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Chrna9 Gene Detail
Summary
  • Symbol
    Chrna9
  • Name
    cholinergic receptor, nicotinic, alpha polypeptide 9
  • Synonyms
    2410015I05Rik, Acra9, Gm8311
  • Feature Type
    protein coding gene
  • IDs
    MGI:1202403
    NCBI Gene: 231252
  • Alliance
    genome feature page
  • Transcription Start Sites
    14 TSS
Location &
Maps
more
  • Sequence Map
    Chr5:66092264-66134669 bp, + strand
    From Ensembl annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 5, 33.84 cM
  • Mapping Data
    4 experiments
Strain
Comparison
more
  • SNPs within 2kb
    1544 from dbSNP Build 142
  • Strain Annotations
    19
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_1202403
 protein coding gene Chr5:66092264-66134823 (+)
129S1/SvImJ ENSMUSG00200035560
 protein coding gene Chr5:61710526-61752900 (+)
A/J ENSMUSG00195032926
 protein coding gene Chr5:61087771-61130156 (+)
AKR/J ENSMUSG00220003513
 protein coding gene Chr5:61221992-61264349 (+)
BALB/cJ ENSMUSG00180005978
 protein coding gene Chr5:60873612-60915982 (+)
C3H/HeJ ENSMUSG00175024931
 protein coding gene Chr5:62907642-62950019 (+)
C57BL/6NJ ENSMUSG00215005575
 protein coding gene Chr5:61639408-61681821 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0027256
 protein coding gene Chr5:59237134-59281575 (+)
CAST/EiJ ENSTCUG00005027164
 protein coding gene Chr5:60790116-60838512 (+)
CBA/J ENSMUSG00210022899
 protein coding gene Chr5:61820578-61862946 (+)
DBA/2J ENSMUSG00185005503
 protein coding gene Chr5:63678071-63720439 (+)
FVB/NJ ENSMUSG00205010544
 protein coding gene Chr5:60621741-60664099 (+)
JF1/MsJ ENSUMUG00000011597
 protein coding gene Chr5:68152259-68200729 (+)
LP/J ENSMUSG00230007024
 protein coding gene Chr5:68323226-68365629 (+)
NOD/ShiLtJ ENSMUSG00190003878
 protein coding gene Chr5:60812750-60855124 (+)
NZO/HlLtJ ENSMUSG00225008423
 protein coding gene Chr5:73448971-73491333 (+)
PWK/PhJ ENSLUMG00010012668
 protein coding gene Chr5:60755122-60797413 (+)
SPRET/EiJ ENSMSPG00010032744
 protein coding gene Chr5:62568890-62611225 (+)
WSB/EiJ ENSIUOG00005017851
 protein coding gene Chr5:63765652-63808003 (+)



Homology
more
  • Human Ortholog
    CHRNA9, cholinergic receptor nicotinic alpha 9 subunit
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    CHRNA9, cholinergic receptor nicotinic alpha 9 subunit
  • Synonyms
    HSA243342, NACHRA9
  • Links
    NCBI Gene ID: 55584
    UniProt: Q9UGM1

  • Chr Location
    4p14; chr4:40335333-40355217 (+)  GRCh38
Human Diseases
more
  • Diseases
    1 with human CHRNA9 associations

Human Disease Mouse Models
      
IDs
Click on a disease name to see all genes associated with that disease.

Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    12 phenotypes from 3 alleles in 4 genetic backgrounds
    79 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.
Homozygous mutation of this gene results in abnormal innervation of the outer hair cells and depressed olivocochlear response.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    57
  • GO References
    13
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
    604
  • Tissues
    5
  • cDNA Data
    9
  • Literature Summary
    3
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000029205 Ensembl Gene Model | MGI Sequence Detail 42406 C57BL/6J ±  kb
    transcript ENSMUST00000031108 Ensembl | MGI Sequence Detail 1843 Not Applicable  
    polypeptide ENSMUSP00000031108 Ensembl | MGI Sequence Detail 479 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      4 Sequences
    • InterPro Domains
      IPR038050 Neuronal acetylcholine receptor
      IPR006201 Neurotransmitter-gated ion-channel
      IPR018000 Neurotransmitter-gated ion-channel, conserved site
      IPR006202 Neurotransmitter-gated ion-channel ligand-binding domain
      IPR036734 Neurotransmitter-gated ion-channel ligand-binding domain superfamily
      IPR006029 Neurotransmitter-gated ion-channel transmembrane domain
      IPR036719 Neurotransmitter-gated ion-channel transmembrane domain superfamily
      IPR002394 Nicotinic acetylcholine receptor
    Molecular
    Reagents
    less
    • All nucleic 9
      cDNA 9

      Microarray probesets 2
    Other
    Accession IDs
    less
    MGI:1917242, MGI:3643549
    References
    more
    • Summaries
      All 123
      Developmental Gene Expression 3
      Gene Ontology 13
      Phenotypes 79
    • Earliest
      J:5021 Batchelor AL, et al., A comparison of the mutagenic effectiveness of chronic neutron- and gamma-irradiation of mouse spermatogonia. Mutat Res. 1966 Jun;3(3):218-29
    • Latest
      J:371589 Quinones PM, et al., The Medial Olivocochlear Efferent Pathway Potentiates Cochlear Amplification in Response to Hearing Loss. J Neurosci. 2025 Apr 9;45(15)
    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
    09/08/2026
    MGI 6.24     		The Jackson Laboratory