Pcdha8 (protocadherin alpha 8) - Rat Genome Database

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Gene: Pcdha8 (protocadherin alpha 8) Rattus norvegicus
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Symbol: Pcdha8 (Ensembl: Pcdha3)
Name: protocadherin alpha 8 (Ensembl:protocadherin alpha 3)
RGD ID: 620338
Description: Predicted to enable calcium ion binding activity. Predicted to be involved in spermatogenesis. Predicted to be located in plasma membrane. Orthologous to human PCDHA8 (protocadherin alpha 8); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride; cadmium dichloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: protocadherin alpha-8
RGD Orthologs
Human
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_6.01829,999,290 - 30,215,896 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,987,206 - 30,215,897 (+)Ensemblrn6Rnor6.0
Rnor_5.01829,696,540 - 29,924,443 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41829,709,960 - 29,928,030 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1828,338,123 - 28,552,754 (+)NCBICelera
RGSC_v3.11829,736,991 - 29,737,250 (+)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. 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:15744052   PMID:17110050  


Genomics

Comparative Map Data
Pcdha8
(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_6.01829,999,290 - 30,215,896 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,987,206 - 30,215,897 (+)Ensemblrn6Rnor6.0
Rnor_5.01829,696,540 - 29,924,443 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41829,709,960 - 29,928,030 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1828,338,123 - 28,552,754 (+)NCBICelera
RGSC_v3.11829,736,991 - 29,737,250 (+)NCBI
Cytogenetic Map18p11NCBI
PCDHA8
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385140,841,187 - 141,012,347 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5140,841,187 - 141,012,347 (+)Ensemblhg38GRCh38
GRCh375140,220,772 - 140,391,932 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,201,091 - 140,372,113 (+)NCBIBuild 36Build 36hg18NCBI36
Build 345140,201,090 - 140,203,535NCBI
Celera5136,297,714 - 136,468,708 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,365,644 - 135,536,628 (+)NCBIHuRef
CHM1_15139,654,096 - 139,825,092 (+)NCBICHM1_1
T2T-CHM13v2.05141,366,514 - 141,537,634 (+)NCBIT2T-CHM13v2.0

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:417
Count of miRNA genes:220
Interacting mature miRNAs:302
Transcripts:ENSRNOT00000027372
Prediction methods: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
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

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
3 10 43 82 48 51 32 19 32 150 72 74 35 41 19

Sequence


RefSeq Acc Id: NM_053942   ⟹   NP_446394
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01829,999,290 - 30,215,896 (+)NCBI
Rnor_5.01829,696,540 - 29,924,443 (+)NCBI
RGSC_v3.41829,709,960 - 29,928,030 (+)RGD
Celera1828,338,123 - 28,552,754 (+)RGD
Protein Sequences
Protein RefSeqs NP_446394 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF87063 (Get FASTA)   NCBI Sequence Viewer  
  AAT77564 (Get FASTA)   NCBI Sequence Viewer  
  BAD06373 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000027372.7
RefSeq Acc Id: NP_446394   ⟸   NM_053942
- Peptide Label: precursor
- UniProtKB: Q767I4 (UniProtKB/TrEMBL),   F7F4G8 (UniProtKB/TrEMBL)
- Sequence:
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:620338 AgrOrtholog
Ensembl Genes ENSRNOG00000020119 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027372.7 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 116781 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PROTOCADHERIN ALPHA-6-RELATED UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
  Cadherin_tail UniProtKB/TrEMBL
PhenoGen Pcdha8 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 F7F4G8 ENTREZGENE
  Q767I4 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary F7F4G8 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Pcdha8  protocadherin alpha 8      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Pcdha8  protocadherin alpha 8      Symbol and Name status set to provisional 70820 PROVISIONAL

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