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Pcdhb9 Gene Detail
Summary
  • Symbol
    Pcdhb9
  • Name
    protocadherin beta 9
  • Synonyms
    Pcdhb4C, PcdhbI
  • Feature Type
    protein coding gene
  • IDs
    MGI:2136744
    NCBI Gene: 93880
  • Member of
    Pcdhb cluster
  • Alliance
    gene page
  • Transcription Start Sites
    1 TSS
Location &
Maps
more
  • Sequence Map
    Chr18:37533908-37536962 bp, + strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 18, 19.48 cM, cytoband B3
  • Mapping Data
    1 experiment
Strain
Comparison
more
  • SNPs within 2kb
    252 from dbSNP Build 142
  • Strain Annotations
    18
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_2136744
 protein coding gene Chr18:37533908-37536962 (+)
129S1/SvImJ MGP_129S1SvImJ_G0024318
 protein coding gene Chr18:35791491-35795938 (+)
A/J MGP_AJ_G0024285
 protein coding gene Chr18:34573233-34576287 (+)
AKR/J MGP_AKRJ_G0024253
 protein coding gene Chr18:35526640-35529694 (+)
BALB/cJ MGP_BALBcJ_G0024284
 protein coding gene Chr18:34613374-34617330 (+)
C3H/HeJ MGP_C3HHeJ_G0024051
 protein coding gene Chr18:35594220-35597274 (+)
C57BL/6NJ MGP_C57BL6NJ_G0024726
 protein coding gene Chr18:37089721-37092897 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0022165
 protein coding gene Chr18:34625492-34628453 (+)
CAST/EiJ MGP_CASTEiJ_G0023527
 protein coding gene Chr18:35564078-35567132 (+)
CBA/J MGP_CBAJ_G0024020
 protein coding gene Chr18:38172051-38180377 (+)
DBA/2J MGP_DBA2J_G0024150
 protein coding gene Chr18:34170724-34173778 (+)
FVB/NJ MGP_FVBNJ_G0024117
 protein coding gene Chr18:33893284-33896338 (+)
LP/J MGP_LPJ_G0024234
 protein coding gene Chr18:35875646-35878700 (+)
NOD/ShiLtJ MGP_NODShiLtJ_G0024147
 protein coding gene Chr18:39449773-39452827 (+)
NZO/HlLtJ MGP_NZOHlLtJ_G0024775
 protein coding gene Chr18:35392224-35395278 (+)
PWK/PhJ MGP_PWKPhJ_G0023271
 protein coding gene Chr18:34405994-34409162 (+)
SPRET/EiJ MGP_SPRETEiJ_G0023076
 protein coding gene Chr18:35628562-35631405 (+)
WSB/EiJ MGP_WSBEiJ_G0023589
 protein coding gene Chr18:35286422-35289476 (+)



Homology
more
  • Human Ortholog
    PCDHB4, protocadherin beta 4
  • Vertebrate Orthologs
    7
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    PCDHB4, protocadherin beta 4
  • Synonyms
    PCDH-BETA4
  • Links
    NCBI Gene ID: 56131
    neXtProt AC: NX_Q9Y5E5
    UniProt: Q9Y5E5

  • Chr Location
    5q31.3; chr5:141121818-141125623 (+)  GRCh38
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    4 phenotypes from 1 allele in 1 genetic background
    8 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    2
  • GO References
    1
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    886
  • Tissues
    42
  • cDNA Data
    14
  • Literature Summary
    5
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 93880 NCBI Gene Model | MGI Sequence Detail 3055 C57BL/6J ±  kb
    transcript NM_053134 RefSeq | MGI Sequence Detail 3055 C57BL/6  
    polypeptide NP_444364 RefSeq | MGI Sequence Detail 828 C57BL/6  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      3 Sequences
    • InterPro Domains
      IPR020894 Cadherin conserved site
      IPR032455 Cadherin, cytoplasmic C-terminal domain
      IPR002126 Cadherin-like
      IPR015919 Cadherin-like superfamily
      IPR013164 Cadherin, N-terminal
      IPR050174 Protocadherin/Cadherin-related Cell Adhesion
    • GlyGen
      E9Q5G2 1 site, 1 N-linked glycan (1 site)
    Molecular
    Reagents
    less
    • All nucleic 17
      cDNA 14
      Primer pair 3

      Microarray probesets 2
    References
    more
    • Summaries
      All 27
      Developmental Gene Expression 5
      Gene Ontology 1
      Phenotypes 8
    • Earliest
      J:67989 Wu Q, et al., Comparative dna sequence analysis of mouse and human protocadherin gene clusters. Genome Res. 2001 Mar;11(3):389-404
    • Latest
      J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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    Funding Information
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    12/10/2024
    MGI 6.24     		The Jackson Laboratory