Cdh2 (cadherin 2) - Rat Genome Database

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Gene: Cdh2 (cadherin 2) Rattus norvegicus
Analyze
Symbol: Cdh2
Name: cadherin 2
RGD ID: 69280
Description: Exhibits beta-catenin binding activity; nitric-oxide synthase binding activity; and protein kinase binding activity. Involved in several processes, including calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules; regulation of glutamatergic synaptic transmission; and regulation of myelination. Localizes to several cellular components, including T-tubule; fascia adherens; and integral component of synaptic membrane. Predicted to colocalize with cortical actin cytoskeleton. Human ortholog(s) of this gene implicated in arrhythmogenic right ventricular cardiomyopathy. Orthologous to human CDH2 (cadherin 2); PARTICIPATES IN cadherin mediated signaling pathway; fibroblast growth factor signaling pathway; N-cadherin signaling pathway; INTERACTS WITH (+)-pilocarpine; 1,1-bis(2-aminoethyl)-2-hydroxy-3-oxotriazane; 1,3-dinitrobenzene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: cadherin 2 type 1 N-cadherin (neuronal); cadherin 2, type 1, N-cadherin (neuronal); cadherin-2; N-cadherin; neural cadherin
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2187,776,704 - 7,990,934 (-)NCBI
Rnor_6.0 Ensembl188,146,971 - 8,360,684 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0188,146,971 - 8,366,037 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0187,997,533 - 8,218,018 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4188,048,920 - 8,267,974 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1188,048,919 - 8,268,462 (-)NCBI
Celera187,938,006 - 8,155,134 (-)NCBICelera
Cytogenetic Map18p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(+)-Tetrandrine  (ISO)
(S)-amphetamine  (ISO)
1,1-bis(2-aminoethyl)-2-hydroxy-3-oxotriazane  (EXP,ISO)
1,2-dichloroethane  (ISO)
1,3-dinitrobenzene  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3-dimethoxynaphthalene-1,4-dione  (ISO)
2,4-Dihydroxybenzophenone  (ISO)
2,4-dinitrotoluene  (EXP)
2-butoxyethanol  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,3'-diindolylmethane  (ISO)
3,4-methylenedioxymethamphetamine  (EXP,ISO)
3-chloropropane-1,2-diol  (EXP)
3-methylcholanthrene  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-tert-Octylphenol  (EXP,ISO)
5-aza-2'-deoxycytidine  (EXP,ISO)
5-azacytidine  (EXP)
6-propyl-2-thiouracil  (EXP)
acrolein  (EXP)
acrylonitrile  (ISO)
aflatoxin B1  (ISO)
alendronic acid  (EXP)
all-trans-retinoic acid  (ISO)
ametryn  (EXP)
ammonium chloride  (EXP)
andrographolide  (ISO)
antroquinonol  (ISO)
arecoline  (ISO)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsenite(3-)  (EXP,ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
berberine  (ISO)
biochanin A  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
calcidiol  (EXP)
calciol  (ISO)
calcitriol  (ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
chloroprene  (ISO)
chloroquine  (EXP)
chrysin  (ISO)
cisatracurium  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cobalt atom  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
corticosterone  (ISO)
coumarin  (ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cyclophosphamide  (EXP)
cyclosporin A  (ISO)
DAPT  (EXP)
DDE  (EXP)
DDT  (ISO)
Deguelin  (ISO)
delphinidin  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibenzo[a,l]pyrene  (ISO)
dibutyl phthalate  (EXP,ISO)
dicrotophos  (ISO)
Dictamnine  (ISO)
dieckol  (ISO)
dieldrin  (EXP)
dioxygen  (ISO)
disodium selenite  (ISO)
disulfiram  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
ethanol  (ISO)
ethyl trans-caffeate  (ISO)
fisetin  (ISO)
flubendazole  (ISO)
fludioxonil  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
genistein  (ISO)
Ginkgoic acid  (ISO)
glafenine  (EXP)
