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Lhx5 Gene Detail
Summary
  • Symbol
    Lhx5
  • Name
    LIM homeobox protein 5
  • Synonyms
    Lim2
  • Feature Type
    protein coding gene
  • IDs
    MGI:107792
    NCBI Gene: 16873
  • Alliance
    genome feature page
  • Transcription Start Sites
    6 TSS
  • Regulated by
    Rr201 (1 regulatory region)
Location &
Maps
more
  • Sequence Map
    Chr5:120569764-120579288 bp, + strand
    From Ensembl annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 5, 60.62 cM
  • Mapping Data
    3 experiments
Strain
Comparison
more
  • SNPs within 2kb
    175 from dbSNP Build 142
  • Strain Annotations
    19
  • RFLP
    1
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_107792
 protein coding gene Chr5:120569764-120579522 (+)
129S1/SvImJ ENSMUSG00200025735
 protein coding gene Chr5:114308965-114318453 (+)
A/J ENSMUSG00195009500
 protein coding gene Chr5:113830075-113839567 (+)
AKR/J ENSMUSG00220045651
 protein coding gene Chr5:113330850-113340347 (+)
BALB/cJ ENSMUSG00180037615
 protein coding gene Chr5:113944665-113954148 (+)
C3H/HeJ ENSMUSG00175020811
 protein coding gene Chr5:115942765-115952205 (+)
C57BL/6NJ ENSMUSG00215043323
 protein coding gene Chr5:113976586-113986124 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0027657
 protein coding gene Chr5:113383735-113393153 (+)
CAST/EiJ ENSTCUG00005040403
 protein coding gene Chr5:113150074-113159556 (+)
CBA/J ENSMUSG00210006056
 protein coding gene Chr5:114693661-114703105 (+)
DBA/2J ENSMUSG00185048982
 protein coding gene Chr5:117752973-117762467 (+)
FVB/NJ ENSMUSG00205018042
 protein coding gene Chr5:113606779-113616272 (+)
JF1/MsJ ENSUMUG00000052426
 protein coding gene Chr5:120589287-120598857 (+)
LP/J ENSMUSG00230038439
 protein coding gene Chr5:121831184-121840661 (+)
NOD/ShiLtJ ENSMUSG00190030001
 protein coding gene Chr5:113640891-113650365 (+)
NZO/HlLtJ ENSMUSG00225015509
 protein coding gene Chr5:129508341-129517832 (+)
PWK/PhJ ENSLUMG00010029118
 protein coding gene Chr5:112489705-112499268 (+)
SPRET/EiJ ENSMSPG00010032128
 protein coding gene Chr5:115807570-115816966 (+)
WSB/EiJ ENSIUOG00005014348
 protein coding gene Chr5:116331942-116341414 (+)



Homology
more
  • Human Ortholog
    LHX5, LIM homeobox 5
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    LHX5, LIM homeobox 5
  • Links
    NCBI Gene ID: 64211
    UniProt: Q9H2C1

  • Chr Location
    12q24.13; chr12:113462033-113472280 (-)  GRCh38
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    22 phenotypes from 2 alleles in 2 genetic backgrounds
    4 phenotypes from multigenic genotypes
    17 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.
Most mice homozygous for a null mutation display defective hippocampal development and die within a few days after birth. Postmitotic hippocampal cells are unable to differentiate properly and migrate to correct positions, resulting in structural anomalies of the Ammon's horn and the dentate gyrus.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    25
  • GO References
    9
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
    1343
  • Tissues
    372
  • cDNA Data
    27
  • Literature Summary
    203
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000029595 Ensembl Gene Model | MGI Sequence Detail 9525 C57BL/6J ±  kb
    transcript ENSMUST00000031591 Ensembl | MGI Sequence Detail 2689 Not Applicable  
    polypeptide ENSMUSP00000031591 Ensembl | MGI Sequence Detail 402 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 47
      Genomic 7
      cDNA 28
      Primer pair 7
      Other 5
      Antibodies 5

      Microarray probesets 3
    Other
    Accession IDs
    less
    MGD-MRK-36369
    References
    more
    • Summaries
      All 245
      Developmental Gene Expression 203
      Gene Ontology 9
      Phenotypes 17
    • 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:388640 Zhang Z, et al., Confined migration induces non-lethal DNA damage in developing neurons. Nature. 2026 Jun;654(8120):1098-1107
    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
    09/01/2026
    MGI 6.24     		The Jackson Laboratory