Pcdha9 (protocadherin alpha 9) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Pcdha9 (protocadherin alpha 9) Rattus norvegicus
Analyze
Symbol: Pcdha9
Name: protocadherin alpha 9
RGD ID: 735153
Description: Predicted to enable calcium ion binding activity. Predicted to be involved in homophilic cell adhesion via plasma membrane adhesion molecules. 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 (+)NCBIRGSC3.4rn4RGSC3.4
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

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 (+)NCBIRGSC3.4rn4RGSC3.4
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.p13 Ensembl5140,847,772 - 141,012,347 (+)EnsemblGRCh38hg38GRCh38
GRCh375140,227,357 - 140,391,932 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,207,541 - 140,372,113 (+)NCBINCBI36hg18NCBI36
Build 345140,207,540 - 140,372,113NCBI
Celera5136,304,162 - 136,468,708 (+)NCBI
Cytogenetic Map5q31.3NCBI
HuRef5135,372,092 - 135,536,628 (+)NCBIHuRef
CHM1_15139,660,543 - 139,825,092 (+)NCBICHM1_1
Pcdha8
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,125,520 - 37,320,710 (+)NCBIGRCm39mm39
GRCm39 Ensembl1837,125,424 - 37,320,710 (+)Ensembl
GRCm381836,992,467 - 37,187,657 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1836,992,371 - 37,187,657 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,152,121 - 37,347,311 (+)NCBIGRCm37mm9NCBIm37
MGSCv361837,118,441 - 37,313,631 (+)NCBImm8
Celera1837,439,238 - 37,441,618 (+)NCBICelera
Cytogenetic Map18B2- B3NCBI
LOC100992160
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15142,280,506 - 142,491,362 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5142,321,070 - 142,488,986 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05136,150,262 - 136,376,530 (+)NCBIMhudiblu_PPA_v0panPan3

Position Markers
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

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.


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_199508 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC097339 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
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  
Reference Sequences
RefSeq Acc Id: NP_955802   ⟸   NM_199508
- Peptide Label: precursor
- UniProtKB: Q767I3 (UniProtKB/TrEMBL)
Protein Domains
Cadherin

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
18 30005470 30005471 T G snv ACI/EurMcwi (MCW), SBH/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), ACI/EurMcwi (2019), ACI/N (2020), LN/MavRrrcAek (2020), SS/JrHsdMcwi (2019)
18 30005952 30005953 T C snv SS/JrHsdMcwi (2019), SR/JrHsd (2020), LN/MavRrrcAek (2020), LL/MavRrrcAek (2020), LH/MavRrrcAek (2020), BUF/N (2020), SS/JrHsdMcwi (MCW), SBH/Ygl (MCW), SR/JrHsd (MCW)
18 30025331 30025332 T A snv ACI/N (2020), ACI/EurMcwi (2019), LH/MavRrrcAek (2020), LL/MavRrrcAek (2020), LN/MavRrrcAek (2020), SR/JrHsd (2020), SS/JrHsdMcwi (2019), ACI/EurMcwi (RGD), ACI/N (MCW), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), SBH/Ygl (MCW), ACI/EurMcwi (MCW), BUF/N (2020)
18 30025862 30025863 T C snv M520/N (MCW)
18 30038729 30038730 G T snv ACI/EurMcwi (MCW), ACI/N (MCW), ACI/EurMcwi (RGD), ACI/EurMcwi (2019), ACI/N (2020)
18 30114825 30114826 G T snv ACI/EurMcwi (MCW), SBH/Ygl (MCW), SS/JrHsdMcwi (2019), SR/JrHsd (2020), LN/MavRrrcAek (2020), LL/MavRrrcAek (2020), LH/MavRrrcAek (2020), BUF/N (2020), ACI/N (2020), ACI/EurMcwi (2019), SS/JrHsdMcwi (RGD), SS/Jr (RGD), SR/JrHsd (RGD), SBH/Ygl (RGD), MNS/Gib (RGD), LL/MavRrrc (RGD), LN/MavRrrc (RGD), LH/MavRrrc (RGD), BBDP/Wor (RGD), ACI/EurMcwi (RGD), Buf/N (MCW), ACI/N (MCW), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW)
18 30116748 30116749 C T snv ACI/EurMcwi (MCW), SS/JrHsdMcwi (2019), LN/MavRrrcAek (2020), LL/MavRrrcAek (2020), LH/MavRrrcAek (2020), BUF/N (2020), ACI/N (2020), ACI/EurMcwi (2019), SS/JrHsdMcwi (RGD), SS/Jr (RGD), SR/JrHsd (RGD), SBH/Ygl (RGD), MNS/Gib (RGD), LL/MavRrrc (RGD), LN/MavRrrc (RGD), LH/MavRrrc (RGD), BBDP/Wor (RGD), ACI/EurMcwi (RGD), Buf/N (MCW), ACI/N (MCW), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), SBH/Ygl (MCW), SR/JrHsd (2020)


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
18 29708303 29708304 C G snv BUF/MNa (KyushuU), ZFDM (KyushuU), ZF (KyushuU)
18 29709599 29709600 G A snv ZFDM (KyushuU), ZF (KyushuU)
18 29709600 29709601 T C snv ZFDM (KyushuU), ZF (KyushuU)
18 29709701 29709702 G A snv ZFDM (KyushuU), ZF (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:735153 AgrOrtholog
Ensembl Genes ENSRNOG00000020119 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000027393 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027393 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
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
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin UniProtKB/TrEMBL
UniProt 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