Pcdha13 (protocadherin alpha 13) - Rat Genome Database

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Gene: Pcdha13 (protocadherin alpha 13) Rattus norvegicus
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Symbol: Pcdha13 (Ensembl: Pcdha2)
Name: protocadherin alpha 13 (Ensembl:protocadherin alpha 2)
RGD ID: 620751
Description: Predicted to enable calcium ion binding activity. Predicted to be involved in homophilic cell adhesion via plasma membrane adhesion molecules. Predicted to be located in plasma membrane. Orthologous to human PCDHA13 (protocadherin alpha 13); INTERACTS WITH 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Cnr5; protocadherin alpha-13
RGD Orthologs
Human
Bonobo
Pig
Alliance Orthologs
More Info more info ...
Related Pseudogenes: Pcdha13-ps1  
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_6.01830,036,887 - 30,215,897 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,987,206 - 30,215,897 (+)Ensemblrn6Rnor6.0
Rnor_5.01829,734,137 - 29,924,444 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41829,747,572 - 29,928,031 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1828,375,720 - 28,552,755 (+)NCBICelera
RGSC_v3.11829,774,939 - 29,952,279 (+)NCBI
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. Cadherin-related neuronal receptors in incisor development. Fukumoto E, etal., J Dent Res 2003 Jan;82(1):17-22.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. 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:15744052   PMID:17110050  


Genomics

Comparative Map Data
Pcdha13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2 Ensembl1828,581,225 - 28,846,211 (+)EnsemblmRatBN7.2
Rnor_6.01830,036,887 - 30,215,897 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,987,206 - 30,215,897 (+)Ensemblrn6Rnor6.0
Rnor_5.01829,734,137 - 29,924,444 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41829,747,572 - 29,928,031 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1828,375,720 - 28,552,755 (+)NCBICelera
RGSC_v3.11829,774,939 - 29,952,279 (+)NCBI
Cytogenetic Map18p11NCBI
PCDHA13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385140,882,124 - 141,012,347 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5140,882,124 - 141,012,347 (+)Ensemblhg38GRCh38
GRCh375140,261,709 - 140,391,932 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,242,038 - 140,372,113 (+)NCBIBuild 36Build 36hg18NCBI36
Build 345140,242,037 - 140,244,464NCBI
Celera5136,338,665 - 136,468,708 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,406,593 - 135,536,628 (+)NCBIHuRef
CHM1_15139,695,046 - 139,825,092 (+)NCBICHM1_1
T2T-CHM13v2.05141,407,449 - 141,537,634 (+)NCBIT2T-CHM13v2.0
PCDHA13
(Pan paniscus - bonobo/pygmy chimpanzee)		 No map positions available.
LOC102160959
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2142,549,516 - 142,552,334 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.12142,547,032 - 142,657,171 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22148,628,826 - 148,631,640 (-)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
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

alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
6 6 31 34 30 18 6 18 6 58 24 19 10 19 12

Sequence


RefSeq Acc Id: NM_053934   ⟹   NP_446386
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01830,036,887 - 30,215,897 (+)NCBI
Rnor_5.01829,734,137 - 29,924,444 (+)NCBI
RGSC_v3.41829,747,572 - 29,928,031 (+)RGD
Celera1828,375,720 - 28,552,755 (+)RGD
Protein Sequences
Protein RefSeqs NP_446386 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAT77557 (Get FASTA)   NCBI Sequence Viewer  
  BAB61764 (Get FASTA)   NCBI Sequence Viewer  
  BAD06378 (Get FASTA)   NCBI Sequence Viewer  
  EDL76330 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000074100.1
RefSeq Acc Id: NP_446386   ⟸   NM_053934
- Peptide Label: precursor
- UniProtKB: I6LBW4 (UniProtKB/TrEMBL),   A0A0G2K783 (UniProtKB/TrEMBL),   Q767H9 (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:620751 AgrOrtholog
Ensembl Genes ENSRNOG00000020119 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000077824.2 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 116742 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PROTOCADHERIN ALPHA-13 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
  Cadherin_tail UniProtKB/TrEMBL
PhenoGen Pcdha13 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 A0A0G2K783 ENTREZGENE, UniProtKB/TrEMBL
  I6LBW4 ENTREZGENE, UniProtKB/TrEMBL
  Q767H9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Pcdha13  protocadherin alpha 13      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Pcdha13  protocadherin alpha 13      Symbol and Name status set to provisional 70820 PROVISIONAL