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Pcdh9 Gene Detail
Summary
  • Symbol
    Pcdh9
  • Name
    protocadherin 9
  • Synonyms
    1500001L12Rik, A730003J17Rik, C530050I23Rik, C630029H24Rik, LOC382930
  • Feature Type
    protein coding gene
  • IDs
    MGI:1306801
    NCBI Gene: 211712
  • Alliance
    gene page
  • Transcription Start Sites
    27 TSS
Location &
Maps
more
  • Sequence Map
    Chr14:93250846-94128115 bp, - strand
    From Ensembl annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 14, 45.80 cM
  • Mapping Data
    4 experiments
Strain
Comparison
more
  • SNPs within 2kb
    9471 from dbSNP Build 142
  • Strain Annotations
    18
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_1306801
 protein coding gene Chr14:93250846-94132619 (-)
129S1/SvImJ MGP_129S1SvImJ_G0021610
 protein coding gene Chr14:88874903-89814765 (-)
A/J MGP_AJ_G0021568
 protein coding gene Chr14:86304495-87162946 (-)
AKR/J MGP_AKRJ_G0021544
 protein coding gene Chr14:88857081-89742657 (-)
BALB/cJ MGP_BALBcJ_G0021574
 protein coding gene Chr14:86441814-87322365 (-)
C3H/HeJ MGP_C3HHeJ_G0021352
 protein coding gene Chr14:88642437-89546593 (-)
C57BL/6NJ MGP_C57BL6NJ_G0022014
 protein coding gene Chr14:92569227-93533240 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0019554
 protein coding gene Chr14:83572750-84417095 (-)
CAST/EiJ MGP_CASTEiJ_G0020869
 protein coding gene Chr14:85757361-86690274 (-)
CBA/J MGP_CBAJ_G0021320
 protein coding gene Chr14:95790788-96805134 (-)
DBA/2J MGP_DBA2J_G0021444
 protein coding gene Chr14:85712955-86599263 (-)
FVB/NJ MGP_FVBNJ_G0021420
 protein coding gene Chr14:84812718-85682919 (-)
LP/J MGP_LPJ_G0021512
 protein coding gene Chr14:89756767-90699919 (-)
NOD/ShiLtJ MGP_NODShiLtJ_G0021448
 protein coding gene Chr14:97172865-98456400 (-)
NZO/HlLtJ MGP_NZOHlLtJ_G0022037
 protein coding gene Chr14:88252475-89167594 (-)
PWK/PhJ MGP_PWKPhJ_G0020612
 protein coding gene Chr14:82568617-83466678 (-)
SPRET/EiJ MGP_SPRETEiJ_G0020450
 protein coding gene Chr14:84161957-85064127 (-)
WSB/EiJ MGP_WSBEiJ_G0020922
 protein coding gene Chr14:88773480-89693792 (-)



Homology
more
  • Human Ortholog
    PCDH9, protocadherin 9
  • Vertebrate Orthologs
    2
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    PCDH9, protocadherin 9
  • Links
    NCBI Gene ID: 5101
    neXtProt AC: NX_Q9HC56
    UniProt: Q9HC56

  • Chr Location
    13q21.32; chr13:66302834-67230336 (-)  GRCh38.p7
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    16 phenotypes from 2 alleles in 2 genetic backgrounds
    6 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
immune system
integument
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
neoplasm
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
vision/eye

Click cells to view annotations.
Mice homozygous for a knock-out allele exhibit impaired long-term social and bject recognition and sensorimotor development.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    6
  • GO References
    4
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 death
cell differentiation
cell population proliferation
cellular component organization
establishment of localization
homeostatic process
immune system process
lipid metabolic process
nucleic acid-templated transcription
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
non-membrane-bounded 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
    851
  • Tissues
    146
  • cDNA Data
    22
  • Literature Summary
    15
  • Comparison Matrix
    Gene Expression + Phenotype
    • Interactions
    less
    Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000055421 Ensembl Gene Model | MGI Sequence Detail 877270 C57BL/6J ±  kb
    transcript ENSMUST00000195826 Ensembl | MGI Sequence Detail 6521 Not Applicable  
    polypeptide ENSMUSP00000141396 Ensembl | MGI Sequence Detail 1237 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 28
      cDNA 25
      Primer pair 1
      Other 2

      Microarray probesets 9
    Other
    Accession IDs
    less
    MGI:1916209, MGI:2444471, MGI:2685143, MGI:2686059, MGI:3510991
    References
    more
    • Summaries
      All 38
      Developmental Gene Expression 15
      Gene Ontology 4
      Phenotypes 6
    • Earliest
      J:50455 Strehl S, et al., Characterization of two novel protocadherins (PCDH8 and PCDH9) localized on human chromosome 13 and mouse chromosome 14. Genomics. 1998 Oct 1;53(1):81-9
    • Latest
      J:288805 Pensold D, et al., Single-Cell Transcriptomics Reveals Regulators of Neuronal Migration and Maturation During Brain Development. J Exp Neurosci. 2018;12:1179069518760783
    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)
    Citing These Resources
    Funding Information
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    Send questions and comments to User Support.     		last database update
    06/14/2022
    MGI 6.19     		The Jackson Laboratory