Cdhr2 (cadherin-related family member 2) - Rat Genome Database

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Gene: Cdhr2 (cadherin-related family member 2) Rattus norvegicus
Analyze
Symbol: Cdhr2
Name: cadherin-related family member 2
RGD ID: 1560576
Description: Predicted to enable cell adhesion molecule binding activity. Predicted to be involved in several processes, including cell-cell adhesion mediated by cadherin; intermicrovillar adhesion; and negative regulation of cell growth involved in contact inhibition. Predicted to be located in apical plasma membrane; brush border membrane; and microvillus membrane. Predicted to be active in plasma membrane. Orthologous to human CDHR2 (cadherin related family member 2); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC291002; Pcdh24; protocadherin 24; RGD1560576; similar to PC-LKC gene product
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8179,881,979 - 9,917,698 (-)NCBIGRCr8
mRatBN7.2179,876,853 - 9,913,356 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl179,876,860 - 9,912,575 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01710,415,044 - 10,450,589 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1710,415,123 - 10,439,691 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01712,540,996 - 12,576,334 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41715,937,987 - 15,962,796 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera179,951,957 - 9,976,839 (-)NCBICelera
Cytogenetic Map17p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12117771   PMID:19056867   PMID:21330445   PMID:23376485   PMID:23533145   PMID:24725409  


Genomics

Comparative Map Data
Cdhr2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8179,881,979 - 9,917,698 (-)NCBIGRCr8
mRatBN7.2179,876,853 - 9,913,356 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl179,876,860 - 9,912,575 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01710,415,044 - 10,450,589 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1710,415,123 - 10,439,691 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01712,540,996 - 12,576,334 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41715,937,987 - 15,962,796 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera179,951,957 - 9,976,839 (-)NCBICelera
Cytogenetic Map17p14NCBI
CDHR2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385176,542,511 - 176,595,974 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5176,542,511 - 176,595,974 (+)EnsemblGRCh38hg38GRCh38
GRCh375175,969,512 - 176,022,975 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365175,908,971 - 175,955,375 (+)NCBINCBI36Build 36hg18NCBI36
Celera5172,478,089 - 172,531,637 (-)NCBICelera
Cytogenetic Map5q35.2NCBI
HuRef5170,893,401 - 170,947,042 (+)NCBIHuRef
CHM1_15175,402,210 - 175,455,196 (+)NCBICHM1_1
T2T-CHM13v2.05177,087,074 - 177,142,566 (+)NCBIT2T-CHM13v2.0
Cdhr2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391354,849,276 - 54,884,475 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1354,849,274 - 54,884,475 (+)EnsemblGRCm39 Ensembl
GRCm381354,701,463 - 54,736,662 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1354,701,461 - 54,736,662 (+)EnsemblGRCm38mm10GRCm38
MGSCv371354,802,824 - 54,838,023 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361354,711,085 - 54,746,277 (+)NCBIMGSCv36mm8
Celera1355,767,386 - 55,802,298 (+)NCBICelera
Cytogenetic Map13B1NCBI
cM Map1329.03NCBI
Cdhr2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540828,832,325 - 28,875,534 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540828,832,362 - 28,871,345 (+)NCBIChiLan1.0ChiLan1.0
CDHR2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v24171,630,262 - 171,676,130 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15169,769,801 - 169,815,669 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v05171,846,538 - 171,893,797 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15178,916,707 - 178,963,944 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5178,916,707 - 178,964,893 (+)Ensemblpanpan1.1panPan2
CDHR2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1436,740,964 - 36,777,118 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl436,740,966 - 36,777,803 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha436,707,763 - 36,743,827 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0437,107,067 - 37,143,175 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl437,107,075 - 37,143,174 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1436,932,892 - 36,968,996 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0437,120,701 - 37,156,839 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0437,628,842 - 37,664,949 (-)NCBIUU_Cfam_GSD_1.0
Cdhr2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213121,785,575 - 121,831,018 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936597831,855 - 857,013 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936597831,895 - 855,925 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CDHR2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl281,318,407 - 81,361,606 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1281,319,179 - 81,361,598 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2282,920,844 - 82,963,238 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CDHR2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12378,571,170 - 78,602,699 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2378,571,792 - 78,602,552 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660759,688,711 - 9,736,431 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cdhr2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473313,535,809 - 13,576,940 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473313,537,363 - 13,582,390 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cdhr2
138 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:37
Count of miRNA genes:37
Interacting mature miRNAs:37
Transcripts:ENSRNOT00000024151
Prediction methods:Miranda, Rnahybrid, 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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
631499Stl1Serum triglyceride level QTL 13.6blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)17327139827389946Rat
2293664Bmd28Bone mineral density QTL 285.10.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)17435448727028127Rat
1582224Epfw4Epididymal fat weight QTL 43.50.0058epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)17920136523653323Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17211514934551001Rat
1582225Bw67Body weight QTL 676.20.0001body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582226Bw64Body weight QTL 644.20.0017body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17452803849528038Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131701463Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
1582208Kidm32Kidney mass QTL 323.90.0018kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17920136523653323Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17429913035837242Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented dorsal coat/hair area to total dorsal coat/hair area ratio (CMO:0001811)17429913021293263Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17452803849528038Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17131990913Rat
1581553Pur14Proteinuria QTL 145.30.0001urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)17797996816317111Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17886846253868462Rat
1582258Bw76Body weight QTL 764.60.0005body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17137830672Rat
1582199Insul5Insulin level QTL 53.40.0119blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)17920136523653323Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
2293648Bmd31Bone mineral density QTL 314.50.0001femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)17435448727028127Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1641902Colcr7Colorectal carcinoma resistance QTL 73.350.0044intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)17211514921881669Rat
1582241Bw70Body weight QTL 704.60.0003body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582245Bw73Body weight QTL 734.60.0004body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
9590316Scort21Serum corticosterone level QTL 214.750.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17122871563Rat


