Pcdhb9 (protocadherin beta 9) - Rat Genome Database

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Gene: Pcdhb9 (protocadherin beta 9) Mus musculus
Analyze
No known orthologs.
Symbol: Pcdhb9
Name: protocadherin beta 9
RGD ID: 1316131
MGI Page MGI
Description: Predicted to be involved in cell adhesion. Is expressed in nervous system and retina. Orthologous to human PCDHB4 (protocadherin beta 4).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Pcdh; Pcdhb4; Pcdhb4C; PcdhbI
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,533,908 - 37,536,962 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,533,908 - 37,536,962 (+)EnsemblGRCm39 Ensembl
GRCm381837,400,855 - 37,403,909 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1837,400,855 - 37,403,909 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,560,509 - 37,563,563 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361837,526,829 - 37,529,883 (+)NCBIMGSCv36mm8
Celera1838,752,174 - 38,755,228 (+)NCBICelera
Cytogenetic Map18B3NCBI
cM Map1819.48NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. MGDs mouse GO annotations MGD data from the GO Consortium
2. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:10380929   PMID:10716726   PMID:11042159   PMID:11076861   PMID:11217851   PMID:11230163   PMID:11322959   PMID:12477932   PMID:16141072   PMID:16141073   PMID:18279309  
PMID:21267068   PMID:21873635   PMID:24952961   PMID:30377227   PMID:32633719  


Genomics

Variants

.
Variants in Pcdhb9
97 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:70
Count of miRNA genes:68
Interacting mature miRNAs:69
Transcripts:ENSMUST00000057228
Prediction methods:Miranda
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.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357603Mom3_mmodifier of Min 3 (mouse)Not determined181403002367098962Mouse
1300685Scc5_mcolon tumor susceptibility 5 (mouse)Not determined183198848065988629Mouse
27226723Tibw9_mtibia width 9, proximal, 16 week (mouse)18320000060933072Mouse
25823167Hrsq5_mhost response to SARS QTL 5, D3% weight (mouse)182724111558827077Mouse
25823171Hrsq10_mhost response to SARS QTL 10, D4% weight (mouse)182724111558827077Mouse
1301400Lmr13_mleishmaniasis resistance 13 (mouse)Not determined182810938062109518Mouse
11532715Sluc41b_msusceptibility to lung cancer 41b (mouse)182261991456620127Mouse
25823173Hrsq12_mhost response to SARS QTL 12, hemorrhage (mouse)182489588178339555Mouse
1302163Bmd16_mbone mineral density 16 (mouse)Not determined182966791463668060Mouse
1301307Phospq1_mphospholipid QTL 1 (mouse)Not determined181813970452139859Mouse
1300877Adip8_madiposity 8 (mouse)Not determined182261991456620127Mouse
1558849W3q15_mweight 3 weeks QTL 15 (mouse)Not determined18504111961272643Mouse
1558743Kcal1_mkilocalorie 1 (mouse)Not determined181901887453018992Mouse
13463476Hctq8_mhematocrit QTL 8 (mouse)182121758055217727Mouse
1357690Vtbt19_mvertebral trabecular bone trait 19 (mouse)Not determined183309104367091221Mouse
11041903Lmr27_mleishmaniasis resistance 27 (mouse)183618756745109518Mouse
4142031Moen1_mmodifier of engrailed QTL 1 (mouse)Not determined182411556058115730Mouse
1300994Pvcan3_mprotection against vaginal candidiasis 3 (mouse)Not determined181619964050199776Mouse
25823174Hrsq11_mhost response to SARS QTL 11, log titer (mouse)182724111558827077Mouse
4142366Chlq10_mcirculating hormone level QTL 10 (mouse)Not determined183629102270291180Mouse
11532709Sluc41_msusceptibility to lung cancer 41 (mouse)182095369457590708Mouse
11532716Sluc41c_msusceptibility to lung cancer 41c (mouse)182261991456620127Mouse
13504732Cath6_mcarotid atherosclerosis 6 (mouse)181363712647637126Mouse
1300638Im7_mimmunoregulatory 7 (mouse)Not determined181901887453018992Mouse
12904950Smmq3_msoleus muscle mass QTL 3 (mouse)182605687560056875Mouse
4141857Mhysq5_mmale hybrid sterility QTL 5 (mouse)Not determined2813060462130739Mouse
11532710Sluc41a_msusceptibility to lung cancer 41a (mouse)182261991456620127Mouse
1558873Hrtfm7_mheart failure modifier 7 (mouse)Not determined18808696442087106Mouse
1301570Sluc14_msusceptibility to lung cancer 14 (mouse)Not determined182261991456620127Mouse
12880412V125Dq12_mvitamin D active form serum level QTL 12 (mouse)183023306764233067Mouse
1301771Pcyts6_mplasmacytoma susceptibility 6 (mouse)Not determined183565863269658851Mouse

