16.
9. T-cadherin-mediated cell growth regulation involves G2 phase arrest and requires p21(CIP1/WAF1) expression. Huang ZY, etal., Mol Cell Biol 2003 Jan;23(2):566-78.
10. T-cadherin upregulation correlates with cell-cycle progression and promotes proliferation of vascular cells. Ivanov D, etal., Cardiovasc Res. 2004 Oct 1;64(1):132-43.
11. Expression of cell adhesion molecule T-cadherin in the human vasculature. Ivanov D, etal., Histochem Cell Biol. 2001 Mar;115(3):231-42.
12. Involvement of H-cadherin (CDH13) on 16q in the region of frequent deletion in ovarian cancer. Kawakami M, etal., Int J Oncol. 1999 Oct;15(4):715-20.
13. Cdh13 and AdipoQ gene knockout alter instrumental and Pavlovian drug conditioning. King CP, etal., Genes Brain Behav. 2017 Sep;16(7):686-698. doi: 10.1111/gbb.12382. Epub 2017 May 2.
14. Expression of adhesion molecule T-cadherin is increased during neointima formation in experimental restenosis. Kudrjashova E, etal., Histochem Cell Biol. 2002 Oct;118(4):281-90. Epub 2002 Sep 27.
15. H-cadherin, a novel cadherin with growth inhibitory functions and diminished expression in human breast cancer. Lee SW Nat Med 1996 Jul;2(7):776-82.
16. Novel epigenetically deregulated genes in testicular cancer include homeobox genes and SCGB3A1 (HIN-1). Lind GE, etal., J Pathol. 2006 Dec;210(4):441-9.
17. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
18. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
19. Aryl hydrocarbon receptor ligands repress T-cadherin expression in vascular smooth muscle cells. Niermann T, etal., Biochem Biophys Res Commun 2003 Jan 24;300(4):943-9.
20. GOA pipeline RGD automated data pipeline
21. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
22. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
23. Comprehensive gene review and curation RGD comprehensive gene curation
24. Cadherin-13, a risk gene for ADHD and comorbid disorders, impacts GABAergic function in hippocampus and cognition. Rivero O, etal., Transl Psychiatry. 2015 Oct 13;5:e655. doi: 10.1038/tp.2015.152.
25. The H-cadherin (CDH13) gene is inactivated in human lung cancer. Sato M, etal., Hum Genet 1998 Jul;103(1):96-101.
26. Comparative expression patterns of T-, N-, E-cadherins, beta-catenin, and polysialic acid neural cell adhesion molecule in rat cochlea during development: implications for the nature of Kolliker's organ. Simonneau L, etal., J Comp Neurol 2003 Apr 28;459(2):113-26.
27. Aneuploidy predicts outcome in patients with endometrial carcinoma and is related to lack of CDH13 hypermethylation. Suehiro Y, etal., Clin Cancer Res. 2008 Jun 1;14(11):3354-61.
28. Loss of expression and aberrant methylation of the CDH13 (H-cadherin) gene in breast and lung carcinomas. Toyooka KO, etal., Cancer Res. 2001 Jun 1;61(11):4556-60.
29. DNA methylation profiling of ovarian carcinomas and their in vitro models identifies HOXA9, HOXB5, SCGB3A1, and CRABP1 as novel targets. Wu Q, etal., Mol Cancer. 2007 Jul 10;6:45.
30. A novel set of DNA methylation markers in urine sediments for sensitive/specific detection of bladder cancer. Yu J, etal., Clin Cancer Res. 2007 Dec 15;13(24):7296-304.
31. beta-Naphthoflavone and 3'-methoxy-4'-nitroflavone exert ambiguous effects on Ah receptor-dependent cell proliferation and gene expression in rat liver 'stem-like' cells. Zatloukalova J, etal., Biochem Pharmacol. 2007 May 15;73(10):1622-34. Epub 2007 Jan 30.
Additional References at PubMed
PMID:9650591   PMID:10601632   PMID:10737605   PMID:11027617   PMID:12060406   PMID:12477932   PMID:14729458   PMID:15210937   PMID:15703273   PMID:15816843   PMID:16013438   PMID:16099944  
PMID:16873731   PMID:17573778   PMID:17912467   PMID:18635739   PMID:21423176   PMID:23376485   PMID:23533145   PMID:25468941   PMID:27068509   PMID:27559042   PMID:28392425   PMID:35352799  