Goe 6976  (EXP)
gossypol  (EXP)
hydrogen peroxide  (ISO)
hydroxyflutamide  (ISO)
isoprenaline  (ISO)
isoprene  (ISO)
jaspamide  (ISO)
L-ascorbic acid  (EXP)
lapatinib  (ISO)
lithium chloride  (ISO)
luteolin  (ISO)
LY294002  (ISO)
mebendazole  (ISO)
menadione  (ISO)
mercury dichloride  (EXP)
methapyrilene  (EXP)
methylarsonic acid  (EXP)
methylmercury chloride  (ISO)
mono(2-ethylhexyl) phthalate  (EXP)
Monobutylphthalate  (ISO)
monocrotaline  (EXP)
morusin  (ISO)
N(6),N(6)-dimethyladenine  (EXP)
N-acetyl-L-cysteine  (EXP,ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-methyl-N-nitrosourea  (EXP)
N-nitrosodiethylamine  (EXP)
nefazodone  (EXP)
niclosamide  (ISO)
nimesulide  (EXP)
nitrogen mustard  (ISO)
Nonylphenol  (EXP,ISO)
novobiocin  (ISO)
oridonin  (ISO)
ouabain  (ISO)
oxaliplatin  (EXP)
p-cresol  (EXP)
p-tert-Amylphenol  (EXP,ISO)
palbociclib  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
pentachlorophenol  (ISO)
perfluorooctane-1-sulfonic acid  (EXP)
perfluorooctanoic acid  (ISO)
phenobarbital  (EXP,ISO)
phenol red  (ISO)
phenylephrine  (EXP)
phenylmercury acetate  (ISO)
phenytoin  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (EXP,ISO)
potassium iodide  (EXP)
pregnenolone 16alpha-carbonitrile  (EXP)
progesterone  (ISO)
quercetin  (EXP,ISO)
raloxifene  (EXP,ISO)
resveratrol  (ISO)
rofecoxib  (ISO)
Salidroside  (ISO)
Salinomycin  (ISO)
SB 431542  (ISO)
sirolimus  (EXP)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sodium fluoride  (ISO)
Soman  (EXP)
sorafenib  (ISO)
streptozocin  (ISO)
sulforaphane  (ISO)
sulfur dioxide  (ISO)
tamoxifen  (ISO)
tauroursodeoxycholic acid  (EXP)
testosterone  (EXP,ISO)
tetrachloromethane  (ISO)
thymoquinone  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
trimethylarsine oxide  (EXP)
Tungsten carbide  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vitamin D  (EXP)
vitamin E  (EXP)
wortmannin  (ISO)
XAV939  (ISO)
zardaverine  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
blood vessel morphogenesis  (IBA,IEA,ISO)
brain development  (IBA)
brain morphogenesis  (IEA,ISO)
calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules  (IEA,IMP,ISO)
cell adhesion  (ISO)
cell migration  (ISO)
cell-cell adhesion  (IDA,ISO)
cell-cell adhesion mediated by cadherin  (IEA,ISO,ISS)
cell-cell adhesion via plasma-membrane adhesion molecules  (IBA)
cell-cell junction assembly  (IEA,ISO,ISS)
cerebral cortex development  (IEA,ISO)
glial cell differentiation  (ISO,ISS)
heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules  (IEA,ISO)
homeostasis of number of cells  (IEA,ISO)
homophilic cell adhesion via plasma membrane adhesion molecules  (IBA,IEA,ISO)
mesenchymal cell migration  (IEA,ISO)
modulation of chemical synaptic transmission  (EXP)
negative regulation of canonical Wnt signaling pathway  (IEA,ISO)
neural crest cell development  (IEA,ISO,ISS)
neuroepithelial cell differentiation  (IEA,ISO)
neuroligin clustering involved in postsynaptic membrane assembly  (IEA,ISO)
neuronal stem cell population maintenance  (IEA,ISO,ISS)
positive regulation of MAPK cascade  (IEA,ISO)
positive regulation of synaptic vesicle clustering  (IEA,ISO)
protein localization to plasma membrane  (IEA,ISO)
radial glial cell differentiation  (IEA,ISO)
regulation of axonogenesis  (IBA,IMP)
regulation of myelination  (IMP)
regulation of oligodendrocyte progenitor proliferation  (IEA,ISO)
regulation of postsynaptic density protein 95 clustering  (IEA,ISO)
regulation of protein localization  (IMP)
regulation of Rho protein signal transduction  (IMP)
regulation of synaptic transmission, glutamatergic  (IBA,IMP)
striated muscle cell differentiation  (IEA,ISO)
synapse assembly  (IBA,IMP)
synaptic membrane adhesion  (IC)
telencephalon development  (ISO)
type B pancreatic cell development  (IEA,ISO,ISS)

Molecular Function

References

