Pcdha7 (protocadherin alpha 7) - Rat Genome Database

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Gene: Pcdha7 (protocadherin alpha 7) Rattus norvegicus
Analyze
Symbol: Pcdha7 (Ensembl: Pcdha5)
Name: protocadherin alpha 7 (Ensembl:protocadherin alpha 5)
RGD ID: 735055
Description: Predicted to enable calcium ion binding activity and identical protein binding activity. Predicted to be involved in cell-cell recognition and homophilic cell adhesion via plasma membrane adhesion molecules. Predicted to be located in plasma membrane. Orthologous to human PCDHA7 (protocadherin alpha 7); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: cadherin-related neuronal receptor 7; protocadherin alpha-7; rCNRv07
RGD Orthologs
Human
Mouse
Bonobo
Dog
Pig
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 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 Ensembl
Rnor_6.01829,993,361 - 30,215,896 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,987,206 - 30,215,897 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01829,690,611 - 29,924,443 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41829,704,031 - 29,928,030 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11829,730,676 - 29,954,676 (+)NCBI
Celera1828,332,194 - 28,552,754 (+)NCBICelera
Cytogenetic Map18p11NCBI


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:14672974   PMID:15347688   PMID:15744052   PMID:17110050   PMID:27161523  


Genomics

Comparative Map Data
Pcdha7
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2 Ensembl1828,581,225 - 28,846,211 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01829,993,361 - 30,215,896 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,987,206 - 30,215,897 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01829,690,611 - 29,924,443 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41829,704,031 - 29,928,030 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11829,730,676 - 29,954,676 (+)NCBI
Celera1828,332,194 - 28,552,754 (+)NCBICelera
Cytogenetic Map18p11NCBI
PCDHA7
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385140,834,269 - 141,012,347 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5140,834,248 - 141,012,347 (+)EnsemblGRCh38hg38GRCh38
GRCh375140,213,854 - 140,391,932 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,194,153 - 140,372,113 (+)NCBINCBI36Build 36hg18NCBI36
Build 345140,194,152 - 140,196,522NCBI
Celera5136,290,778 - 136,468,708 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,358,715 - 135,536,628 (+)NCBIHuRef
CHM1_15139,647,162 - 139,825,092 (+)NCBICHM1_1
T2T-CHM13v2.05141,359,603 - 141,537,634 (+)NCBIT2T-CHM13v2.0
Pcdha7
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,106,864 - 37,320,716 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,106,855 - 37,320,710 (+)EnsemblGRCm39 Ensembl
GRCm381836,973,811 - 37,187,663 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1836,973,802 - 37,187,657 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,133,578 - 37,347,311 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361837,099,898 - 37,313,631 (+)NCBIMGSCv36mm8
Celera1837,420,703 - 37,450,919 (+)NCBICelera
Cytogenetic Map18B2- B3NCBI
cM Map1819.46NCBI
LOC100995259
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15142,313,905 - 142,316,338 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5142,301,336 - 142,316,338 (+)Ensemblpanpan1.1panPan2
PCDHA7
(Canis lupus familiaris - dog)		 No map positions available.
LOC102160218
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.12142,504,123 - 142,511,445 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22148,453,693 - 148,455,294 (+)NCBISscrofa10.2Sscrofa10.2susScr3

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


Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000027340   ⟹   ENSRNOP00000027340
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1828,802,566 - 28,846,211 (+)Ensembl
Rnor_6.0 Ensembl1830,172,740 - 30,215,896 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000027343   ⟹   ENSRNOP00000027343
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1830,114,708 - 30,215,896 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000027372   ⟹   ENSRNOP00000027372
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1828,629,247 - 28,846,211 (+)Ensembl
Rnor_6.0 Ensembl1829,999,290 - 30,215,896 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000027383   ⟹   ENSRNOP00000027383
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1828,617,395 - 28,846,211 (+)Ensembl
Rnor_6.0 Ensembl1829,987,206 - 30,215,896 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000027393   ⟹   ENSRNOP00000027393
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1828,596,122 - 28,846,211 (+)Ensembl
Rnor_6.0 Ensembl1830,004,565 - 30,215,896 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000027402   ⟹   ENSRNOP00000027402
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1828,581,225 - 28,846,211 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000071366   ⟹   ENSRNOP00000065957
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1828,590,221 - 28,846,211 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000074028   ⟹   ENSRNOP00000066853
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1828,595,962 - 28,846,211 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000075810   ⟹   ENSRNOP00000066774
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1828,590,221 - 28,846,211 (+)Ensembl
Rnor_6.0 Ensembl1829,993,361 - 30,215,896 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000077824   ⟹   ENSRNOP00000074100
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1828,666,964 - 28,846,211 (+)Ensembl
Rnor_6.0 Ensembl1830,036,887 - 30,215,897 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000079008   ⟹   ENSRNOP00000069635
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1830,023,828 - 30,215,896 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000079794   ⟹   ENSRNOP00000075260
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1828,602,540 - 28,846,211 (+)Ensembl
Rnor_6.0 Ensembl1830,017,918 - 30,215,896 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000084132   ⟹   ENSRNOP00000074164
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1830,010,918 - 30,215,896 (+)Ensembl
RefSeq Acc Id: NM_199507   ⟹   NP_955801
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01829,993,361 - 30,215,896 (+)NCBI
Rnor_5.01829,690,611 - 29,924,443 (+)NCBI
RGSC_v3.41829,704,031 - 29,928,030 (+)RGD
Celera1828,332,194 - 28,552,754 (+)RGD
Protein Sequences
Protein RefSeqs NP_955801 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAD06372 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_955801   ⟸   NM_199507
- Peptide Label: precursor
- UniProtKB: Q767I5 (UniProtKB/TrEMBL),   M0RB51 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000069635   ⟸   ENSRNOT00000079008
RefSeq Acc Id: ENSRNOP00000075260   ⟸   ENSRNOT00000079794
RefSeq Acc Id: ENSRNOP00000066774   ⟸   ENSRNOT00000075810
RefSeq Acc Id: ENSRNOP00000074100   ⟸   ENSRNOT00000077824
RefSeq Acc Id: ENSRNOP00000074164   ⟸   ENSRNOT00000084132
RefSeq Acc Id: ENSRNOP00000027372   ⟸   ENSRNOT00000027372
RefSeq Acc Id: ENSRNOP00000027383   ⟸   ENSRNOT00000027383
RefSeq Acc Id: ENSRNOP00000027393   ⟸   ENSRNOT00000027393
RefSeq Acc Id: ENSRNOP00000027340   ⟸   ENSRNOT00000027340
RefSeq Acc Id: ENSRNOP00000027343   ⟸   ENSRNOT00000027343
RefSeq Acc Id: ENSRNOP00000066853   ⟸   ENSRNOT00000074028
RefSeq Acc Id: ENSRNOP00000027402   ⟸   ENSRNOT00000027402
RefSeq Acc Id: ENSRNOP00000065957   ⟸   ENSRNOT00000071366
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:735055 AgrOrtholog
Ensembl Genes ENSRNOG00000020119 Ensembl
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
NCBI Gene 393089 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PROTOCADHERIN ALPHA-9 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
  Cadherin_tail UniProtKB/TrEMBL
PhenoGen Pcdha7 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 M0RB51 ENTREZGENE
  Q767I5 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary M0RB51 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-10-12 Pcdha7        Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localizes to the synaptic junction 1302433
gene_domains protein contains an N-terminal variable extracellular domain and a C-terminal constant intracellular domain 1302433
gene_homology percentage identity of coding regions at the nucleic acid level is 93.6% between rat and mouse and 82.8% between rat and human 1302433