Pcdha10 (protocadherin alpha 10) - Rat Genome Database

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Gene: Pcdha10 (protocadherin alpha 10) Rattus norvegicus
Analyze
Symbol: Pcdha10 (Ensembl: Pcdha5)
Name: protocadherin alpha 10 (Ensembl:protocadherin alpha 5)
RGD ID: 620749
Description: Predicted to be involved in spermatogenesis. Predicted to act upstream of or within circulatory system development; embryonic placenta development; and gene expression. Predicted to be located in membrane. Predicted to be active in cell-cell contact zone. Orthologous to human PCDHA10 (protocadherin alpha 10); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; cadmium dichloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cadherin-related neuronal receptor 10; protocadherin alpha-10; rCNRv10
RGD Orthologs
Human
Mouse
Bonobo
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
mRatBN7.2 Ensembl1828,581,225 - 28,846,211 (+)EnsemblmRatBN7.2
Rnor_6.01830,010,918 - 30,215,896 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,987,206 - 30,215,897 (+)Ensemblrn6Rnor6.0
Rnor_5.01829,708,168 - 29,924,443 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41829,721,603 - 29,928,030 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1828,349,751 - 28,552,754 (+)NCBICelera
RGSC_v3.11829,748,724 - 29,748,983 (+)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

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.
Additional References at PubMed
PMID:14672974   PMID:15347688   PMID:15744052   PMID:17110050  


Genomics

Comparative Map Data
Pcdha10
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2 Ensembl1828,581,225 - 28,846,211 (+)EnsemblmRatBN7.2
Rnor_6.01830,010,918 - 30,215,896 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,987,206 - 30,215,897 (+)Ensemblrn6Rnor6.0
Rnor_5.01829,708,168 - 29,924,443 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41829,721,603 - 29,928,030 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1828,349,751 - 28,552,754 (+)NCBICelera
RGSC_v3.11829,748,724 - 29,748,983 (+)NCBI
Cytogenetic Map18p11NCBI
PCDHA10
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385140,855,897 - 141,012,347 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5140,855,883 - 141,012,347 (+)Ensemblhg38GRCh38
GRCh375140,235,482 - 140,391,932 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,215,818 - 140,372,113 (+)NCBIBuild 36Build 36hg18NCBI36
Build 345140,215,817 - 140,372,113NCBI
Celera5136,312,442 - 136,468,708 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,380,373 - 135,536,628 (+)NCBIHuRef
CHM1_15139,668,823 - 139,825,092 (+)NCBICHM1_1
T2T-CHM13v2.05141,381,222 - 141,537,634 (+)NCBIT2T-CHM13v2.0
Pcdha9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,130,933 - 37,320,710 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,130,933 - 37,320,710 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381836,997,880 - 37,187,657 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1836,997,880 - 37,187,657 (+)Ensemblmm10GRCm38
MGSCv371837,157,534 - 37,347,311 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361837,123,854 - 37,313,631 (+)NCBIMGSCv36mm8
MGSCv361837,184,986 - 37,374,763 (+)NCBIMGSCv36mm8
Celera1837,444,653 - 37,447,133 (+)NCBICelera
Cytogenetic Map18B2- B3NCBI
cM Map1819.46NCBI
PCDHA10
(Pan paniscus - bonobo/pygmy chimpanzee)		 No map positions available.
PCDHA10
(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
GRCr8 Ensembl1829,076,678 - 29,120,224 (+)Ensembl
mRatBN7.2 Ensembl1828,802,566 - 28,846,211 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000027372   ⟹   ENSRNOP00000027372
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1828,903,452 - 29,120,224 (+)Ensembl
mRatBN7.2 Ensembl1828,629,247 - 28,846,211 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000027383   ⟹   ENSRNOP00000027383
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1828,866,578 - 29,120,224 (+)Ensembl
mRatBN7.2 Ensembl1828,617,395 - 28,846,211 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000027393   ⟹   ENSRNOP00000027393
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1828,915,080 - 29,120,227 (+)Ensembl
mRatBN7.2 Ensembl1828,596,122 - 28,846,211 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000027402   ⟹   ENSRNOP00000027402
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1828,855,256 - 29,120,227 (+)Ensembl
mRatBN7.2 Ensembl1828,581,225 - 28,846,211 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000071366   ⟹   ENSRNOP00000065957
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1828,903,452 - 29,120,227 (+)Ensembl
mRatBN7.2 Ensembl1828,590,221 - 28,846,211 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000074028   ⟹   ENSRNOP00000066853
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1828,866,104 - 29,120,227 (+)Ensembl
mRatBN7.2 Ensembl1828,595,962 - 28,846,211 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000075810   ⟹   ENSRNOP00000066774
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1828,897,523 - 29,120,224 (+)Ensembl
mRatBN7.2 Ensembl1828,590,221 - 28,846,211 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000077824   ⟹   ENSRNOP00000074100
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1828,915,158 - 29,120,224 (+)Ensembl
mRatBN7.2 Ensembl1828,666,964 - 28,846,211 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000079794   ⟹   ENSRNOP00000075260
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1828,891,368 - 29,120,224 (+)Ensembl
mRatBN7.2 Ensembl1828,602,540 - 28,846,211 (+)Ensembl
RefSeq Acc Id: NM_053939   ⟹   NP_446391
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01830,010,918 - 30,215,896 (+)NCBI
Rnor_5.01829,708,168 - 29,924,443 (+)NCBI
RGSC_v3.41829,721,603 - 29,928,030 (+)RGD
Celera1828,349,751 - 28,552,754 (+)RGD
Protein Sequences
Protein RefSeqs NP_446391 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF87059 (Get FASTA)   NCBI Sequence Viewer  
  AAT77554 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_446391   ⟸   NM_053939
- UniProtKB: Q767I2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000074100   ⟸   ENSRNOT00000077824
Ensembl Acc Id: ENSRNOP00000075260   ⟸   ENSRNOT00000079794
Ensembl Acc Id: ENSRNOP00000066774   ⟸   ENSRNOT00000075810
Ensembl Acc Id: ENSRNOP00000066853   ⟸   ENSRNOT00000074028
Ensembl Acc Id: ENSRNOP00000027393   ⟸   ENSRNOT00000027393
Ensembl Acc Id: ENSRNOP00000027372   ⟸   ENSRNOT00000027372
Ensembl Acc Id: ENSRNOP00000027402   ⟸   ENSRNOT00000027402
Ensembl Acc Id: ENSRNOP00000027340   ⟸   ENSRNOT00000027340
Ensembl Acc Id: ENSRNOP00000027383   ⟸   ENSRNOT00000027383
Ensembl 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:620749 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
  Protocadherin/Cadherin-CA UniProtKB/TrEMBL
NCBI Gene 116778 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PROTOCADHERIN ALPHA-10 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
  Cadherin_tail UniProtKB/TrEMBL
PhenoGen Pcdha10 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 Q767I2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Pcdha10  protocadherin alpha 10      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Pcdha10  protocadherin alpha 10      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in testis 68759