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
nervous system
renal system
reproductive system
respiratory system
9 11 48 113 91 90 59 25 59 6 217 96 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000024151   ⟹   ENSRNOP00000024151
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl179,876,860 - 9,912,575 (-)Ensembl
Rnor_6.0 Ensembl1710,415,123 - 10,439,691 (-)Ensembl
RefSeq Acc Id: NM_001427596   ⟹   NP_001414525
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8179,881,979 - 9,917,698 (-)NCBI
RefSeq Acc Id: XM_039096512   ⟹   XP_038952440
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8179,881,979 - 9,901,991 (-)NCBI
mRatBN7.2179,876,853 - 9,896,683 (-)NCBI
RefSeq Acc Id: XM_039096513   ⟹   XP_038952441
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8179,881,979 - 9,902,008 (-)NCBI
mRatBN7.2179,876,853 - 9,896,885 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001414525 (Get FASTA)   NCBI Sequence Viewer  
  XP_038952440 (Get FASTA)   NCBI Sequence Viewer  
  XP_038952441 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000024151.5
Ensembl Acc Id: ENSRNOP00000024151   ⟸   ENSRNOT00000024151
RefSeq Acc Id: XP_038952441   ⟸   XM_039096513
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038952440   ⟸   XM_039096512
- Peptide Label: isoform X1
- UniProtKB: A6KAX4 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001414525   ⟸   NM_001427596
- Peptide Label: precursor
- UniProtKB: D3ZAN2 (UniProtKB/TrEMBL)
Protein Domains
Cadherin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZAN2-F1-model_v2 AlphaFold D3ZAN2 1-1310 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560576 AgrOrtholog
BioCyc Gene G2FUF-10179 BioCyc
Ensembl Genes ENSRNOG00000017917 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024151.8 UniProtKB/TrEMBL
Gene3D-CATH Cadherins UniProtKB/TrEMBL
InterPro Cadherin UniProtKB/TrEMBL
  Cadherin UniProtKB/TrEMBL
  Cadherin-like UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
NCBI Gene 291002 ENTREZGENE
PANTHER CADHERIN-23 UniProtKB/TrEMBL
  CADHERIN-RELATED FAMILY MEMBER 5-LIKE ISOFORM X1 UniProtKB/TrEMBL
  FAT ATYPICAL CADHERIN-RELATED UniProtKB/TrEMBL
  FAT-LIKE CADHERIN-RELATED TUMOR SUPPRESSOR HOMOLOG UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
PhenoGen Cdhr2 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000017917 RatGTEx
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin UniProtKB/TrEMBL
UniProt A6KAX4 ENTREZGENE, UniProtKB/TrEMBL
  D3ZAN2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-02 Cdhr2  cadherin-related family member 2  Pcdh24  protocadherin 24  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-28 Pcdh24  protocadherin 24  RGD1560576_predicted  similar to PC-LKC gene product (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1560576_predicted  similar to PC-LKC gene product (predicted)  LOC291002  similar to PC-LKC gene product  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC291002  similar to PC-LKC gene product      Symbol and Name status set to provisional 70820 PROVISIONAL