Genomics

Comparative Map Data
Cdh13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81963,258,251 - 64,296,122 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1963,258,122 - 64,296,119 (+)EnsemblGRCr8
mRatBN7.21946,349,562 - 47,387,462 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1946,349,430 - 47,387,459 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1953,154,689 - 54,181,827 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01953,822,337 - 54,862,256 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01956,050,181 - 57,076,905 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01950,848,793 - 51,971,618 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1950,848,736 - 51,972,103 (+)Ensemblrn6Rnor6.0
Rnor_5.01962,345,236 - 62,720,155 (+)NCBIRnor_5.0Rnor_5.0rn5
Rnor_5.01961,621,434 - 62,245,798 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41948,507,173 - 49,575,123 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1945,613,369 - 46,646,704 (+)NCBICelera
RGSC_v3.11948,512,053 - 49,580,001 (+)NCBI
Cytogenetic Map19q12NCBI
CDH13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381682,626,969 - 83,800,640 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1682,626,965 - 83,800,640 (+)Ensemblhg38GRCh38
GRCh371682,660,574 - 83,834,245 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361681,218,079 - 82,387,702 (+)NCBIBuild 36Build 36hg18NCBI36
Build 341681,218,078 - 82,387,698NCBI
Celera1666,958,625 - 68,131,309 (+)NCBICelera
Cytogenetic Map16q23.3NCBI
HuRef1668,413,614 - 69,581,731 (+)NCBIHuRef
CHM1_11684,071,783 - 85,241,595 (+)NCBICHM1_1
T2T-CHM13v2.01688,691,276 - 89,866,370 (+)NCBIT2T-CHM13v2.0
Cdh13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398119,010,150 - 120,051,668 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8119,010,472 - 120,051,660 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm388118,140,017 - 119,324,929 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8118,283,733 - 119,324,921 (+)Ensemblmm10GRCm38
MGSCv378120,807,655 - 121,847,348 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv368121,169,722 - 122,209,431 (+)NCBIMGSCv36mm8
Celera8122,501,087 - 123,539,200 (+)NCBICelera
Cytogenetic Map8E1NCBI
cM Map865.97NCBI
Cdh13
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955564408,730 - 1,426,841 (-)Ensembl
ChiLan1.0NW_004955564407,120 - 1,549,880 (-)NCBIChiLan1.0ChiLan1.0
CDH13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21892,377,952 - 93,541,587 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11698,297,600 - 99,460,039 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01663,255,482 - 64,418,053 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11682,651,203 - 83,810,566 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1682,883,184 - 83,808,996 (+)EnsemblpanPan2panpan1.1
CDH13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1568,491,156 - 69,586,119 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl568,492,022 - 69,489,255 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha568,504,431 - 69,504,811 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0568,788,965 - 69,796,268 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl568,788,965 - 69,795,981 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1568,736,496 - 69,737,712 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0568,572,996 - 69,574,406 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0568,989,116 - 69,991,896 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Cdh13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934928,171,641 - 28,469,935 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366413,931,033 - 4,224,101 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366413,925,185 - 4,223,421 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CDH13
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl64,808,255 - 5,832,415 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.164,809,752 - 5,832,188 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.265,214,298 - 5,364,555 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CDH13
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1568,048,655 - 69,213,102 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl568,451,894 - 69,211,534 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660476,608,086 - 7,783,994 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cdh13
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247463,698,196 - 4,759,442 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247463,696,608 - 4,759,693 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Cdh13
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11737,937,303 - 38,980,550 (+)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:316
Count of miRNA genes:191
Interacting mature miRNAs:208
Transcripts:ENSRNOT00000019298
Prediction methods:Microtar, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)191922068964220689Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032907674246245Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)194622677874246245Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)193236531174246245Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)193628974246245Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)192409397369093973Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191083361874246245Rat
2303628Vencon9Ventilatory control QTL 90.005respiration trait (VT:0001943)minute ventilation (CMO:0000132)192318858668188586Rat
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)194438513474246245Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)193253961574246245Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)196124916174246245Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)193177788874246245Rat
1554318Bmd5Bone mineral density QTL 512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)192318858668188586Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)192010930665109306Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19219431774246245Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)194172254674246245Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19219431774246245Rat