Markers in Region
Pcdhb9  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381837,403,555 - 37,403,840UniSTSGRCm38
MGSCv371837,563,209 - 37,563,494UniSTSGRCm37
Celera1838,754,874 - 38,755,159UniSTS
Cytogenetic Map18B3UniSTS
cM Map18 UniSTS


Expression


Sequence


RefSeq Acc Id: ENSMUST00000057228   ⟹   ENSMUSP00000058801
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1837,533,908 - 37,536,962 (+)Ensembl
GRCm38.p6 Ensembl1837,400,855 - 37,403,909 (+)Ensembl
RefSeq Acc Id: NM_053134   ⟹   NP_444364
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391837,533,908 - 37,536,962 (+)NCBI
GRCm381837,400,855 - 37,403,909 (+)ENTREZGENE
MGSCv371837,560,509 - 37,563,563 (+)RGD
Celera1838,752,174 - 38,755,228 (+)RGD
cM Map18 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_444364 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH55319 (Get FASTA)   NCBI Sequence Viewer  
  AAH62640 (Get FASTA)   NCBI Sequence Viewer  
  AAK26080 (Get FASTA)   NCBI Sequence Viewer  
  AAK53227 (Get FASTA)   NCBI Sequence Viewer  
  BAC27957 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000058801
  ENSMUSP00000058801.2
RefSeq Acc Id: NP_444364   ⟸   NM_053134
- UniProtKB: E9Q5G2 (UniProtKB/TrEMBL),   Q91XZ1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000058801   ⟸   ENSMUST00000057228
Protein Domains
Cadherin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-E9Q5G2-F1-model_v2 AlphaFold E9Q5G2 1-828 view protein structure

Promoters
RGD ID:13677536
Promoter ID:EPDNEW_M22918
Type:multiple initiation site
Name:Pcdhb9_1
Description:Mus musculus protocadherin beta 9 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381837,400,868 - 37,400,928EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2136744 AgrOrtholog
Ensembl Genes ENSMUSG00000051242 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000057228 ENTREZGENE
  ENSMUST00000057228.2 UniProtKB/TrEMBL
Gene3D-CATH Cadherins UniProtKB/TrEMBL
InterPro Cadherin UniProtKB/TrEMBL
  Cadherin-like UniProtKB/TrEMBL
  Cadherin_C UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
  Cadherin_N UniProtKB/TrEMBL
KEGG Report mmu:93880 UniProtKB/TrEMBL
MGD MGI:2136744 ENTREZGENE
NCBI Gene 93880 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PROTOCADHERIN BETA 9 UniProtKB/TrEMBL
  PROTOCADHERIN BETA-10 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
  Cadherin_C_2 UniProtKB/TrEMBL
PhenoGen Pcdhb9 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin UniProtKB/TrEMBL
UniProt E9Q5G2 ENTREZGENE, UniProtKB/TrEMBL
  Q8CCK1_MOUSE UniProtKB/TrEMBL
  Q91XZ1 ENTREZGENE, UniProtKB/TrEMBL
  Q925L3_MOUSE UniProtKB/TrEMBL