References - curated
1. Bakkaloglu B, etal., Am J Hum Genet. 2008 Jan;82(1):165-73. doi: 10.1016/j.ajhg.2007.09.017.
2. Bozdagi O, etal., Neuron. 2000 Oct;28(1):245-59.
3. Chen YM, etal., Biol Reprod. 2003 Aug;69(2):656-72. Epub 2003 Apr 16.
4. Chung SS, etal., Endocrinology 1998 Apr;139(4):1853-62.
5. Fasen K, etal., J Neuropathol Exp Neurol 2002 Oct;61(10):903-13.
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. Gorski JA, etal., Mol Biol Cell. 2005 Aug;16(8):3574-90. Epub 2005 Jun 1.
9. Hermiston ML and Gordon JI, Science 1995 Nov 17;270(5239):1203-7.
10. Hertig CM, etal., J Cell Sci. 1996 Jan;109 ( Pt 1):11-20.
11. Johnson KJ, etal., Endocrinology 2000 Feb;141(2):675-83.
12. Jones M, etal., Arterioscler Thromb Vasc Biol 2002 Dec 1;22(12):1972-7.
13. Kwon YT, etal., Curr Biol. 2000 Apr 6;10(7):363-72.
14. Lee NP, etal., Biol Reprod. 2003 Feb;68(2):489-508.
15. Lee NP, etal., Biol Reprod. 2005 Sep;73(3):458-71. Epub 2005 Apr 27.
16. Liang JR and Yang H, Biomed Pharmacother. 2020 May;125:109585. doi: 10.1016/j.biopha.2019.109585. Epub 2020 Feb 25.
17. Matsuda T, etal., J Mol Cell Cardiol. 2006 Apr;40(4):495-502. Epub 2006 Mar 2.
18. Mayosi BM, etal., Circ Cardiovasc Genet. 2017 Apr;10(2). pii: CIRCGENETICS.116.001605. doi: 10.1161/CIRCGENETICS.116.001605.
19. MGD data from the GO Consortium
20. Mohler PJ, etal., Proc Natl Acad Sci U S A. 2004 Dec 14;101(50):17533-8. Epub 2004 Dec 3.
21. NCBI rat LocusLink and RefSeq merged data July 26, 2002
22. Pipeline to import KEGG annotations from KEGG into RGD
23. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
24. Poskanzer K, etal., J Neurosci 2003 Mar 15;23(6):2294-305.
25. Ranchoux B, etal., Circulation. 2015 Mar 17;131(11):1006-18. doi: 10.1161/CIRCULATIONAHA.114.008750. Epub 2015 Jan 15.
