U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Lhx1 LIM homeobox protein 1 [ Mus musculus (house mouse) ]

Gene ID: 16869, updated on 8-Feb-2024

Summary

Official Symbol
Lhx1provided by MGI
Official Full Name
LIM homeobox protein 1provided by MGI
Primary source
MGI:MGI:99783
See related
Ensembl:ENSMUSG00000018698 AllianceGenome:MGI:99783
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Lim1
Summary
Enables DNA-binding transcription factor activity and cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including animal organ development; generation of neurons; and regulation of transcription, DNA-templated. Acts upstream of or within several processes, including animal organ development; gastrulation; and regionalization. Located in nucleus. Part of transcription regulator complex. Is expressed in several structures, including central nervous system; embryo mesoderm; genitourinary system; gut; and sensory organ. Orthologous to human LHX1 (LIM homeobox 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in whole brain E14.5 (RPKM 11.5), CNS E11.5 (RPKM 10.7) and 5 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See Lhx1 in Genome Data Viewer
Location:
11 C; 11 51.31 cM
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (84408801..84416360, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (84517975..84525534, complement)

Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene acetyl-Coenzyme A carboxylase alpha Neighboring gene 60S ribosomal protein L35 pseudogene Neighboring gene STARR-seq mESC enhancer starr_30214 Neighboring gene STARR-positive B cell enhancer mm9_chr11:84077985-84078286 Neighboring gene STARR-seq mESC enhancer starr_30216 Neighboring gene STARR-seq mESC enhancer starr_30218 Neighboring gene STARR-seq mESC enhancer starr_30219 Neighboring gene apoptosis antagonizing transcription factor Neighboring gene STARR-seq mESC enhancer starr_30220 Neighboring gene LIM homeobox 1, opposite strand Neighboring gene STARR-seq mESC enhancer starr_30221 Neighboring gene RIKEN cDNA 1700109G15 gene Neighboring gene STARR-seq mESC enhancer starr_30223

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Process Evidence Code Pubs
involved_in S-shaped body morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within anatomical structure formation involved in morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within anatomical structure formation involved in morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within anatomical structure morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within anterior/posterior axis specification IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within anterior/posterior pattern specification IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in branching involved in ureteric bud morphogenesis IEP
Inferred from Expression Pattern
more info
PubMed 
acts_upstream_of_or_within cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cell-cell signaling IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within cerebellar Purkinje cell differentiation IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within cerebellum development IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in cervix development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in comma-shaped body morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within dorsal/ventral pattern formation IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within ectoderm formation IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within embryonic pattern specification IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in embryonic retina morphogenesis in camera-type eye IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in embryonic viscerocranium morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within endoderm development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within endoderm formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in epithelium development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within forebrain regionalization IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within gastrulation with mouth forming second IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within head development IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in head development IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within kidney development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in lateral motor column neuron migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of mesendoderm development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in mesonephros development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in metanephric S-shaped body morphogenesis IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in metanephric renal vesicle morphogenesis IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in metanephros development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in motor neuron axon guidance IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in nephric duct elongation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in nephric duct morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within nervous system development IEA
Inferred from Electronic Annotation
more info
 
involved_in neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in oviduct development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in oviduct epithelium development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in paramesonephric duct development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within pattern specification process IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within pattern specification process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of DNA-templated transcription IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in positive regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of anterior head development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of branching involved in ureteric bud morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of embryonic development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of gastrulation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of nephron tubule epithelial cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within post-embryonic development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within primitive streak formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in pronephros development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in renal vesicle morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in retina development in camera-type eye IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in retina layer formation IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in retina layer formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within somite rostral/caudal axis specification IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in spinal cord association neuron differentiation IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in spinal cord development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in telencephalon development IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within ureter morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within ureteric bud development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within urogenital system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in uterine epithelium development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in uterus development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in vagina development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in ventral spinal cord development IEP
Inferred from Expression Pattern
more info
PubMed 
Component Evidence Code Pubs
located_in intracellular anatomical structure IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of transcription regulator complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
LIM/homeobox protein Lhx1
Names
LIM homeo box protein 1
homeobox protein Lim-1

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_008498.3NP_032524.1  LIM/homeobox protein Lhx1

    See identical proteins and their annotated locations for NP_032524.1

    Status: VALIDATED

    Source sequence(s)
    AL603708
    Consensus CDS
    CCDS25187.1
    UniProtKB/Swiss-Prot
    P63006
    UniProtKB/TrEMBL
    Q3URX6, Q569N5
    Related
    ENSMUSP00000018842.7, ENSMUST00000018842.14
    Conserved Domains (4) summary
    cd09367
    Location:455
    LIM1_Lhx1_Lhx5; The first LIM domain of Lhx1 (also known as Lim1) and Lhx5
    cd09375
    Location:63118
    LIM2_Lhx1_Lhx5; The second LIM domain of Lhx1 (also known as Lim1) and Lhx5
    PRK14086
    Location:263382
    dnaA; chromosomal replication initiator protein DnaA
    pfam00046
    Location:183237
    Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000077.7 Reference GRCm39 C57BL/6J

    Range
    84408801..84416360 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)