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Lhx3 LIM homeobox protein 3 [ Mus musculus (house mouse) ]

Gene ID: 16871, updated on 17-Jul-2024

Summary

Official Symbol
Lhx3provided by MGI
Official Full Name
LIM homeobox protein 3provided by MGI
Primary source
MGI:MGI:102673
See related
Ensembl:ENSMUSG00000026934 AllianceGenome:MGI:102673
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
Lim3; P-LIM; mLIM3; mLim-3
Summary
Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and RNA polymerase II-specific DNA-binding transcription factor binding activity. Involved in positive regulation of transcription, DNA-templated. Acts upstream of or within several processes, including nervous system development; placenta development; and positive regulation of transcription by RNA polymerase II. Part of transcription regulator complex. Is expressed in several structures, including alimentary system; cardiovascular system; central nervous system; genitourinary system; and sensory organ. Used to study hypopituitarism. Human ortholog(s) of this gene implicated in panhypopituitarism. Orthologous to human LHX3 (LIM homeobox 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

See Lhx3 in Genome Data Viewer
Location:
2 A3; 2 18.44 cM
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (26090224..26098261, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (26200212..26208249, complement)

Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene transmembrane protein 250 Neighboring gene predicted gene, 35745 Neighboring gene STARR-seq mESC enhancer starr_03976 Neighboring gene quiescin Q6 sulfhydryl oxidase 2 Neighboring gene STARR-seq mESC enhancer starr_03977 Neighboring gene STARR-positive B cell enhancer ABC_E10086 Neighboring gene STARR-seq mESC enhancer starr_03978 Neighboring gene predicted gene, 52504

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)

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Process Evidence Code Pubs
acts_upstream_of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within dorsal/ventral pattern formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within medial motor column neuron differentiation IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within motor neuron axon guidance IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within negative regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within pituitary gland development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within placenta development IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within prolactin secreting cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within somatotropin secreting cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within spinal cord association neuron differentiation IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within spinal cord motor neuron cell fate specification IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within thyroid-stimulating hormone-secreting cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within ventral spinal cord interneuron specification IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
part_of chromatin IDA
Inferred from Direct Assay
more info
PubMed 
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 ISO
Inferred from Sequence Orthology
more info
PubMed 
part_of transcription regulator complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
LIM/homeobox protein Lhx3
Names
LIM homeo box protein 3
homeobox protein LIM-3
homeobox protein P-LIM

NCBI Reference Sequences (RefSeq)

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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_001039653.2NP_001034742.1  LIM/homeobox protein Lhx3 isoform a

    See identical proteins and their annotated locations for NP_001034742.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AL773595, CD741809, L38248
    Consensus CDS
    CCDS38081.1
    UniProtKB/TrEMBL
    A2ALD8
    Related
    ENSMUSP00000028302.7, ENSMUST00000028302.8
    Conserved Domains (3) summary
    cd09376
    Location:95150
    LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family
    cd09467
    Location:3387
    LIM1_Lhx3b; The first LIM domain of Lhx3b
    pfam00046
    Location:165218
    Homeobox; Homeobox domain
  2. NM_010711.2NP_034841.2  LIM/homeobox protein Lhx3 isoform b

    See identical proteins and their annotated locations for NP_034841.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' terminal exon, and it thus differs in the 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    AL773595, CD741809, L38248
    Consensus CDS
    CCDS71004.1
    UniProtKB/Swiss-Prot
    A2ALD9, P50481, Q61800, Q61801
    Related
    ENSMUSP00000056822.10, ENSMUST00000054099.16
    Conserved Domains (3) summary
    cd09376
    Location:93148
    LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family
    cd09467
    Location:3185
    LIM1_Lhx3b; The first LIM domain of Lhx3b
    pfam00046
    Location:163216
    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_000068.8 Reference GRCm39 C57BL/6J

    Range
    26090224..26098261 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011239031.2XP_011237333.1  LIM/homeobox protein Lhx3 isoform X1

    Conserved Domains (1) summary
    pfam00046
    Location:2781
    Homeobox; Homeobox domain