26. RGD automated data pipeline
27. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
28. RGD automated import pipeline for gene-chemical interactions
29. Sato M, etal., J Biol Chem. 2009 Nov 6;284(45):31431-40. doi: 10.1074/jbc.M109.014068. Epub 2009 Sep 1.
30. Schnadelbach O, etal., Mol Cell Neurosci. 2001 Jun;17(6):1084-93.
31. Shan W, etal., J Neurosci Res 2002 Aug 1;69(3):292-304.
32. Simonneau L, etal., J Comp Neurol 2003 Apr 28;459(2):113-26.
33. Tang L, etal., Neuron. 1998 Jun;20(6):1165-75.
34. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
35. Turkowski KL, etal., Congenit Heart Dis. 2017 Mar;12(2):226-235. doi: 10.1111/chd.12462. Epub 2017 Mar 21.
36. Xia W, etal., J Biol Chem. 2006 Jun 16;281(24):16799-813. Epub 2006 Apr 13.
Additional References at PubMed
PMID:7650039   PMID:8270638   PMID:9531566   PMID:9655503   PMID:11732910   PMID:12052883   PMID:12203715   PMID:12695331   PMID:12738802   PMID:14561752   PMID:14622577   PMID:14657280  
PMID:15383621   PMID:15389538   PMID:15569714   PMID:15691707   PMID:15741167   PMID:15750591   PMID:15809310   PMID:16580782   PMID:16831887   PMID:16886205   PMID:16892058   PMID:16955247  
PMID:16973135   PMID:17028923   PMID:17188238   PMID:17884088   PMID:17959753   PMID:17988630   PMID:18064706   PMID:18067145   PMID:18239929   PMID:18617695   PMID:19075000   PMID:19101069  
PMID:19377287   PMID:19546590   PMID:19830702   PMID:20160094   PMID:20190754   PMID:20333303   PMID:20457910   PMID:20534458   PMID:20623533   PMID:20638445   PMID:20668183   PMID:20848607  
PMID:20881055   PMID:21056983   PMID:21250828   PMID:21257918   PMID:21296051   PMID:21300292   PMID:21414924   PMID:21423176   PMID:21520058   PMID:21572446   PMID:21720156   PMID:21720765  
PMID:21947081   PMID:22199283   PMID:22328515   PMID:22354041   PMID:22467863   PMID:22489706   PMID:22698587   PMID:22735489   PMID:22871113   PMID:23271561   PMID:23292232   PMID:23376485  
PMID:23392350   PMID:24046456   PMID:24223993   PMID:24338362   PMID:24412534   PMID:24891510   PMID:24952463   PMID:25100583   PMID:25232112   PMID:25512490   PMID:25724647   PMID:26187182  
PMID:26345922   PMID:26403541   PMID:26545901   PMID:27559042   PMID:27816814   PMID:28008617   PMID:28169360   PMID:28213972   PMID:28641114   PMID:29131030   PMID:29133434   PMID:29238079  
PMID:29257288   PMID:29768261  


Genomics

Comparative Map Data
Cdh2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2187,776,704 - 7,990,934 (-)NCBI
Rnor_6.0 Ensembl188,146,971 - 8,360,684 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0188,146,971 - 8,366,037 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0187,997,533 - 8,218,018 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4188,048,920 - 8,267,974 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1188,048,919 - 8,268,462 (-)NCBI
Celera187,938,006 - 8,155,134 (-)NCBICelera
Cytogenetic Map18p13NCBI
CDH2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1827,932,879 - 28,177,946 (-)EnsemblGRCh38hg38GRCh38
GRCh381827,932,878 - 28,177,130 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371825,530,930 - 25,757,094 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361823,784,933 - 24,011,189 (-)NCBINCBI36hg18NCBI36
Build 341823,784,933 - 24,011,189NCBI
Celera1822,342,317 - 22,568,868 (-)NCBI
Cytogenetic Map18q12.1NCBI
HuRef1822,383,072 - 22,579,896 (-)NCBIHuRef
CHM1_11825,458,398 - 25,684,881 (-)NCBICHM1_1
Cdh2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391816,721,934 - 16,942,303 (-)NCBIGRCm39mm39
GRCm39 Ensembl1816,721,934 - 16,942,303 (-)Ensembl
GRCm381816,588,877 - 16,809,246 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1816,588,877 - 16,809,246 (-)EnsemblGRCm38mm10GRCm38
MGSCv371816,747,386 - 16,967,558 (-)NCBIGRCm37mm9NCBIm37
MGSCv361816,732,027 - 16,952,264 (-)NCBImm8
Celera1817,099,283 - 17,328,154 (-)NCBICelera
Cytogenetic Map18A1NCBI
cM Map1810.1NCBI
Cdh2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540215,831,110 - 16,049,890 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540215,829,895 - 16,049,874 (-)NCBIChiLan1.0ChiLan1.0
CDH2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11824,812,019 - 25,008,249 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1824,812,019 - 25,008,325 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01821,210,001 - 21,435,919 (-)NCBIMhudiblu_PPA_v0panPan3
CDH2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1760,736,760 - 60,950,477 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl760,736,760 - 60,951,034 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha760,142,523 - 60,355,795 (+)NCBI
