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    LMX1A LIM homeobox transcription factor 1 alpha [ Homo sapiens (human) ]

    Gene ID: 4009, updated on 2-Nov-2024

    Summary

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    Official Symbol
    LMX1Aprovided by HGNC
    Official Full Name
    LIM homeobox transcription factor 1 alphaprovided by HGNC
    Primary source
    HGNC:HGNC:6653
    See related
    Ensembl:ENSG00000162761 MIM:600298; AllianceGenome:HGNC:6653
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LMX1; DFNA7; LMX1.1
    Summary
    This gene encodes a homeodomain and LIM-domain containing protein. The encoded protein is a transcription factor that acts as a positive regulator of insulin gene transcription. This gene also plays a role in the development of dopamine producing neurons during embryogenesis. Mutations in this gene are associated with an increased risk of developing Parkinson's disease. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2012]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See LMX1A in Genome Data Viewer
    Location:
    1q23.3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (165201867..165356715, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (164548251..164703069, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (165171104..165325952, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 755, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1497 Neighboring gene uncharacterized LOC107985452 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1498 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:165131828-165132328 Neighboring gene LMX1A antisense RNA 2 Neighboring gene LMX1A antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr1:165223074-165223646 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_852 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2015 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:165370087-165370588 Neighboring gene retinoid X receptor gamma Neighboring gene ReSE screen-validated silencer GRCh37_chr1:165446262-165446483 Neighboring gene LRRC52 antisense RNA 1 Neighboring gene PRELID1 pseudogene 7

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Forced LMX1A expression induces dorsal neural fates and disrupts patterning of human embryonic stem cells into ventral midbrain dopaminergic neurons.
      Title: Forced LMX1A expression induces dorsal neural fates and disrupts patterning of human embryonic stem cells into ventral midbrain dopaminergic neurons.
    2. ceRNA network of lncRNA MIR210HG/miR-377-3p/LMX1A in malignant proliferation of glioma cells.
      Title: ceRNA network of lncRNA MIR210HG/miR-377-3p/LMX1A in malignant proliferation of glioma cells.
    3. Novel Molecular Genetic Etiology of Asymmetric Hearing Loss: Autosomal-Dominant LMX1A Variants.
      Title: Novel Molecular Genetic Etiology of Asymmetric Hearing Loss: Autosomal-Dominant LMX1A Variants.
    4. Update on CD164 and LMX1A genes to strengthen their causative role in autosomal dominant hearing loss.
      Title: Update on CD164 and LMX1A genes to strengthen their causative role in autosomal dominant hearing loss.
    5. Novel genotype-phenotype correlation of functionally characterized LMX1A variants linked to sensorineural hearing loss.
      Title: Novel genotype-phenotype correlation of functionally characterized LMX1A variants linked to sensorineural hearing loss.
    6. Epigenetic Silencing of LMX1A Contributes to Cancer Progression in Lung Cancer Cells.
      Title: Epigenetic Silencing of LMX1A Contributes to Cancer Progression in Lung Cancer Cells.
    7. Circular RNA circMTO1 Suppresses RCC Cancer Cell Progression via miR9/LMX1A Axis.
      Title: Circular RNA circMTO1 Suppresses RCC Cancer Cell Progression via miR9/LMX1A Axis.
    8. LINC00682 inhibits gastric cancer cell progression via targeting microRNA-9-LMX1A signaling axis.
      Title: LINC00682 inhibits gastric cancer cell progression via targeting microRNA-9-LMX1A signaling axis.
    9. Knockdown of LncRNA SCAMP1 suppressed malignant biological behaviours of glioma cells via modulating miR-499a-5p/LMX1A/NLRC5 pathway.
      Title: Knockdown of LncRNA SCAMP1 suppressed malignant biological behaviours of glioma cells via modulating miR-499a-5p/LMX1A/NLRC5 pathway.
    10. Knockdown of ANGPTL4 rescued the tumor suppressive phenotype of LMX1A overexpression, which indicated that LMX1A upregulates ANGPTL4 to exert its role. Mechanistically, we found that LMX1A inhibited the expression of the oncogene C-Myc, which is alleviated by ANGPTL4 knockdown.
      Title: LMX1A inhibits C-Myc expression through ANGPTL4 to exert tumor suppressive role in gastric cancer.
    Submit: New GeneRIF Correction See all GeneRIFs (33)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Autosomal dominant nonsyndromic hearing loss 7
    MedGen: C1832379 OMIM: 601412 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    Acetaminophen-NAPQI hepatotoxicity: a cell line model system genome-wide association study.
    EBI GWAS Catalog
    Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC87616

