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 have several functions, including adiponectin binding activity; cadherin binding activity; and low-density lipoprotein particle binding activity. Involved in mitotic cell cycle and response to organic substance. Localizes to GABA-ergic synapse; perinuclear region of cytoplasm; and plasma membrane. 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
Also known as: cadherin-13; Cdht; MGC93172; T-cadherin; Tcad
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Cdh13em1Mcwi  
Genetic Models: SS-Cdh13em1Mcwi
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21946,349,562 - 47,387,462 (+)NCBI
Rnor_6.0 Ensembl1950,848,736 - 51,972,103 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01950,848,793 - 51,971,618 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01961,621,434 - 62,245,798 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01962,345,236 - 62,720,155 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41948,507,173 - 49,575,123 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11948,512,053 - 49,580,001 (+)NCBI
Celera1945,613,369 - 46,646,704 (+)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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-acetamidofluorene  (EXP)
3-Chloro-4-(dichloromethyl)-5-hydroxy-2(5H)-furanone  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (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  (ISO)
all-trans-retinoic acid  (ISO)
alpha-naphthoflavone  (EXP)
ammonium chloride  (EXP)
anthracen-2-amine  (EXP)
atrazine  (EXP)
benzo[a]pyrene  (EXP,ISO)
beta-naphthoflavone  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
chlorpyrifos  (EXP)
chrysene  (ISO)
clobetasol  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (ISO)
daunorubicin  (ISO)
decabromodiphenyl ether  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (EXP,ISO)
dimethylarsinic acid  (EXP)
dioxygen  (ISO)
Domiphen bromide  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
fenvalerate  (EXP)
flutamide  (EXP)
folic acid  (ISO)
furan  (EXP)
glycine betaine  (EXP)
glyphosate  (EXP)
graphite  (EXP)
indole-3-methanol  (EXP)
isoprenaline  (ISO)
kainic acid  (ISO)
L-ascorbic acid  (ISO)
lipopolysaccharide  (ISO)
mercury dibromide  (ISO)
methamphetamine  (ISO)
methylmercury chloride  (ISO)
N-acetyl-L-cysteine  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
ozone  (ISO)
paracetamol  (ISO)
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)
trichostatin A  (ISO)
triclosan  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
1. Alumkal JJ, etal., Urology. 2008 Apr 1;.
2. Blanco D, etal., Neoplasia. 2007 Oct;9(10):840-52.
3. Doyle DD, etal., J Biol Chem. 1998 Mar 20;273(12):6937-43.
4. Feng Q, etal., Cancer Epidemiol Biomarkers Prev. 2007 Jun;16(6):1178-84.
5. Feng W, etal., Breast Cancer Res. 2007;9(4):R57.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. GOA data from the GO Consortium
8. Hebbard LW, etal., Cancer Res. 2008 Mar 1;68(5):1407-16.
9. Huang ZY, etal., Mol Cell Biol 2003 Jan;23(2):566-78.
10. Ivanov D, etal., Cardiovasc Res. 2004 Oct 1;64(1):132-43.
11. Ivanov D, etal., Histochem Cell Biol. 2001 Mar;115(3):231-42.
12. Kawakami M, etal., Int J Oncol. 1999 Oct;15(4):715-20.
13. King CP, etal., Genes Brain Behav. 2017 Sep;16(7):686-698. doi: 10.1111/gbb.12382. Epub 2017 May 2.
14. Kudrjashova E, etal., Histochem Cell Biol. 2002 Oct;118(4):281-90. Epub 2002 Sep 27.
15. Lee SW Nat Med 1996 Jul;2(7):776-82.
16. Lind GE, etal., J Pathol. 2006 Dec;210(4):441-9.
17. MGD data from the GO Consortium
18. NCBI rat LocusLink and RefSeq merged data July 26, 2002
19. Niermann T, etal., Biochem Biophys Res Commun 2003 Jan 24;300(4):943-9.
20. RGD automated data pipeline
21. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
22. RGD automated import pipeline for gene-chemical interactions
23. RGD comprehensive gene curation
24. Rivero O, etal., Transl Psychiatry. 2015 Oct 13;5:e655. doi: 10.1038/tp.2015.152.
25. Sato M, etal., Hum Genet 1998 Jul;103(1):96-101.
26. Simonneau L, etal., J Comp Neurol 2003 Apr 28;459(2):113-26.
27. Suehiro Y, etal., Clin Cancer Res. 2008 Jun 1;14(11):3354-61.
28. Toyooka KO, etal., Cancer Res. 2001 Jun 1;61(11):4556-60.
29. Wu Q, etal., Mol Cancer. 2007 Jul 10;6:45.
30. Yu J, etal., Clin Cancer Res. 2007 Dec 15;13(24):7296-304.
31. 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  


