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Lhx9 Gene Detail
Summary
  • Symbol
    Lhx9
  • Name
    LIM homeobox protein 9
  • Synonyms
    3110009O07Rik, LH2B, Lhx9 alpha
  • Feature Type
    protein coding gene
  • IDs
    MGI:1316721
    NCBI Gene: 16876
  • Alliance
    genome feature page
  • Transcription Start Sites
    5 TSS
Location &
Maps
more
  • Sequence Map
    Chr1:138752924-138776315 bp, - strand
    From Ensembl annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 1, 60.82 cM, cytoband G-H2
  • Mapping Data
    4 experiments
Strain
Comparison
more
  • SNPs within 2kb
    543 from dbSNP Build 142
  • Strain Annotations
    19
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_1316721
 protein coding gene Chr1:138752924-138776577 (-)
129S1/SvImJ ENSMUSG00200008212
 protein coding gene Chr1:136385224-136408631 (-)
A/J ENSMUSG00195016040
 protein coding gene Chr1:135454335-135477738 (-)
AKR/J ENSMUSG00220002631
 protein coding gene Chr1:135338731-135362135 (-)
BALB/cJ ENSMUSG00180011295
 protein coding gene Chr1:135982738-136006136 (-)
C3H/HeJ ENSMUSG00175006373
 protein coding gene Chr1:135671881-135695276 (-)
C57BL/6NJ ENSMUSG00215010234
 protein coding gene Chr1:135684828-135708228 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0014663
 protein coding gene Chr1:130386668-130410310 (-)
CAST/EiJ ENSTCUG00005012911
 protein coding gene Chr1:134599778-134623286 (-)
CBA/J ENSMUSG00210013748
 protein coding gene Chr1:135617834-135641245 (-)
DBA/2J ENSMUSG00185027701
 protein coding gene Chr1:139990940-140014361 (-)
FVB/NJ ENSMUSG00205002312
 protein coding gene Chr1:134979939-135003332 (-)
JF1/MsJ ENSUMUG00000048836
 protein coding gene Chr1:139074049-139097515 (-)
LP/J ENSMUSG00230037935
 protein coding gene Chr1:139516905-139540300 (-)
NOD/ShiLtJ ENSMUSG00190002104
 protein coding gene Chr1:135617533-135640940 (-)
NZO/HlLtJ ENSMUSG00225000086
 protein coding gene Chr1:143291483-143314874 (-)
PWK/PhJ ENSLUMG00010001780
 protein coding gene Chr1:134697792-134721289 (-)
SPRET/EiJ ENSMSPG00010011971
 protein coding gene Chr1:137593315-137613555 (-)
WSB/EiJ ENSIUOG00005025474
 protein coding gene Chr1:135410895-135433583 (-)



Homology
more
  • Human Ortholog
    LHX9, LIM homeobox 9
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    LHX9, LIM homeobox 9
  • Links
    NCBI Gene ID: 56956
    UniProt: Q9NQ69

  • Chr Location
    1q31.3; chr1:197911902-197935478 (+)  GRCh38
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    19 phenotypes from 2 alleles in 2 genetic backgrounds
    1 phenotype from multigenic genotypes
    1 images
    19 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.
Homozygotes for a targeted null mutation exhibit failed proliferation of the somatic cells of the genital ridge resulting in lack of discrete gonad formation, infertility in both sexes, and female-like genitalia in genetically male mice.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    21
  • GO References
    10
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
    1457
  • Tissues
    396
  • cDNA Data
    40
  • Literature Summary
    168
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000019230 Ensembl Gene Model | MGI Sequence Detail 23392 C57BL/6J ±  kb
    transcript ENSMUST00000112026 Ensembl | MGI Sequence Detail 2065 Not Applicable  
    polypeptide ENSMUSP00000107657 Ensembl | MGI Sequence Detail 397 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 80
      Genomic 1
      cDNA 43
      Primer pair 21
      Other 15
      Antibodies 11

      Microarray probesets 6
    Other
    Accession IDs
    less
    MGI:1920327, MGI:2138632
    References
    more
    • Summaries
      All 220
      Developmental Gene Expression 168
      Gene Ontology 10
      Phenotypes 19
    • Earliest
      J:134667 Roderick TH, et al., Two radiation-induced chromosomal inversions in mice (Mus musculus). Proc Natl Acad Sci U S A. 1970 Oct;67(2):961-7
    • Latest
      J:388885 Lin CY, et al., A 3D amphioxus brain atlas illuminates the blueprint of the ancestral chordate brain and highlights unique vertebrate innovations. Sci Adv. 2026 Jul 3;12(27):eaee5076
    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