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

Gene ID: 4009, updated on 1-Jun-2020

Summary

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
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

Genomic context

See LMX1A in Genome Data Viewer
Location:
1q23.3
Exon count:
12
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (165201867..165356715, complement)
105 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 uncharacterized LOC107985452 Neighboring gene LMX1A antisense RNA 2 Neighboring gene LMX1A antisense RNA 1 Neighboring gene retinoid X receptor gamma Neighboring gene LRRC52 antisense RNA 1 Neighboring gene leucine rich repeat containing 52

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Deafness, autosomal dominant 7
MedGen: C1832379 OMIM: 601412 GeneReviews: Not available
not available

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC87616

Gene Ontology Provided by GOA

Process Evidence Code Pubs
axon guidance IEA
Inferred from Electronic Annotation
more info
 
cerebellum development IEA
Inferred from Electronic Annotation
more info
 
dentate gyrus development IEA
Inferred from Electronic Annotation
more info
 
dopaminergic neuron differentiation TAS
Traceable Author Statement
more info
PubMed 
locomotory behavior IEA
Inferred from Electronic Annotation
more info
 
memory IEA
Inferred from Electronic Annotation
more info
 
midbrain dopaminergic neuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
midbrain dopaminergic neuron differentiation TAS
Traceable Author Statement
more info
PubMed 
negative regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
olfactory behavior IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cell growth IEA
Inferred from Electronic Annotation
more info
 
synapse organization IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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

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_001174069.1NP_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, AL160058, AL390730, BM678780
    Consensus CDS
    CCDS1247.1
    UniProtKB/Swiss-Prot
    Q8TE12
    Related
    ENSP00000294816.2, ENST00000294816.6
    Conserved Domains (3) summary
    cd09370
    Location:3586
    LIM1_Lmx1a; The first LIM domain of Lmx1a
    cd09378
    Location:94148
    LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
    pfam00046
    Location:198252
    Homeobox; Homeobox domain
  2. NM_177398.4NP_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
    Q8TE12
    Related
    ENSP00000340226.3, ENST00000342310.7
    Conserved Domains (3) summary
    cd09370
    Location:3586
    LIM1_Lmx1a; The first LIM domain of Lmx1a
    cd09378
    Location:94148
    LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
    pfam00046
    Location:198252
    Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_011509538.3XP_011507840.1  LIM homeobox transcription factor 1-alpha isoform X1

    Conserved Domains (2) summary
    cd09378
    Location:1468
    LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
    pfam00046
    Location:118171
    Homeobox; Homeobox domain
  2. XM_011509540.2XP_011507842.1  LIM homeobox transcription factor 1-alpha isoform X2

    Conserved Domains (3) summary
    cd09370
    Location:3586
    LIM1_Lmx1a; The first LIM domain of Lmx1a
    pfam00046
    Location:198251
    Homeobox; Homeobox domain
    cl02475
    Location:94148
    LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

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.
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