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    Lhx6 LIM homeobox protein 6 [ Mus musculus (house mouse) ]

    Gene ID: 16874, updated on 7-Aug-2018

    Summary

    Official Symbol
    Lhx6provided by MGI
    Official Full Name
    LIM homeobox protein 6provided by MGI
    Primary source
    MGI:MGI:1306803
    See related
    Ensembl:ENSMUSG00000026890 Vega:OTTMUSG00000012098
    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
    Lhx6.1
    Expression
    Broad expression in CNS E18 (RPKM 4.6), whole brain E14.5 (RPKM 3.8) and 18 other tissues See more
    Orthologs

    Genomic context

    See Lhx6 in Genome Data Viewer
    Location:
    2; 2 B
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 2 NC_000068.7 (36081950..36105998, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (35937473..35960928, complement)

    Chromosome 2 - NC_000068.7Genomic Context describing neighboring genes Neighboring gene NADH:ubiquinone oxidoreductase subunit A8 Neighboring gene MORN repeat containing 5 Neighboring gene RNA binding motif protein 18 Neighboring gene mitochondrial ribosome recycling factor Neighboring gene predicted gene, 46735

    Genomic regions, transcripts, and products

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Variation

    Alleles

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

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    DNA-binding transcription factor activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    cell maturation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cerebral cortex GABAergic interneuron migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cerebral cortex neuron differentiation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    cerebral cortex radially oriented cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cerebral cortex tangential migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    forebrain neuron development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    forebrain neuron fate commitment IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    multicellular organism development IEA
    Inferred from Electronic Annotation
    more info
     
    nervous system development IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    LIM/homeobox protein Lhx6
    Names
    LIM-homeodomain protein 6.1
    LIM/homeobox protein Lhx6.1

    NCBI Reference Sequences (RefSeq)

    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_001083125.1NP_001076594.1  LIM/homeobox protein Lhx6 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the 3' coding region resulting in a frameshift and a shorter 3' UTR compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AK140987, CO042780
      Consensus CDS
      CCDS38110.1
      UniProtKB/TrEMBL
      E9QN32
      Related
      ENSMUSP00000108591.4, OTTMUSP00000057726, ENSMUST00000112967.11, OTTMUST00000103353
      Conserved Domains (3) summary
      cd09380
      Location:99152
      LIM1_Lhx6; The first LIM domain of Lhx6
      cd09382
      Location:160214
      LIM2_Lhx6; The second LIM domain of Lhx6
      pfam00046
      Location:252304
      Homeobox; Homeobox domain
    2. NM_001083126.1NP_001076595.1  LIM/homeobox protein Lhx6 isoform 3

      See identical proteins and their annotated locations for NP_001076595.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) represents the use of an alternate promoter, differs in the 5' UTR and uses a downstream start codon compared to variant 1. The encoded isoform (3, also known as Lhx6.1a) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AB031040, BC065077
      Consensus CDS
      CCDS38113.1
      UniProtKB/Swiss-Prot
      Q9R1R0
      Related
      ENSMUSP00000108585.3, OTTMUSP00000013029, ENSMUST00000112961.9, OTTMUST00000028785
      Conserved Domains (3) summary
      cd09380
      Location:70123
      LIM1_Lhx6; The first LIM domain of Lhx6
      cd09382
      Location:131185
      LIM2_Lhx6; The second LIM domain of Lhx6
      pfam00046
      Location:223275
      Homeobox; Homeobox domain
    3. NM_001083127.1NP_001076596.1  LIM/homeobox protein Lhx6 isoform 4

      See identical proteins and their annotated locations for NP_001076596.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) represents the use of an alternate promoter and has multiple differences compared to variant 1. These differences result in distinct 5' and 3' UTRs, the use of a downstream start codon and a translational frameshift in the 3' coding region compared to variant 1. The encoded isoform (4, also known as Lhx6.1b) has a shorter N-terminus and a distinct C-terminus compared to isoform 1. Variants 4 and 5 both encode the same isoform (4).
      Source sequence(s)
      AB031039, BC065077
      Consensus CDS
      CCDS38111.1
      UniProtKB/Swiss-Prot
      Q9R1R0
      Related
      ENSMUSP00000108590.3, OTTMUSP00000013030, ENSMUST00000112966.9, OTTMUST00000028786
      Conserved Domains (3) summary
      cd09380
      Location:70123
      LIM1_Lhx6; The first LIM domain of Lhx6
      cd09382
      Location:131185
      LIM2_Lhx6; The second LIM domain of Lhx6
      pfam00046
      Location:223275
      Homeobox; Homeobox domain
    4. NM_001355125.1NP_001342054.1  LIM/homeobox protein Lhx6 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) has multiple differences compared to variant 1. These differences result in distinct 5' and 3' UTRs, the use of a downstream start codon and a translational frameshift in the 3' coding region compared to variant 1. The encoded isoform (4, also known as Lhx6.1b) has a shorter N-terminus and a distinct C-terminus compared to isoform 1. Variants 4 and 5 both encode the same isoform (4).
      Source sequence(s)
      AL773525
      Conserved Domains (3) summary
      cd09380
      Location:70123
      LIM1_Lhx6; The first LIM domain of Lhx6
      cd09382
      Location:131185
      LIM2_Lhx6; The second LIM domain of Lhx6
      pfam00046
      Location:223275
      Homeobox; Homeobox domain
    5. NM_008500.2NP_032526.2  LIM/homeobox protein Lhx6 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AK140987, BC065077
      Consensus CDS
      CCDS38112.1
      UniProtKB/Swiss-Prot
      Q9R1R0
      UniProtKB/TrEMBL
      H9H9T0
      Related
      ENSMUSP00000108584.1, OTTMUSP00000013031, ENSMUST00000112960.7, OTTMUST00000028787
      Conserved Domains (3) summary
      cd09380
      Location:99152
      LIM1_Lhx6; The first LIM domain of Lhx6
      cd09382
      Location:160214
      LIM2_Lhx6; The second LIM domain of Lhx6
      pfam00046
      Location:252304
      Homeobox; Homeobox domain

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000068.7 Reference GRCm38.p4 C57BL/6J

      Range
      36081950..36105998 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017315869.1XP_017171358.1  LIM/homeobox protein Lhx6 isoform X2

      UniProtKB/Swiss-Prot
      Q9R1R0
      Related
      ENSMUSP00000135693.3, OTTMUSP00000057727, ENSMUST00000148852.3, OTTMUST00000103354
      Conserved Domains (3) summary
      cd09380
      Location:70123
      LIM1_Lhx6; The first LIM domain of Lhx6
      cd09382
      Location:131185
      LIM2_Lhx6; The second LIM domain of Lhx6
      pfam00046
      Location:223275
      Homeobox; Homeobox domain
    2. XM_006497744.3XP_006497807.1  LIM/homeobox protein Lhx6 isoform X1

      See identical proteins and their annotated locations for XP_006497807.1

      UniProtKB/Swiss-Prot
      Q9R1R0
      Conserved Domains (3) summary
      cd09380
      Location:70123
      LIM1_Lhx6; The first LIM domain of Lhx6
      cd09382
      Location:131185
      LIM2_Lhx6; The second LIM domain of Lhx6
      pfam00046
      Location:223275
      Homeobox; Homeobox domain

    RNA

    1. XR_374064.3 RNA Sequence

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