Pcdha1 (protocadherin alpha 1) - Rat Genome Database

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Pathways
Gene: Pcdha1 (protocadherin alpha 1) Rattus norvegicus
Analyze
Symbol: Pcdha1 (Ensembl: Pcdha3)
Name: protocadherin alpha 1 (Ensembl:protocadherin alpha 3)
RGD ID: 735016
Description: Orthologous to human PCDHA1 (protocadherin alpha 1); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; diuron.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: cadherin-related neuronal receptor 1; LOC364840; protocadherin alpha-1; rCNRv01
RGD Orthologs
Human
Mouse
Chinchilla
Dog
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
GRCr8 Ensembl1828,855,256 - 29,120,227 (+)EnsemblGRCr8
mRatBN7.2 Ensembl1828,581,225 - 28,846,211 (+)EnsemblmRatBN7.2
Rnor_6.01829,951,094 - 30,215,896 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01829,648,344 - 29,924,443 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41829,661,560 - 29,928,030 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1828,289,927 - 28,552,754 (+)NCBICelera
RGSC_v3.11829,688,205 - 29,954,676 (+)NCBI
Cytogenetic Map18p11NCBI



Disease 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
Pcdha1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8 Ensembl1828,855,256 - 29,120,227 (+)EnsemblGRCr8
mRatBN7.2 Ensembl1828,581,225 - 28,846,211 (+)EnsemblmRatBN7.2
Rnor_6.01829,951,094 - 30,215,896 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01829,648,344 - 29,924,443 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41829,661,560 - 29,928,030 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1828,289,927 - 28,552,754 (+)NCBICelera
RGSC_v3.11829,688,205 - 29,954,676 (+)NCBI
Cytogenetic Map18p11NCBI
PCDHA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385140,786,140 - 141,012,347 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5140,786,136 - 141,012,347 (+)Ensemblhg38GRCh38
GRCh375140,165,721 - 140,391,932 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,146,060 - 140,372,113 (+)NCBIBuild 36Build 36hg18NCBI36
Build 345140,146,059 - 140,372,113NCBI
Celera5136,242,652 - 136,468,708 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,311,159 - 135,536,628 (+)NCBIHuRef
CHM1_15139,599,068 - 139,825,092 (+)NCBICHM1_1
T2T-CHM13v2.05141,311,473 - 141,537,634 (+)NCBIT2T-CHM13v2.0
Pcdha1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,063,338 - 37,320,710 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,063,237 - 37,320,714 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381836,930,285 - 37,187,657 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1836,930,184 - 37,187,661 (+)Ensemblmm10GRCm38
MGSCv371837,089,939 - 37,347,311 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361837,056,259 - 37,313,631 (+)NCBIMGSCv36mm8
MGSCv361837,117,391 - 37,374,763 (+)NCBIMGSCv36mm8
Celera1837,377,057 - 37,397,935 (+)NCBICelera
Cytogenetic Map18B2- B3NCBI
cM Map1819.46NCBI
Pcdha1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955611363,566 - 396,184 (-)NCBIChiLan1.0ChiLan1.0
PCDHA1
(Canis lupus familiaris - dog)
No map positions available.

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


Ensembl Acc Id: ENSRNOT00000027340   ⟹   ENSRNOP00000027340
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1828,802,566 - 28,846,211 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000027372   ⟹   ENSRNOP00000027372
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1828,629,247 - 28,846,211 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000027383   ⟹   ENSRNOP00000027383
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1828,617,395 - 28,846,211 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000027393   ⟹   ENSRNOP00000027393
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1828,596,122 - 28,846,211 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000027402   ⟹   ENSRNOP00000027402
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1828,581,225 - 28,846,211 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000071366   ⟹   ENSRNOP00000065957
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1828,590,221 - 28,846,211 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000074028   ⟹   ENSRNOP00000066853
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1828,595,962 - 28,846,211 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000075810   ⟹   ENSRNOP00000066774
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1828,590,221 - 28,846,211 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000077824   ⟹   ENSRNOP00000074100
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1828,666,964 - 28,846,211 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000079794   ⟹   ENSRNOP00000075260
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1828,602,540 - 28,846,211 (+)Ensembl
RefSeq Acc Id: NM_199503   ⟹   NP_955797
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01829,951,094 - 30,215,896 (+)NCBI
Rnor_5.01829,648,344 - 29,924,443 (+)NCBI
RGSC_v3.41829,661,560 - 29,928,030 (+)RGD
Celera1828,289,927 - 28,552,754 (+)RGD
Protein Sequences
Protein RefSeqs NP_955797 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAT77553 (Get FASTA)   NCBI Sequence Viewer  
  BAD06366 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000027402.4
RefSeq Acc Id: NP_955797   ⟸   NM_199503
- Peptide Label: precursor
- UniProtKB: Q767J1 (UniProtKB/TrEMBL),   E9PSN7 (UniProtKB/TrEMBL),   A6J343 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000065957   ⟸   ENSRNOT00000071366
Ensembl Acc Id: ENSRNOP00000027393   ⟸   ENSRNOT00000027393
Ensembl Acc Id: ENSRNOP00000027340   ⟸   ENSRNOT00000027340
Ensembl Acc Id: ENSRNOP00000066774   ⟸   ENSRNOT00000075810
Ensembl Acc Id: ENSRNOP00000074100   ⟸   ENSRNOT00000077824
Ensembl Acc Id: ENSRNOP00000027372   ⟸   ENSRNOT00000027372
Ensembl Acc Id: ENSRNOP00000027383   ⟸   ENSRNOT00000027383
Ensembl Acc Id: ENSRNOP00000027402   ⟸   ENSRNOT00000027402
Ensembl Acc Id: ENSRNOP00000075260   ⟸   ENSRNOT00000079794
Ensembl Acc Id: ENSRNOP00000066853   ⟸   ENSRNOT00000074028
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:735016 AgrOrtholog
Ensembl Genes ENSRNOG00000020119 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027402.5 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 393085 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PTHR24028:SF92 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
  Cadherin_tail UniProtKB/TrEMBL
PhenoGen Pcdha1 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 A6J343 ENTREZGENE, UniProtKB/TrEMBL
  E9PSN7 ENTREZGENE
  Q767J1 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary E9PSN7 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-25 Pcdha1  protocadherin alpha 1  Pcdha2_predicted  protocadherin alpha 2 (predicted)  Data merged from RGD:1307020 737654 APPROVED
2005-10-12 Pcdha1        Symbol and Name status set to provisional 70820 PROVISIONAL
2005-04-20   protocadherin alpha 1  Pcdha1  cadherin-related neuronal receptor 1  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2005-01-12 Pcdha2_predicted  protocadherin alpha 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED