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    Lhx2 LIM homeobox protein 2 [ Mus musculus (house mouse) ]

    Gene ID: 16870, updated on 9-Dec-2024

    Summary

    Official Symbol
    Lhx2provided by MGI
    Official Full Name
    LIM homeobox protein 2provided by MGI
    Primary source
    MGI:MGI:96785
    See related
    Ensembl:ENSMUSG00000000247 AllianceGenome:MGI:96785
    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
    ap; LH2A; Lh-2; Lim2; apterous
    Summary
    Enables DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Involved in several processes, including nervous system development; positive regulation of neural precursor cell proliferation; and regulation of gene expression. Acts upstream of or within several processes, including hair follicle development; maintenance of epithelial cell apical/basal polarity; and nervous system development. Located in nucleus. Is expressed in several structures, including branchial arch; future brain; limb primordium; nervous system; and sensory organ. Orthologous to human LHX2 (LIM homeobox 2). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in CNS E14 (RPKM 42.9), whole brain E14.5 (RPKM 35.2) and 6 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See Lhx2 in Genome Data Viewer
    Location:
    2 B; 2 24.31 cM
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (38229282..38259747)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (38339271..38369737)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene spermatid perinuclear RNA binding protein Neighboring gene microRNA 5128 Neighboring gene STARR-positive B cell enhancer ABC_E9511 Neighboring gene STARR-seq mESC enhancer starr_04315 Neighboring gene STARR-positive B cell enhancer ABC_E5909 Neighboring gene DENN domain containing 1A Neighboring gene crumbs family member 2 Neighboring gene STARR-seq mESC enhancer starr_04318 Neighboring gene STARR-seq mESC enhancer starr_04319 Neighboring gene STARR-seq mESC enhancer starr_04321 Neighboring gene STARR-seq mESC enhancer starr_04322 Neighboring gene predicted gene, 46736 Neighboring gene STARR-seq mESC enhancer starr_04324 Neighboring gene predicted gene 27197 Neighboring gene predicted gene 13584 Neighboring gene NIMA (never in mitosis gene a)-related expressed kinase 6 Neighboring gene predicted gene, 39799 Neighboring gene predicted gene, 25081 Neighboring gene thymosin, beta 10 pseudogene

    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)
    • Endonuclease-mediated (1) 
    • Targeted (8)  1 citation

    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
    acts_upstream_of_or_within anatomical structure formation involved in morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within axon extension IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within brain development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cerebral cortex development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cerebral cortex development 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 hair follicle development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within maintenance of epithelial cell apical/basal polarity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within mesoderm development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of gene expression, epigenetic IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of neurogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of transcription regulatory region DNA binding IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within nervous system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within neural tube closure IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within neurogenesis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within neuron differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within olfactory bulb development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of neural precursor cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in 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 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
     
    acts_upstream_of_or_within retina development in camera-type eye IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within telencephalon development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within telencephalon regionalization IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within telencephalon regionalization IMP
    Inferred from Mutant Phenotype
    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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 

    General protein information

    Preferred Names
    LIM/homeobox protein Lhx2
    Names
    LIM homeo box protein 2
    homeobox protein LH-2

    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_001290646.2NP_001277575.1  LIM/homeobox protein Lhx2 isoform b

      See identical proteins and their annotated locations for NP_001277575.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate 5' terminal exon and it thus differs in the 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a. Variants 2, 5, and 6 all encode the same isoform (b).
      Source sequence(s)
      AL929186, BX813320
      Consensus CDS
      CCDS71048.1
      UniProtKB/TrEMBL
      F6Z9H5
      Related
      ENSMUSP00000114797.3, ENSMUST00000143783.9
      Conserved Domains (4) summary
      cd09377
      Location:70128
      LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
      cd09469
      Location:265
      LIM1_Lhx2; The first LIM domain of Lhx2
      COG5576
      Location:206337
      COG5576; Homeodomain-containing transcription factor [Transcription]
      pfam00046
      Location:229282
      Homeobox; Homeobox domain
    2. NM_001420354.1NP_001407283.1  LIM/homeobox protein Lhx2 isoform c

      Status: VALIDATED

      Source sequence(s)
      AL929186, BX813320
    3. NM_001420355.1NP_001407284.1  LIM/homeobox protein Lhx2 isoform d

      Status: VALIDATED

      Source sequence(s)
      AL929186, BX813320
    4. NM_001420356.1NP_001407285.1  LIM/homeobox protein Lhx2 isoform b

      Status: VALIDATED

      Source sequence(s)
      AL929186, BX813320
      UniProtKB/TrEMBL
      F6Z9H5
    5. NM_001420357.1NP_001407286.1  LIM/homeobox protein Lhx2 isoform b

      Status: VALIDATED

      Source sequence(s)
      AL929186, BX813320
      UniProtKB/TrEMBL
      F6Z9H5
    6. NM_001420359.1NP_001407288.1  LIM/homeobox protein Lhx2 isoform e

      Status: VALIDATED

      Source sequence(s)
      AL929186, BX813320
    7. NM_010710.5NP_034840.1  LIM/homeobox protein Lhx2 isoform a

      See identical proteins and their annotated locations for NP_034840.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform a.
      Source sequence(s)
      AL929186, BX813320
      Consensus CDS
      CCDS16008.1
      UniProtKB/Swiss-Prot
      Q9Z0S2
      UniProtKB/TrEMBL
      Q543C6
      Related
      ENSMUSP00000000253.6, ENSMUST00000000253.6
      Conserved Domains (4) summary
      cd09377
      Location:111169
      LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
      cd09469
      Location:43106
      LIM1_Lhx2; The first LIM domain of Lhx2
      COG5576
      Location:247378
      COG5576; Homeodomain-containing transcription factor [Transcription]
      pfam00046
      Location:270323
      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
      38229282..38259747
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006497735.3XP_006497798.1  LIM/homeobox protein Lhx2 isoform X2

      See identical proteins and their annotated locations for XP_006497798.1

      Conserved Domains (4) summary
      cd09377
      Location:78136
      LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
      cd09469
      Location:265
      LIM1_Lhx2; The first LIM domain of Lhx2
      COG5576
      Location:214345
      COG5576; Homeodomain-containing transcription factor [Transcription]
      pfam00046
      Location:237290
      Homeobox; Homeobox domain
    2. XM_006497736.4XP_006497799.1  LIM/homeobox protein Lhx2 isoform X2

      See identical proteins and their annotated locations for XP_006497799.1

      Conserved Domains (4) summary
      cd09377
      Location:78136
      LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family
      cd09469
      Location:265
      LIM1_Lhx2; The first LIM domain of Lhx2
      COG5576
      Location:214345
      COG5576; Homeodomain-containing transcription factor [Transcription]
      pfam00046
      Location:237290
      Homeobox; Homeobox domain