Genomics

Comparative Map Data
Cdh13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21946,349,562 - 47,387,462 (+)NCBI
Rnor_6.0 Ensembl1950,848,736 - 51,972,103 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01950,848,793 - 51,971,618 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01961,621,434 - 62,245,798 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01962,345,236 - 62,720,155 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41948,507,173 - 49,575,123 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11948,512,053 - 49,580,001 (+)NCBI
Celera1945,613,369 - 46,646,704 (+)NCBICelera
Cytogenetic Map19q12NCBI
CDH13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1682,626,965 - 83,800,640 (+)EnsemblGRCh38hg38GRCh38
GRCh381682,626,823 - 83,800,640 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371682,660,574 - 83,834,245 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361681,218,079 - 82,387,702 (+)NCBINCBI36hg18NCBI36
Build 341681,218,078 - 82,387,698NCBI
Celera1666,958,625 - 68,131,309 (+)NCBI
Cytogenetic Map16q23.3NCBI
HuRef1668,413,614 - 69,581,731 (+)NCBIHuRef
CHM1_11684,071,783 - 85,241,595 (+)NCBICHM1_1
Cdh13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398119,010,150 - 120,051,668 (+)NCBIGRCm39mm39
GRCm39 Ensembl8119,010,472 - 120,051,660 (+)Ensembl
GRCm388118,140,017 - 119,324,929 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8118,283,733 - 119,324,921 (+)EnsemblGRCm38mm10GRCm38
MGSCv378120,807,655 - 121,847,348 (+)NCBIGRCm37mm9NCBIm37
MGSCv368121,169,722 - 122,209,431 (+)NCBImm8
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 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955564407,120 - 1,549,880 (-)NCBIChiLan1.0ChiLan1.0
CDH13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11682,651,203 - 83,810,566 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1682,883,184 - 83,808,996 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01663,255,482 - 64,418,053 (+)NCBIMhudiblu_PPA_v0panPan3
CDH13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl568,492,022 - 69,489,255 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1568,491,156 - 69,586,119 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Cdh13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 - 5,832,188 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.164,809,752 - 5,832,188 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.265,214,298 - 5,364,555 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CDH13
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1568,048,655 - 69,213,102 (+)NCBI
ChlSab1.1 Ensembl568,451,894 - 69,211,534 (+)Ensembl
Cdh13
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247463,696,608 - 4,759,693 (-)NCBI

Position Markers
D19Mit11  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
RGSC_v3.11949,569,903 - 49,570,236RGD
Celera1946,636,612 - 46,636,804UniSTS
RH 3.4 Map19648.7UniSTS
RH 3.4 Map19648.7RGD
RH 2.0 Map19641.8RGD
Cytogenetic Map19q12UniSTS
D19Rat107  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01950,921,416 - 50,921,540NCBIRnor6.0
Rnor_5.01961,693,845 - 61,693,969UniSTSRnor5.0
RGSC_v3.41948,580,097 - 48,580,222RGDRGSC3.4
RGSC_v3.41948,580,098 - 48,580,222UniSTSRGSC3.4
RGSC_v3.11948,584,978 - 48,585,103RGD
Celera1945,685,912 - 45,686,036UniSTS
SHRSP x BN Map1941.4898UniSTS
SHRSP x BN Map1941.4898RGD
Cytogenetic Map19q12UniSTS
D19Got53  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01951,448,264 - 51,448,465NCBIRnor6.0
Rnor_5.01962,204,148 - 62,204,349UniSTSRnor5.0
RGSC_v3.41949,122,393 - 49,122,595RGDRGSC3.4
RGSC_v3.41949,122,394 - 49,122,595UniSTSRGSC3.4
RGSC_v3.11949,127,275 - 49,127,476RGD
Celera1946,125,257 - 46,125,458UniSTS
RH 3.4 Map19612.6RGD
RH 3.4 Map19612.6UniSTS
RH 2.0 Map19644.1RGD
Cytogenetic Map19q12UniSTS
BE119741  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
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
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
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
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
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
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


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191702800352538299Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191899398262275575Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191917749562275575Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)192140778762275575Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192481825762275575Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)193299439262275575Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193791679960220451Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193791679960220451Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194883071260220581Rat


Genetic Models
This gene Cdh13 is modified in the following models/strains
miRNA Target Status

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.


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 circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 31 1 8 11 64 14 11 4 8
Low 3 12 47 31 18 31 10 21 30 7
Below cutoff 10 10 10

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000019298   ⟹   ENSRNOP00000019298
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1951,317,425 - 51,972,103 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000077053   ⟹   ENSRNOP00000068368
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1950,848,736 - 51,971,615 (+)Ensembl
RefSeq Acc Id: NM_138889   ⟹   NP_620244
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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:
RefSeq Acc Id: XM_017601173   ⟹   XP_017456662
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01951,543,366 - 51,971,618 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601174   ⟹   XP_017456663
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01951,599,233 - 51,971,618 (+)NCBI
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  
Reference Sequences
RefSeq Acc Id: NP_620244   ⟸   NM_138889
- UniProtKB: Q8R490 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456662   ⟸   XM_017601173
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017456663   ⟸   XM_017601174
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000068368   ⟸   ENSRNOT00000077053
RefSeq Acc Id: ENSRNOP00000019298   ⟸   ENSRNOT00000019298
Protein Domains
Cadherin

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619745 AgrOrtholog
Ensembl Genes ENSRNOG00000014371 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000019298 UniProtKB/TrEMBL
  ENSRNOP00000068368 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019298 UniProtKB/TrEMBL
  ENSRNOT00000077053 ENTREZGENE, 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
  CDH13 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
SMART Cadherin_pro UniProtKB/TrEMBL
  SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin UniProtKB/TrEMBL
UniProt F1M7X3_RAT UniProtKB/TrEMBL
  Q8R490 ENTREZGENE, 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