Pcdha9 (protocadherin alpha 9) - Rat Genome Database

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Gene: Pcdha9 (protocadherin alpha 9) Rattus norvegicus
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Symbol: Pcdha9 (Ensembl: Pcdha13)
Name: protocadherin alpha 9 (Ensembl:protocadherin alpha 13)
RGD ID: 735153
Description: Predicted to be located in membrane. Orthologous to human PCDHA9 (protocadherin alpha 9); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: cadherin-related neuronal receptor 9; protocadherin alpha-9; rCNRv09
RGD Orthologs
Human
Mouse
Bonobo
Alliance Genes
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
Rnor_6.01830,004,565 - 30,215,897 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,987,206 - 30,215,897 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01829,701,815 - 29,924,444 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41829,715,235 - 29,928,031 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11829,741,880 - 29,954,676 (+)NCBI
Celera1828,343,398 - 28,552,755 (+)NCBICelera
Cytogenetic Map18p11NCBI


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (ISO)

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:14672974   PMID:15347688   PMID:15744052   PMID:17110050  


Genomics

Comparative Map Data
Pcdha9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01830,004,565 - 30,215,897 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,987,206 - 30,215,897 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01829,701,815 - 29,924,444 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41829,715,235 - 29,928,031 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11829,741,880 - 29,954,676 (+)NCBI
Celera1828,343,398 - 28,552,755 (+)NCBICelera
Cytogenetic Map18p11NCBI
PCDHA9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385140,847,772 - 141,012,347 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5140,847,772 - 141,012,347 (+)EnsemblGRCh38hg38GRCh38
GRCh375140,227,357 - 140,391,932 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,207,541 - 140,372,113 (+)NCBINCBI36Build 36hg18NCBI36
Build 345140,207,540 - 140,372,113NCBI
Celera5136,304,162 - 136,468,708 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,372,092 - 135,536,628 (+)NCBIHuRef
CHM1_15139,660,543 - 139,825,092 (+)NCBICHM1_1
T2T-CHM13v2.05141,373,097 - 141,537,634 (+)NCBIT2T-CHM13v2.0
Pcdha8
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,125,520 - 37,320,710 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,125,424 - 37,320,710 (+)EnsemblGRCm39 Ensembl
GRCm381836,992,467 - 37,187,657 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1836,992,371 - 37,187,657 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,152,121 - 37,347,311 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361837,118,441 - 37,313,631 (+)NCBIMGSCv36mm8
Celera1837,439,238 - 37,441,618 (+)NCBICelera
Cytogenetic Map18B2- B3NCBI
cM Map1819.46NCBI
LOC100992160
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v24136,039,789 - 136,269,711 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15134,179,338 - 134,408,495 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v05136,150,262 - 136,376,530 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15142,280,506 - 142,491,362 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5142,321,070 - 142,488,986 (+)Ensemblpanpan1.1panPan2

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:959
Count of miRNA genes:329
Interacting mature miRNAs:451
Transcripts:ENSRNOT00000027393
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
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


Sequence


RefSeq Acc Id: NM_199508   ⟹   NP_955802
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01830,004,565 - 30,215,897 (+)NCBI
Rnor_5.01829,701,815 - 29,924,444 (+)NCBI
RGSC_v3.41829,715,235 - 29,928,031 (+)RGD
Celera1828,343,398 - 28,552,755 (+)RGD
Protein Sequences
Protein RefSeqs NP_955802 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAT77565 (Get FASTA)   NCBI Sequence Viewer  
  BAD06374 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_955802   ⟸   NM_199508
- Peptide Label: precursor
- UniProtKB: Q767I3 (UniProtKB/TrEMBL),   F1LM35 (UniProtKB/TrEMBL),   A6J351 (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:735153 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 393090 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PROTOCADHERIN ALPHA-9 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
  Cadherin_tail UniProtKB/TrEMBL
PhenoGen Pcdha9 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 A6J351 ENTREZGENE, UniProtKB/TrEMBL
  F1LM35 ENTREZGENE
  Q767I3 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary F1LM35 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-10-12 Pcdha9        Symbol and Name status set to provisional 70820 PROVISIONAL