ROS_Cfam_1.0760,754,899 - 60,968,628 (+)NCBI
UMICH_Zoey_3.1760,431,048 - 60,644,193 (+)NCBI
UNSW_CanFamBas_1.0760,442,612 - 60,655,854 (+)NCBI
UU_Cfam_GSD_1.0760,744,933 - 60,958,801 (+)NCBI
Cdh2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494456,749,166 - 56,930,675 (+)NCBI
SpeTri2.0NW_0049365506,885,484 - 7,067,001 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CDH2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6112,396,721 - 112,628,432 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16112,396,713 - 112,629,073 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26105,317,507 - 105,518,900 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CDH2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11852,426,381 - 52,652,986 (+)NCBI
ChlSab1.1 Ensembl1852,426,077 - 52,654,828 (+)Ensembl
Vero_WHO_p1.0NW_02366605027,147,394 - 27,374,174 (+)NCBI
Cdh2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247704,333,643 - 4,540,817 (+)NCBI

Position Markers
D18Got6  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2187,939,002 - 7,939,178 (+)MAPPER
Rnor_6.0188,309,243 - 8,309,418NCBIRnor6.0
Rnor_5.0188,161,224 - 8,161,399UniSTSRnor5.0
RGSC_v3.4188,211,177 - 8,211,405RGDRGSC3.4
RGSC_v3.4188,211,180 - 8,211,355UniSTSRGSC3.4
RGSC_v3.1188,211,180 - 8,211,355RGD
Celera188,099,385 - 8,099,560UniSTS
RH 3.4 Map1866.1RGD
RH 3.4 Map1866.1UniSTS
Cytogenetic Map18p13UniSTS
D18Chm84  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2187,866,120 - 7,866,271 (+)MAPPER
Rnor_6.0188,236,422 - 8,236,572NCBIRnor6.0
Rnor_5.0188,088,405 - 8,088,555UniSTSRnor5.0
RGSC_v3.4188,138,359 - 8,138,509UniSTSRGSC3.4
Celera188,026,453 - 8,026,603UniSTS
Cytogenetic Map18p13UniSTS
D18Wox24  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2187,776,887 - 7,777,044 (+)MAPPER
Rnor_6.0188,147,155 - 8,147,311NCBIRnor6.0
Rnor_5.0187,997,717 - 7,997,873UniSTSRnor5.0
RGSC_v3.4188,049,104 - 8,049,260UniSTSRGSC3.4
Cytogenetic Map18p13UniSTS
RH130775  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2187,777,618 - 7,777,813 (+)MAPPER
Rnor_6.0188,147,886 - 8,148,080NCBIRnor6.0
Rnor_5.0187,998,448 - 7,998,642UniSTSRnor5.0
RGSC_v3.4188,049,835 - 8,050,029UniSTSRGSC3.4
Celera187,938,903 - 7,939,097UniSTS
RH 3.4 Map1868.0UniSTS
Cytogenetic Map18p13UniSTS
BF387008  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2187,859,971 - 7,860,169 (+)MAPPER
Rnor_6.0188,230,273 - 8,230,470NCBIRnor6.0
Rnor_5.0188,082,256 - 8,082,453UniSTSRnor5.0
RGSC_v3.4188,132,210 - 8,132,407UniSTSRGSC3.4
Celera188,020,304 - 8,020,501UniSTS
RH 3.4 Map1882.31UniSTS
Cytogenetic Map18p13UniSTS
BF396900  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2187,932,939 - 7,933,165 (+)MAPPER
Rnor_6.0188,303,180 - 8,303,405NCBIRnor6.0
Rnor_5.0188,155,161 - 8,155,386UniSTSRnor5.0
RGSC_v3.4188,205,117 - 8,205,342UniSTSRGSC3.4
Celera188,093,321 - 8,093,546UniSTS
RH 3.4 Map1866.41UniSTS
Cytogenetic Map18p13UniSTS
AU046659  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2187,895,010 - 7,895,134 (+)MAPPER
Rnor_6.0188,265,309 - 8,265,435NCBIRnor6.0
Rnor_5.0188,117,292 - 8,117,418UniSTSRnor5.0
RGSC_v3.4188,167,246 - 8,167,372UniSTSRGSC3.4
Cytogenetic Map18p13UniSTS
RH134928  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2187,956,439 - 7,956,630 (+)MAPPER
Rnor_6.0188,326,678 - 8,326,868NCBIRnor6.0
Rnor_5.0188,178,659 - 8,178,849UniSTSRnor5.0
RGSC_v3.4188,228,615 - 8,228,805UniSTSRGSC3.4
Celera188,115,783 - 8,115,973UniSTS
RH 3.4 Map1868.0UniSTS
Cytogenetic Map18p13UniSTS
REN16027  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2187,810,266 - 7,810,521 (+)MAPPER
Rnor_6.0188,180,549 - 8,180,803NCBIRnor6.0
Rnor_5.0188,031,420 - 8,031,674UniSTSRnor5.0
RGSC_v3.4188,082,486 - 8,082,740UniSTSRGSC3.4
Celera187,971,154 - 7,971,408UniSTS
Cytogenetic Map18p13UniSTS
UniSTS:498368  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2187,776,763 - 7,777,432 (+)MAPPER
Rnor_6.0188,147,031 - 8,147,699NCBIRnor6.0
Rnor_5.0187,997,593 - 7,998,261UniSTSRnor5.0
RGSC_v3.4188,048,980 - 8,049,648UniSTSRGSC3.4
Celera187,938,066 - 7,938,716UniSTS
Cytogenetic Map18p13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590248Scort10Serum corticosterone level QTL 1019.710.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)18125999214Rat
8552968Pigfal19Plasma insulin-like growth factor 1 level QTL 1911.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)18125999214Rat