Markers in Region
D19Mit11  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81964,286,029 - 64,286,222 (+)Marker Load Pipeline
mRatBN7.21947,377,369 - 47,377,562 (+)MAPPERmRatBN7.2
Rnor_6.01951,961,523 - 51,961,715NCBIRnor6.0
Rnor_5.01962,710,063 - 62,710,255UniSTSRnor5.0
RGSC_v3.41949,565,030 - 49,565,223RGDRGSC3.4
RGSC_v3.41949,565,031 - 49,565,223UniSTSRGSC3.4
Celera1946,636,612 - 46,636,804UniSTS
RGSC_v3.11949,569,903 - 49,570,236RGD
RH 3.4 Map19648.7UniSTS
RH 3.4 Map19648.7RGD
RH 2.0 Map19641.8RGD
Cytogenetic Map19q12UniSTS
D19Rat107  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81963,330,863 - 63,330,988 (+)Marker Load Pipeline
mRatBN7.21946,422,168 - 46,422,293 (+)MAPPERmRatBN7.2
Rnor_6.01950,921,416 - 50,921,540NCBIRnor6.0
Rnor_5.01961,693,845 - 61,693,969UniSTSRnor5.0
RGSC_v3.41948,580,098 - 48,580,222UniSTSRGSC3.4
RGSC_v3.41948,580,097 - 48,580,222RGDRGSC3.4
Celera1945,685,912 - 45,686,036UniSTS
RGSC_v3.11948,584,978 - 48,585,103RGD
SHRSP x BN Map1941.4898RGD
SHRSP x BN Map1941.4898UniSTS
Cytogenetic Map19q12UniSTS
D19Got53  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21946,863,392 - 46,863,594 (+)MAPPERmRatBN7.2
Rnor_6.01951,448,264 - 51,448,465NCBIRnor6.0
Rnor_5.01962,204,148 - 62,204,349UniSTSRnor5.0
RGSC_v3.41949,122,394 - 49,122,595UniSTSRGSC3.4
RGSC_v3.41949,122,393 - 49,122,595RGDRGSC3.4
Celera1946,125,257 - 46,125,458UniSTS
RGSC_v3.11949,127,275 - 49,127,476RGD
RH 3.4 Map19612.6UniSTS
RH 3.4 Map19612.6RGD
RH 2.0 Map19644.1RGD
Cytogenetic Map19q12UniSTS
BE119741  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21947,003,862 - 47,004,022 (+)MAPPERmRatBN7.2
Rnor_6.01951,589,004 - 51,589,163NCBIRnor6.0
Rnor_5.01962,340,062 - 62,340,221UniSTSRnor5.0
RGSC_v3.41949,272,400 - 49,272,559UniSTSRGSC3.4
Celera1946,265,431 - 46,265,590UniSTS
RH 3.4 Map19633.4UniSTS
Cytogenetic Map19q12UniSTS
RH128547  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21947,387,581 - 47,387,762 (+)MAPPERmRatBN7.2
Rnor_6.01951,971,735 - 51,971,915NCBIRnor6.0
Rnor_5.01962,720,275 - 62,720,455UniSTSRnor5.0
RGSC_v3.41949,575,243 - 49,575,423UniSTSRGSC3.4
Celera1946,646,824 - 46,647,004UniSTS
RH 3.4 Map19655.0UniSTS
Cytogenetic Map19q12UniSTS
RH132183  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21947,387,250 - 47,387,438 (+)MAPPERmRatBN7.2
Rnor_6.01951,971,404 - 51,971,591NCBIRnor6.0
Rnor_5.01962,719,944 - 62,720,131UniSTSRnor5.0
RGSC_v3.41949,574,912 - 49,575,099UniSTSRGSC3.4
Celera1946,646,493 - 46,646,680UniSTS
RH 3.4 Map19649.8UniSTS
Cytogenetic Map19q12UniSTS
BG376843  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81963,555,534 - 63,555,761 (+)Marker Load Pipeline
mRatBN7.21946,646,856 - 46,647,083 (+)MAPPERmRatBN7.2
Rnor_6.01951,143,490 - 51,143,716NCBIRnor6.0
Rnor_5.01961,914,796 - 61,915,022UniSTSRnor5.0
RGSC_v3.41948,810,495 - 48,810,721UniSTSRGSC3.4
Celera1945,909,812 - 45,910,038UniSTS
RH 3.4 Map19656.4UniSTS
Cytogenetic Map19q12UniSTS
BE112937  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21946,668,049 - 46,668,222 (+)MAPPERmRatBN7.2
Rnor_6.01951,164,661 - 51,164,833NCBIRnor6.0
Rnor_5.01961,934,759 - 61,934,931UniSTSRnor5.0
RGSC_v3.41948,842,269 - 48,842,441UniSTSRGSC3.4
Celera1945,929,977 - 45,930,149UniSTS
RH 3.4 Map19634.3UniSTS
Cytogenetic Map19q12UniSTS
BF391658  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21947,340,646 - 47,340,844 (+)MAPPERmRatBN7.2
Rnor_6.01951,925,114 - 51,925,311NCBIRnor6.0
Rnor_5.01962,673,654 - 62,673,851UniSTSRnor5.0
RGSC_v3.41949,528,622 - 49,528,819UniSTSRGSC3.4
Celera1946,600,294 - 46,600,491UniSTS
RH 3.4 Map19654.0UniSTS
Cytogenetic Map19q12UniSTS
AU048918  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21946,891,380 - 46,891,669 (+)MAPPERmRatBN7.2
Rnor_6.01951,476,127 - 51,476,415NCBIRnor6.0
Rnor_5.01962,231,661 - 62,231,949UniSTSRnor5.0
RGSC_v3.41949,151,370 - 49,151,658UniSTSRGSC3.4
Celera1946,153,207 - 46,153,495UniSTS
Cytogenetic Map19q12UniSTS


