Pcdha2 (protocadherin alpha 2) - Rat Genome Database

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Gene: Pcdha2 (protocadherin alpha 2) Rattus norvegicus
Analyze
Symbol: Pcdha2
Name: protocadherin alpha 2
RGD ID: 735182
Description: Orthologous to human PCDHA2 (protocadherin alpha 2); INTERACTS WITH 17alpha-ethynylestradiol; bisphenol A; 5-azacytidine (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: cadherin-related neuronal receptor 2; protocadherin alpha-2; rCNRv02
RGD Orthologs
Human
Mouse
Bonobo
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
NCBI Annotation Information: Genome Annotation Status: not in current annotation release
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2 Ensembl1828,581,225 - 28,846,211 (+)EnsemblmRatBN7.2
Rnor_6.01829,960,072 - 30,215,896 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01829,657,322 - 29,924,443 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41829,670,538 - 29,928,030 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1828,298,905 - 28,552,754 (+)NCBICelera
RGSC_v3.11829,697,183 - 29,954,676 (+)NCBI
Cytogenetic Map18p11NCBI



Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOA pipeline RGD automated data pipeline
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Genomic sequence and organization of the family of CNR/Pcdhalpha genes in rat. Yanase H, etal., Genomics 2004 Apr;83(4):717-26.
Additional References at PubMed
PMID:11401448   PMID:14672974   PMID:15347688   PMID:15744052   PMID:17110050  


Genomics

Comparative Map Data
Pcdha2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2 Ensembl1828,581,225 - 28,846,211 (+)EnsemblmRatBN7.2
Rnor_6.01829,960,072 - 30,215,896 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01829,657,322 - 29,924,443 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41829,670,538 - 29,928,030 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1828,298,905 - 28,552,754 (+)NCBICelera
RGSC_v3.11829,697,183 - 29,954,676 (+)NCBI
Cytogenetic Map18p11NCBI
PCDHA2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385140,794,852 - 141,012,347 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5140,794,852 - 141,012,347 (+)Ensemblhg38GRCh38
GRCh375140,174,437 - 140,391,932 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,154,628 - 140,372,113 (+)NCBIBuild 36Build 36hg18NCBI36
Build 345140,154,627 - 140,165,386NCBI
Celera5136,251,221 - 136,468,708 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,319,158 - 135,536,628 (+)NCBIHuRef
CHM1_15139,607,636 - 139,825,092 (+)NCBICHM1_1
T2T-CHM13v2.05141,320,185 - 141,537,634 (+)NCBIT2T-CHM13v2.0
Pcdha2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,072,258 - 37,320,714 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,072,258 - 37,320,710 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381836,939,205 - 37,187,661 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1836,939,205 - 37,187,657 (+)Ensemblmm10GRCm38
MGSCv371837,098,859 - 37,347,315 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361837,065,292 - 37,313,631 (+)NCBIMGSCv36mm8
MGSCv361837,126,424 - 37,374,763 (+)NCBIMGSCv36mm8
Celera1837,385,976 - 37,388,476 (+)NCBICelera
Cytogenetic Map18B2- B3NCBI
cM Map1819.46NCBI
LOC100994239
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15142,274,257 - 142,276,995 (+)NCBIPanPan1.1PanPan1.1panPan2

