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Aliases for LMX1A Gene

Aliases for LMX1A Gene

  • LIM Homeobox Transcription Factor 1 Alpha 2 3 5
  • LIM/Homeobox Protein 1.1 3 4
  • LIM Homeobox Transcription Factor 1, Alpha 2
  • LIM Homeobox Transcription Factor 1-Alpha 3
  • LIM/Homeobox Protein LMX1A 4
  • LMX-1.1 4
  • LMX1.1 3
  • LMX1 3

External Ids for LMX1A Gene

Previous HGNC Symbols for LMX1A Gene

  • LMX1

Previous GeneCards Identifiers for LMX1A Gene

  • GC01U990100
  • GC01M160823
  • GC01M161868
  • GC01M162360
  • GC01M162358
  • GC01M161902
  • GC01M163437
  • GC01M136417

Summaries for LMX1A Gene

Entrez Gene Summary for LMX1A Gene

  • 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]

GeneCards Summary for LMX1A Gene

LMX1A (LIM Homeobox Transcription Factor 1 Alpha) is a Protein Coding gene. Among its related pathways are Dopaminergic Neurogenesis. GO annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is LMX1B.

UniProtKB/Swiss-Prot for LMX1A Gene

  • Acts as a transcriptional activator by binding to an A/T-rich sequence, the FLAT element, in the insulin gene promoter. Required for development of the roof plate and, in turn, for specification of dorsal cell fates in the CNS and developing vertebrae (By similarity).

Gene Wiki entry for LMX1A Gene

Additional gene information for LMX1A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LMX1A Gene

Genomics for LMX1A Gene

Regulatory Elements for LMX1A Gene

Enhancers for LMX1A Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01H165593 0.7 ENCODE 10 -236.4 -236414 0 CTCF ZNF654 TRIM22 REST ZNF2 RAD21 CC2D1A ZNF121 SKIL SMC3 MGST3 RXRG LMX1A TRK-CTT13-1 LOC400794
GH01H165162 0.6 ENCODE 10.9 +193.8 193762 1 STAT1 NFIB MNT ZSCAN21 GATA3 ZSCAN16 ZBTB48 ZNF600 FOS ZFX LOC102725140 LMX1A LOC105371561 GC01M164980 RNU6-755P
GH01H165383 0.4 ENCODE 11.4 -26.7 -26727 0 NRF1 FOS LMX1A RXRG GC01M165392
GH01H165350 0.3 FANTOM5 8.9 +6.4 6429 0 LMX1A LOC102725140
GH01H165375 1 Ensembl ENCODE 0.4 -19.9 -19910 1 ZNF664 GLIS2 ZNF366 ZBTB48 PATZ1 ZNF600 ZBTB20 MAZ SOX6 L3MBTL2 LMX1A GC01M165392
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LMX1A on UCSC Golden Path with GeneCards custom track

Genomic Location for LMX1A Gene

Chromosome:
1
Start:
165,201,867 bp from pter
End:
165,356,715 bp from pter
Size:
154,849 bases
Orientation:
Minus strand

Genomic View for LMX1A Gene

Genes around LMX1A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LMX1A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LMX1A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LMX1A Gene

Proteins for LMX1A Gene

  • Protein details for LMX1A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TE12-LMX1A_HUMAN
    Recommended name:
    LIM homeobox transcription factor 1-alpha
    Protein Accession:
    Q8TE12
    Secondary Accessions:
    • B3KXP6
    • Q0VDB5
    • Q5VWG4
    • Q8TE11

    Protein attributes for LMX1A Gene

    Size:
    382 amino acids
    Molecular mass:
    42747 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for LMX1A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LMX1A Gene

Post-translational modifications for LMX1A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LMX1A Gene

No data available for DME Specific Peptides for LMX1A Gene

Domains & Families for LMX1A Gene

Gene Families for LMX1A Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for LMX1A Gene

Suggested Antigen Peptide Sequences for LMX1A Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LMX1A: view

No data available for UniProtKB/Swiss-Prot for LMX1A Gene

Function for LMX1A Gene

Molecular function for LMX1A Gene

GENATLAS Biochemistry:
transcriptional regulator of insulin gene,with the LIM-homeo domain (lmx-1),expressed in pancreatic islets,expressed in limb mesenchyme through WNT7A induction,involved in dorsoventral polarity of vertebrate limb (dorsal differentiation)
UniProtKB/Swiss-Prot Function:
Acts as a transcriptional activator by binding to an A/T-rich sequence, the FLAT element, in the insulin gene promoter. Required for development of the roof plate and, in turn, for specification of dorsal cell fates in the CNS and developing vertebrae (By similarity).

Phenotypes From GWAS Catalog for LMX1A Gene

Gene Ontology (GO) - Molecular Function for LMX1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding ISS --
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding IEA --
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 25814554
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with LMX1A: view
genes like me logo Genes that share phenotypes with LMX1A: view

Animal Models for LMX1A Gene

MGI Knock Outs for LMX1A:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for LMX1A
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LMX1A Gene

Localization for LMX1A Gene

Subcellular locations from UniProtKB/Swiss-Prot for LMX1A Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LMX1A gene
Compartment Confidence
nucleus 5
golgi apparatus 3
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LMX1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with LMX1A: view

Pathways & Interactions for LMX1A Gene

SuperPathways for LMX1A Gene

SuperPathway Contained pathways
1 Dopaminergic Neurogenesis
genes like me logo Genes that share pathways with LMX1A: view

Pathways by source for LMX1A Gene

1 BioSystems pathway for LMX1A Gene

Gene Ontology (GO) - Biological Process for LMX1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001558 regulation of cell growth IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription from RNA polymerase II promoter IEA --
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with LMX1A: view

No data available for SIGNOR curated interactions for LMX1A Gene

Drugs & Compounds for LMX1A Gene

No Compound Related Data Available

Transcripts for LMX1A Gene

mRNA/cDNA for LMX1A Gene

(6) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(9) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for LMX1A Gene

LIM homeobox transcription factor 1, alpha:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for LMX1A
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for LMX1A Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13
SP1: - - - -
SP2: - - -
SP3:

Relevant External Links for LMX1A Gene

GeneLoc Exon Structure for
LMX1A
ECgene alternative splicing isoforms for
LMX1A

Expression for LMX1A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LMX1A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LMX1A Gene

This gene is overexpressed in Pituitary (x14.1) and Testis (x7.4).