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
    		  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in axon guidance IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in central nervous system neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cerebellum development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in dentate gyrus development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in dopaminergic neuron differentiation TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in locomotory behavior IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in memory IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in midbrain dopaminergic neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in midbrain dopaminergic neuron differentiation TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in olfactory behavior IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of cell growth 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
    		  
    involved_in synapse organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    LIM homeobox transcription factor 1-alpha
    Names
    LIM/homeobox protein 1.1

    NCBI Reference Sequences (RefSeq)

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    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_001174069.2 → NP_001167540.1  LIM homeobox transcription factor 1-alpha

      See identical proteins and their annotated locations for NP_001167540.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Both variants 1 and 4 encode the same protein.
      Source sequence(s)
      AK122800, AK127724, AL390730, BM678780
      Consensus CDS
      CCDS1247.1
      UniProtKB/Swiss-Prot
      B3KXP6, Q0VDB5, Q5VWG4, Q8TE11, Q8TE12
      Related
      ENSP00000294816.2, ENST00000294816.6
      Conserved Domains (3) summary
      cd09370
      Location:35 → 86
      LIM1_Lmx1a; The first LIM domain of Lmx1a
      cd09378
      Location:94 → 148
      LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
      pfam00046
      Location:198 → 252
      Homeobox; Homeobox domain

    2. NM_177398.4 → NP_796372.1  LIM homeobox transcription factor 1-alpha

      See identical proteins and their annotated locations for NP_796372.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 4 encode the same protein.
      Source sequence(s)
      AK122800, AK127724, AL160058, AL390730, BM678780
      Consensus CDS
      CCDS1247.1
      UniProtKB/Swiss-Prot
      B3KXP6, Q0VDB5, Q5VWG4, Q8TE11, Q8TE12
      Related
      ENSP00000340226.3, ENST00000342310.7
      Conserved Domains (3) summary
      cd09370
      Location:35 → 86
      LIM1_Lmx1a; The first LIM domain of Lmx1a
      cd09378
      Location:94 → 148
      LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
      pfam00046
      Location:198 → 252
      Homeobox; Homeobox domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      165201867..165356715 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011509538.4 → XP_011507840.1  LIM homeobox transcription factor 1-alpha isoform X1

      Conserved Domains (2) summary
      cd09378
      Location:14 → 68
      LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
      pfam00046
      Location:118 → 171
      Homeobox; Homeobox domain

    2. XM_011509540.3 → XP_011507842.1  LIM homeobox transcription factor 1-alpha isoform X2

      Conserved Domains (3) summary
      cd09370
      Location:35 → 86
      LIM1_Lmx1a; The first LIM domain of Lmx1a
      pfam00046
      Location:198 → 251
      Homeobox; Homeobox domain
      cl02475
      Location:94 → 148
      LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      164548251..164703069 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336594.1 → XP_054192569.1  LIM homeobox transcription factor 1-alpha isoform X1

    2. XM_054336595.1 → XP_054192570.1  LIM homeobox transcription factor 1-alpha isoform X2

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001033507.1: Suppressed sequence

      Description
      NM_001033507.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

    2. NM_177399.2: Suppressed sequence

      Description
      NM_177399.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TE12.1 GenPept UniProtKB/Swiss-Prot:Q8TE12

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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