Markers in Region
WI-19540  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21828,845,892 - 28,846,156 (+)MAPPERmRatBN7.2
Rnor_6.01830,215,579 - 30,215,842NCBIRnor6.0
Rnor_5.01829,924,126 - 29,924,389UniSTSRnor5.0
RGSC_v3.41829,927,713 - 29,927,976UniSTSRGSC3.4
Celera1828,552,437 - 28,552,700UniSTS
Cytogenetic Map18p11UniSTS
RH65516  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21828,845,204 - 28,845,379 (+)MAPPERmRatBN7.2
Rnor_6.01830,214,891 - 30,215,065NCBIRnor6.0
Rnor_5.01829,923,438 - 29,923,612UniSTSRnor5.0
RGSC_v3.41829,927,025 - 29,927,199UniSTSRGSC3.4
Celera1828,551,749 - 28,551,923UniSTS
Cytogenetic Map18p11UniSTS
IB766  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21828,845,918 - 28,846,149 (+)MAPPERmRatBN7.2
Rnor_6.01830,215,605 - 30,215,835NCBIRnor6.0
Rnor_5.01829,924,152 - 29,924,382UniSTSRnor5.0
RGSC_v3.41829,927,739 - 29,927,969UniSTSRGSC3.4
Celera1828,552,463 - 28,552,693UniSTS
Cytogenetic Map18p11UniSTS
PMC311048P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21828,818,659 - 28,818,748 (+)MAPPERmRatBN7.2
Rnor_6.01830,188,352 - 30,188,440NCBIRnor6.0
Rnor_5.01829,896,899 - 29,896,987UniSTSRnor5.0
RGSC_v3.41829,900,486 - 29,900,574UniSTSRGSC3.4
Celera1828,525,314 - 28,525,402UniSTS
Cytogenetic Map18p11UniSTS
RH91795  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21828,843,505 - 28,843,650 (+)MAPPERmRatBN7.2
Rnor_6.01830,213,192 - 30,213,336NCBIRnor6.0
Rnor_5.01829,921,739 - 29,921,883UniSTSRnor5.0
RGSC_v3.41829,925,326 - 29,925,470UniSTSRGSC3.4
Celera1828,550,050 - 28,550,194UniSTS
Cytogenetic Map18p11UniSTS
BF389688  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21828,749,911 - 28,750,152 (+)MAPPERmRatBN7.2
Rnor_6.01830,119,568 - 30,119,808NCBIRnor6.0
Rnor_5.01829,815,629 - 29,815,869UniSTSRnor5.0
RGSC_v3.41829,831,514 - 29,831,754UniSTSRGSC3.4
Celera1828,458,199 - 28,458,439UniSTS
RH 3.4 Map18420.79UniSTS
Cytogenetic Map18p11UniSTS
PMC311048P3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21828,641,804 - 28,641,941 (+)MAPPERmRatBN7.2
Rnor_6.01830,011,467 - 30,011,603NCBIRnor6.0
Rnor_5.01829,708,717 - 29,708,853UniSTSRnor5.0
RGSC_v3.41829,722,152 - 29,722,288UniSTSRGSC3.4
Celera1828,350,300 - 28,350,436UniSTS
Cytogenetic Map18p11UniSTS
PMC312645P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21828,843,709 - 28,843,897 (+)MAPPERmRatBN7.2
Rnor_6.01830,213,396 - 30,213,583NCBIRnor6.0
Rnor_5.01829,921,943 - 29,922,130UniSTSRnor5.0
RGSC_v3.41829,925,530 - 29,925,717UniSTSRGSC3.4
Celera1828,550,254 - 28,550,441UniSTS
Cytogenetic Map18p11UniSTS
UniSTS:547524  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21828,843,567 - 28,844,209 (+)MAPPERmRatBN7.2
Rnor_6.01830,213,254 - 30,213,895NCBIRnor6.0
Rnor_5.01829,921,801 - 29,922,442UniSTSRnor5.0
Celera1828,550,112 - 28,550,753UniSTS
Cytogenetic Map18p11UniSTS


Expression

RNA-SEQ Expression


Sequence


RefSeq Acc Id: NM_199504   ⟹   NP_955798
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01829,960,072 - 30,215,896 (+)NCBI
Rnor_5.01829,657,322 - 29,924,443 (+)NCBI
RGSC_v3.41829,670,538 - 29,928,030 (+)RGD
Celera1828,298,905 - 28,552,754 (+)RGD
Protein Sequences
Protein RefSeqs NP_955798 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAT77558 (Get FASTA)   NCBI Sequence Viewer  
  BAD06367 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000065957.3
  ENSRNOP00000066774.4
RefSeq Acc Id: NP_955798   ⟸   NM_199504
- Peptide Label: precursor
- UniProtKB: Q767J0 (UniProtKB/TrEMBL),   M0R8Z9 (UniProtKB/TrEMBL),   A0A8J8XGC7 (UniProtKB/TrEMBL)
Protein Domains
Cadherin

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:735182 AgrOrtholog
Ensembl Genes ENSRNOG00000020119 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000071366.3 UniProtKB/TrEMBL
  ENSRNOT00000075810.4 UniProtKB/TrEMBL
Gene3D-CATH Cadherins UniProtKB/TrEMBL
InterPro Cadherin UniProtKB/TrEMBL
  Cadherin-like UniProtKB/TrEMBL
  Cadherin_CBD UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
  Cadherin_N UniProtKB/TrEMBL
  Protocadherin/Cadherin-CA UniProtKB/TrEMBL
NCBI Gene 393086 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PROTOCADHERIN ALPHA-2 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
  Cadherin_tail UniProtKB/TrEMBL
PhenoGen Pcdha2 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000020119 RatGTEx
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin UniProtKB/TrEMBL
UniProt A0A8J8XGC7 ENTREZGENE, UniProtKB/TrEMBL
  A0ABZ3NN59_RAT UniProtKB/TrEMBL
  M0R8Z9 ENTREZGENE
  Q767J0 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary M0R8Z9 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-10-12 Pcdha2        Symbol and Name status set to provisional 70820 PROVISIONAL
2005-04-20   protocadherin alpha 2  Pcdha2  cadherin-related neuronal receptor 2  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED