Pcdhac2 (protocadherin alpha subfamily C, 2) - Rat Genome Database

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Gene: Pcdhac2 (protocadherin alpha subfamily C, 2) Rattus norvegicus
Analyze
Symbol: Pcdhac2 (Ensembl: Pcdha3)
Name: protocadherin alpha subfamily C, 2 (Ensembl:protocadherin alpha 3)
RGD ID: 735216
Description: Orthologous to human PCDHAC2 (protocadherin alpha subfamily C, 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,4-methylenedioxymethamphetamine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: cadherin-related neuronal receptor c2; protocadherin alpha c2; protocadherin alpha subfamily C 2; protocadherin alpha-C2; rCNRvc2
RGD Orthologs
Human
Mouse
Bonobo
Dog
Pig
Black Rat
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_6.01830,172,740 - 30,215,896 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,987,206 - 30,215,897 (+)Ensemblrn6Rnor6.0
Rnor_5.01829,881,386 - 29,924,443 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41829,884,685 - 29,928,030 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1828,509,807 - 28,552,754 (+)NCBICelera
RGSC_v3.11829,911,330 - 29,954,676 (+)NCBI
Cytogenetic Map18p11NCBI



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:12508039   PMID:14672974   PMID:15744052   PMID:17110050  


Genomics

Comparative Map Data
Pcdhac2
(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_6.01830,172,740 - 30,215,896 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,987,206 - 30,215,897 (+)Ensemblrn6Rnor6.0
Rnor_5.01829,881,386 - 29,924,443 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41829,884,685 - 29,928,030 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1828,509,807 - 28,552,754 (+)NCBICelera
RGSC_v3.11829,911,330 - 29,954,676 (+)NCBI
Cytogenetic Map18p11NCBI
PCDHAC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385140,966,476 - 141,012,347 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5140,966,470 - 141,012,347 (+)Ensemblhg38GRCh38
GRCh375140,346,061 - 140,391,932 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,326,536 - 140,372,113 (+)NCBIBuild 36Build 36hg18NCBI36
Build 345140,326,535 - 140,329,190NCBI
Celera5136,422,531 - 136,468,708 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,490,462 - 135,536,628 (+)NCBIHuRef
CHM1_15139,778,941 - 139,825,092 (+)NCBICHM1_1
T2T-CHM13v2.05141,491,769 - 141,537,634 (+)NCBIT2T-CHM13v2.0
Pcdhac2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,276,731 - 37,320,716 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,276,556 - 37,320,710 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381837,143,678 - 37,187,663 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1837,143,503 - 37,187,657 (+)Ensemblmm10GRCm38
MGSCv371837,303,623 - 37,347,311 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361837,269,943 - 37,313,631 (+)NCBIMGSCv36mm8
MGSCv361837,331,075 - 37,374,763 (+)NCBIMGSCv36mm8
Cytogenetic Map18B3NCBI
cM Map1819.46NCBI
PCDHAC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15142,445,483 - 142,448,709 (+)NCBIPanPan1.1PanPan1.1panPan2
LOC111089960
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1235,954,126 - 36,096,661 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl235,910,402 - 36,095,110 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha232,989,113 - 33,114,899 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
LOC100621701
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2142,460,178 - 142,688,089 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.12142,477,627 - 142,687,684 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22148,423,053 - 148,427,771 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pcdhac2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v115750,100 - 793,891 (+)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:1000
Count of miRNA genes:249
Interacting mature miRNAs:325
Transcripts:ENSRNOT00000027340, ENSRNOT00000027343
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

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
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_201422   ⟹   NP_958825
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01830,172,740 - 30,215,896 (+)NCBI
Rnor_5.01829,881,386 - 29,924,443 (+)NCBI
RGSC_v3.41829,884,685 - 29,928,030 (+)RGD
Celera1828,509,807 - 28,552,754 (+)RGD
Protein Sequences
Protein RefSeqs NP_958825 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAT77567 (Get FASTA)   NCBI Sequence Viewer  
  BAD06380 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000027340.3
RefSeq Acc Id: NP_958825   ⟸   NM_201422
- Peptide Label: precursor
- UniProtKB: Q767H7 (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:735216 AgrOrtholog
Ensembl Genes ENSRNOG00000020119 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027340.7 UniProtKB/TrEMBL
Gene3D-CATH Cadherins UniProtKB/TrEMBL
InterPro Cadherin UniProtKB/TrEMBL
  Cadherin-like UniProtKB/TrEMBL
  Cadherin_C UniProtKB/TrEMBL
  Cadherin_CBD UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
  Cadherin_N UniProtKB/TrEMBL
  Protocadherin/Cadherin-CA UniProtKB/TrEMBL
NCBI Gene 393092 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PTHR24028:SF119 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
  Cadherin_C_2 UniProtKB/TrEMBL
  Cadherin_tail UniProtKB/TrEMBL
PhenoGen Pcdhac2 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 Q767H7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-10-12 Pcdhac2        Symbol and Name status set to provisional 70820 PROVISIONAL