Pcdha12 (protocadherin alpha 12) - Rat Genome Database

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Gene: Pcdha12 (protocadherin alpha 12) Rattus norvegicus
Analyze
Symbol: Pcdha12 (Ensembl: Pcdha5)
Name: protocadherin alpha 12 (Ensembl:protocadherin alpha 5)
RGD ID: 620750
Description: Predicted to be located in membrane. Orthologous to human PCDHA12 (protocadherin alpha 12); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride; furan.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Pcdha11; protocadherin alpha 11; protocadherin alpha-11; protocadherin alpha-12; rCNRv12
RGD Orthologs
Human
Mouse
Bonobo
Dog
Alliance Orthologs
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_6.01830,023,828 - 30,215,896 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,987,206 - 30,215,897 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01829,721,078 - 29,924,443 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41829,734,513 - 29,928,030 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11829,755,248 - 29,954,676 (+)NCBI
Celera1828,362,661 - 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

Cellular Component
membrane  (ISO)

References

References - curated
# Reference Title Reference Citation
1. Multiple cadherin superfamily members with unique expression profiles are produced in rat testis. Johnson KJ, etal., Endocrinology 2000 Feb;141(2):675-83.
2. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
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.
7. Multiple variable first exons: a mechanism for cell- and tissue-specific gene regulation. Zhang T, etal., Genome Res 2004 Jan;14(1):79-89. Epub 2003 Dec 12.
Additional References at PubMed
PMID:15347688   PMID:15744052   PMID:17110050  


Genomics

Comparative Map Data
Pcdha12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2 Ensembl1828,581,225 - 28,846,211 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01830,023,828 - 30,215,896 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,987,206 - 30,215,897 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01829,721,078 - 29,924,443 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41829,734,513 - 29,928,030 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11829,755,248 - 29,954,676 (+)NCBI
Celera1828,362,661 - 28,552,754 (+)NCBICelera
Cytogenetic Map18p11NCBI
PCDHA12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385140,875,308 - 141,012,347 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5140,875,302 - 141,012,347 (+)EnsemblGRCh38hg38GRCh38
GRCh375140,254,893 - 140,391,932 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,235,115 - 140,372,113 (+)NCBINCBI36Build 36hg18NCBI36
Build 345140,235,114 - 140,237,620NCBI
Celera5136,331,742 - 136,468,708 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,399,670 - 135,536,628 (+)NCBIHuRef
CHM1_15139,688,123 - 139,825,092 (+)NCBICHM1_1
T2T-CHM13v2.05141,400,633 - 141,537,634 (+)NCBIT2T-CHM13v2.0
Pcdha12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,153,283 - 37,320,710 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,153,202 - 37,320,710 (+)EnsemblGRCm39 Ensembl
GRCm381837,020,230 - 37,187,657 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1837,020,149 - 37,187,657 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,179,884 - 37,347,311 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361837,146,204 - 37,313,631 (+)NCBIMGSCv36mm8
MGSCv361837,207,336 - 37,374,763 (+)NCBIMGSCv36mm8
Celera1837,466,988 - 37,469,381 (+)NCBICelera
Cytogenetic Map18B3NCBI
cM Map1819.46NCBI
PCDHA12
(Pan paniscus - bonobo/pygmy chimpanzee)		 No map positions available.
PCDHA12
(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
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: NM_053940   ⟹   NP_446392
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01830,023,828 - 30,215,896 (+)NCBI
Rnor_5.01829,721,078 - 29,924,443 (+)NCBI
RGSC_v3.41829,734,513 - 29,928,030 (+)RGD
Celera1828,362,661 - 28,552,754 (+)RGD
Protein Sequences
Protein RefSeqs NP_446392 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF87060 (Get FASTA)   NCBI Sequence Viewer  
  AAT77556 (Get FASTA)   NCBI Sequence Viewer  
  BAD06377 (Get FASTA)   NCBI Sequence Viewer  
  EDL76329 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_446392   ⟸   NM_053940
- Peptide Label: precursor
- UniProtKB: Q767I0 (UniProtKB/TrEMBL),   Q593Y1 (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:620750 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 116779 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PROTOCADHERIN ALPHA-11 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
  Cadherin_tail UniProtKB/TrEMBL
PhenoGen Pcdha12 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 Q593Y1 ENTREZGENE, UniProtKB/TrEMBL
  Q767I0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-11-07 Pcdha12  protocadherin alpha 12  Pcdha11  protocadherin alpha 11  Symbol and Name updated 1299863 APPROVED