61388Bp2Blood pressure QTL 23.23arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)18135097280Rat
2300180Bmd67Bone mineral density QTL 674.80.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)18138195967Rat
2293661Bss50Bone structure and strength QTL 504.640.0003lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)18138195967Rat
9589153Insul31Insulin level QTL 317.150.05blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)18138753381Rat
1641910Colcr3Colorectal carcinoma resistance QTL 35.020.000007intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor surface area measurement (CMO:0002078)18247709623184414Rat
1641910Colcr3Colorectal carcinoma resistance QTL 35.020.000007intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)18247709623184414Rat
2312598Bp340Blood pressure QTL 3400.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)18371954732487870Rat
2299160Iddm35Insulin dependent diabetes mellitus QTL 352.79blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)18440751362570466Rat
2312568Glom21Glomerulus QTL 2120.005kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)18543013441781619Rat
2301409Cm70Cardiac mass QTL 700.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)18705776915274626Rat
11565454Kidm59Kidney mass QTL 590.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)18705776915274626Rat
12904714Cm131Cardiac mass QTL 1310.002heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)18705776915274626Rat
12904715Cm132Cardiac mass QTL 1320.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)18705776915274626Rat
12904716Am21Aortic mass QTL 210.005aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)18705776915274626Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:156
Count of miRNA genes:109
Interacting mature miRNAs:132
Transcripts:ENSRNOT00000021170
Prediction methods:Miranda, Targetscan
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 43 44 41 2 41 74 35 31
Low 3 13 17 8 10 10 11 8
Below cutoff 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000021170   ⟹   ENSRNOP00000021170
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl188,146,971 - 8,360,684 (-)Ensembl
RefSeq Acc Id: NM_031333   ⟹   NP_112623
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2187,776,704 - 7,990,934 (-)NCBI
Rnor_6.0188,146,971 - 8,366,037 (-)NCBI
Rnor_5.0187,997,533 - 8,218,018 (-)NCBI
RGSC_v3.4188,048,920 - 8,267,974 (-)RGD
Celera187,938,006 - 8,155,134 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_112623   ⟸   NM_031333
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000021170   ⟸   ENSRNOT00000021170
Protein Domains
Cadherin

Transcriptome

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

Promoters
RGD ID:13700649
Promoter ID:EPDNEW_R11173
Type:multiple initiation site
Name:Cdh2_1
Description:cadherin 2
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_6.0188,360,413 - 8,360,473EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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:69280 AgrOrtholog
Ensembl Genes ENSRNOG00000015602 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000021170 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021170 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 4.10.900.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Cadherin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_cytoplasmic-dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_pro_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Catenin_binding_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CDH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:83501 UniProtKB/Swiss-Prot
NCBI Gene 83501 ENTREZGENE
PANTHER PTHR24027 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR24027:SF79 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_pro UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cdh2 PhenoGen
PRINTS CADHERIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Cadherin_pro UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49313 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC218644
UniProt CADH2_RAT UniProtKB/Swiss-Prot
  G3V803_RAT UniProtKB/TrEMBL
  Q9Z1Y3 ENTREZGENE
UniProt Secondary Q9R0T5 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Cdh2  cadherin 2      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease increased expression occurs after balloon catheter injury of the carotid artery 68759
gene_process may be involved in facilitating germ cell migration during spermatogenesis 68761