Protein differential expression in normal tissues from HIPED for LMX1A Gene

This gene is overexpressed in Adipocyte (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LMX1A Gene



Protein tissue co-expression partners for LMX1A Gene

NURSA nuclear receptor signaling pathways regulating expression of LMX1A Gene:

LMX1A

SOURCE GeneReport for Unigene cluster for LMX1A Gene:

Hs.667312

mRNA Expression by UniProt/SwissProt for LMX1A Gene:

Q8TE12-LMX1A_HUMAN
Tissue specificity: Isoform 1 is expressed in many tissues. Not found in heart, liver, spleen and testis. Relatively highly expressed in fetal brain. Isoform LMX1A-4AB is expressed in testis.

Evidence on tissue expression from TISSUES for LMX1A Gene

  • Nervous system(2.4)
genes like me logo Genes that share expression patterns with LMX1A: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for LMX1A Gene

Orthologs for LMX1A Gene

This gene was present in the common ancestor of animals.

Orthologs for LMX1A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LMX1A 33 34
  • 99.65 (n)
cow
(Bos Taurus)
Mammalia LMX1A 33 34
  • 94.07 (n)
oppossum
(Monodelphis domestica)
Mammalia LMX1A 34
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LMX1A 33 34
  • 93.11 (n)
rat
(Rattus norvegicus)
Mammalia Lmx1a 33
  • 91.1 (n)
mouse
(Mus musculus)
Mammalia Lmx1a 33 16 34
  • 90.92 (n)
chicken
(Gallus gallus)
Aves LMX1A 33 34
  • 80.96 (n)
lizard
(Anolis carolinensis)
Reptilia LMX1A 34
  • 77 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100492433 33
  • 72.49 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.12464 33
zebrafish
(Danio rerio)
Actinopterygii lmx1a 34
  • 55 (a)
OneToOne
Dr.13964 33
fruit fly
(Drosophila melanogaster)
Insecta CG4328 34
  • 26 (a)
ManyToMany
CG32105 34
  • 25 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea lim-6 34
  • 37 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 32 (a)
ManyToMany
-- 34
  • 23 (a)
ManyToMany
Species where no ortholog for LMX1A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for LMX1A Gene

ENSEMBL:
Gene Tree for LMX1A (if available)
TreeFam:
Gene Tree for LMX1A (if available)

Paralogs for LMX1A Gene

Paralogs for LMX1A Gene

(11) SIMAP similar genes for LMX1A Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with LMX1A: view

Variants for LMX1A Gene

Sequence variations from dbSNP and Humsavar for LMX1A Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1000005810 -- 165,355,980(+) AAGAG(A/T)GGGTA intron-variant
rs1000015353 -- 165,271,915(+) TAAGG(C/T)ATCTC intron-variant
rs1000044796 -- 165,271,684(+) CCCCA(C/T)CATAA intron-variant
rs1000052172 -- 165,349,696(+) CGTCC(C/T)GAAGT intron-variant
rs1000091407 -- 165,202,559(+) ATATA(C/T)TCTTC upstream-variant-2KB, utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for LMX1A Gene

Variant ID Type Subtype PubMed ID
dgv57e214 CNV loss 21293372
esv1005410 CNV deletion 20482838
esv1310421 CNV deletion 17803354
esv2678124 CNV deletion 23128226
esv2719084 CNV deletion 23290073
esv3587802 CNV gain 21293372
nsv1119734 CNV deletion 24896259
nsv952229 CNV deletion 24416366

Variation tolerance for LMX1A Gene

Residual Variation Intolerance Score: 15.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.83; 17.39% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LMX1A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LMX1A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LMX1A Gene

Disorders for LMX1A Gene

Relevant External Links for LMX1A

Genetic Association Database (GAD)
LMX1A
Human Genome Epidemiology (HuGE) Navigator
LMX1A
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LMX1A

No disorders were found for LMX1A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LMX1A Gene

Publications for LMX1A Gene

  1. Cloning, expression and genomic structure of human LMX1A, and variant screening in Pima Indians. (PMID: 12062816) Thameem F … Prochazka M (Gene 2002) 3 4 45 60
  2. Acetaminophen-NAPQI hepatotoxicity: a cell line model system genome-wide association study. (PMID: 21177773) Moyer AM … Weinshilboum RM (Toxicological sciences : an official journal of the Society of Toxicology 2011) 3 45 60
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 45 60
  4. Preliminary evidence that polymorphisms in dopamine-related transcription factors LMX1A, LMX1B and PITX3 are associated with schizophrenia. (PMID: 20570600) Bergman O … Eriksson E (Progress in neuro-psychopharmacology & biological psychiatry 2010) 3 45 60
  5. Follow-up of a major linkage peak on chromosome 1 reveals suggestive QTLs associated with essential hypertension: GenNet study. (PMID: 19536175) Ehret GB … Chakravarti A (European journal of human genetics : EJHG 2009) 3 45 60

Products for LMX1A Gene

Sources for LMX1A Gene

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