Genetic Models
This gene Cdh13 is modified in the following models/strains:
SS-Cdh13em1Mcwi    


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 161 91 90 59 61 59 6 324 161 11 140 80 94 31 16 16

Sequence


Ensembl Acc Id: ENSRNOT00000019298   ⟹   ENSRNOP00000019298
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1963,434,028 - 64,296,119 (+)Ensembl
mRatBN7.2 Ensembl1946,349,575 - 47,387,452 (+)Ensembl
Rnor_6.0 Ensembl1951,317,425 - 51,972,103 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000077053   ⟹   ENSRNOP00000068368
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1963,258,122 - 64,296,119 (+)Ensembl
mRatBN7.2 Ensembl1946,349,430 - 47,387,459 (+)Ensembl
Rnor_6.0 Ensembl1950,848,736 - 51,971,615 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000096949   ⟹   ENSRNOP00000080752
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1946,572,115 - 47,378,814 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000098921   ⟹   ENSRNOP00000078354
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1946,572,624 - 47,386,361 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000114490   ⟹   ENSRNOP00000077903
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1946,823,655 - 47,378,814 (+)Ensembl
RefSeq Acc Id: NM_138889   ⟹   NP_620244
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81963,258,251 - 64,296,122 (+)NCBI
mRatBN7.21946,349,562 - 47,387,462 (+)NCBI
Rnor_6.01950,848,793 - 51,971,615 (+)NCBI
Rnor_5.01961,621,434 - 62,245,798 (+)NCBI
Rnor_5.01962,345,236 - 62,720,155 (+)NCBI
RGSC_v3.41948,507,173 - 49,575,123 (+)RGD
Celera1945,613,369 - 46,646,704 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_620244 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH85699 (Get FASTA)   NCBI Sequence Viewer  
  AAM14607 (Get FASTA)   NCBI Sequence Viewer  
  EDL92658 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000019298.8
  ENSRNOP00000068368
  ENSRNOP00000068368.1
RefSeq Acc Id: NP_620244   ⟸   NM_138889
- Peptide Label: precursor
- UniProtKB: Q8R490 (UniProtKB/TrEMBL),   A6IZI0 (UniProtKB/TrEMBL),   A0A8I6G502 (UniProtKB/TrEMBL),   A0A096MK38 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000068368   ⟸   ENSRNOT00000077053
Ensembl Acc Id: ENSRNOP00000019298   ⟸   ENSRNOT00000019298
Ensembl Acc Id: ENSRNOP00000080752   ⟸   ENSRNOT00000096949
Ensembl Acc Id: ENSRNOP00000078354   ⟸   ENSRNOT00000098921
Ensembl Acc Id: ENSRNOP00000077903   ⟸   ENSRNOT00000114490
Protein Domains
Cadherin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8R490-F1-model_v2 AlphaFold Q8R490 1-714 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13701176
Promoter ID:EPDNEW_R11698
Type:initiation region
Name:Cdh13_1
Description:cadherin 13
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01950,848,806 - 50,848,866EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619745 AgrOrtholog
BioCyc Gene G2FUF-5531 BioCyc
Ensembl Genes ENSRNOG00000014371 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019298.9 UniProtKB/TrEMBL
  ENSRNOT00000077053 ENTREZGENE
  ENSRNOT00000077053.4 UniProtKB/TrEMBL
Gene3D-CATH Cadherins UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7106186 IMAGE-MGC_LOAD
InterPro Cadherin UniProtKB/TrEMBL
  Cadherin UniProtKB/TrEMBL
  Cadherin-like UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
  Cadherin_pro UniProtKB/TrEMBL
KEGG Report rno:192248 UniProtKB/TrEMBL
MGC_CLONE MGC:93172 IMAGE-MGC_LOAD
NCBI Gene 192248 ENTREZGENE
PANTHER PTHR24027 UniProtKB/TrEMBL
  PTHR24027:SF80 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_pro UniProtKB/TrEMBL
PharmGKB CDH13 RGD
PhenoGen Cdh13 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000014371 RatGTEx
SMART Cadherin_pro UniProtKB/TrEMBL
  SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin UniProtKB/TrEMBL
UniProt A0A096MK38 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6G502 ENTREZGENE
  A6IZI0 ENTREZGENE
  F1M7X3_RAT UniProtKB/TrEMBL
  Q8R490 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary A6IZI0 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Cdh13  cadherin 13      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Cdh13  cadherin 13      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in fibrocyte and pillar cells of cochlea during development 1299192
gene_process mediates growth arrest that is dependent on p21(CIP1/WAF1) expression 632358
gene_regulation expression is negatively regulated through aryl hydrocarbon receptor/aryl hydrocarbon nuclear translocator (AHR) signaling 632357