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Lmx1a Gene Detail
Summary
  • Symbol
    Lmx1a
  • Name
    LIM homeobox transcription factor 1 alpha
  • Synonyms
    Lmx1.1, shaker short-tail
  • Feature Type
    protein coding gene
  • IDs
    MGI:1888519
    NCBI Gene: 110648
  • Gene Overview
    MyGene.info: LMX1A
  • Alliance
  • Transcription Start Sites
    5 TSS
Location &
Maps
more
  • Sequence Map
    Chr1:167689237-167848741 bp, + strand
  • From Ensembl annotation of GRCm38

    View this region in JBrowse

  • Genome Browsers
  • Genetic Map
    Chromosome 1, 75.08 cM
  • Mapping Data
    14 experiments
Strain
Comparison
more
  • SNPs within 2kb
    1524 from dbSNP Build 142
  • Strain Annotations
    18
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_1888519
protein coding gene Chr1:167688900-167848741 (.)
129S1/SvImJ MGP_129S1SvImJ_G0016717
protein coding gene Chr1:173282710-173444048 (+)
A/J MGP_AJ_G0016697
protein coding gene Chr1:166204717-166356733 (+)
AKR/J MGP_AKRJ_G0016663
protein coding gene Chr1:171234341-171403333 (+)
BALB/cJ MGP_BALBcJ_G0016658
protein coding gene Chr1:166690373-166846722 (+)
C3H/HeJ MGP_C3HHeJ_G0016482
protein coding gene Chr1:171467023-171624734 (+)
C57BL/6NJ MGP_C57BL6NJ_G0017119
protein coding gene Chr1:179062453-179235735 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0014828
protein coding gene Chr1:158039005-158185139 (+)
CAST/EiJ MGP_CASTEiJ_G0016062
protein coding gene Chr1:171074584-171231259 (+)
CBA/J MGP_CBAJ_G0016457
protein coding gene Chr1:185449659-185622485 (+)
DBA/2J MGP_DBA2J_G0016563
protein coding gene Chr1:165042595-165202278 (+)
FVB/NJ MGP_FVBNJ_G0016561
protein coding gene Chr1:163506092-163655478 (+)
LP/J MGP_LPJ_G0016634
protein coding gene Chr1:174343507-174510766 (+)
NOD/ShiLtJ MGP_NODShiLtJ_G0016586
protein coding gene Chr1:192818360-192975511 (+)
NZO/HlLtJ MGP_NZOHlLtJ_G0017156
protein coding gene Chr1:171100179-171269909 (+)
PWK/PhJ MGP_PWKPhJ_G0015848
protein coding gene Chr1:164253357-164408051 (+)
SPRET/EiJ MGP_SPRETEiJ_G0015634
protein coding gene Chr1:169869910-170034797 (+)
WSB/EiJ MGP_WSBEiJ_G0016124
protein coding gene Chr1:171212865-171376117 (+)



Homology
more
  • Human Ortholog
    LMX1A, LIM homeobox transcription factor 1 alpha
  • Vertebrate Orthologs
    9
  • Human Ortholog
    LMX1A, LIM homeobox transcription factor 1 alpha
    Orthology source: HomoloGene, HGNC
  • Synonyms
    LMX1, LMX1.1
  • Links
    NCBI Gene ID: 4009
    neXtProt AC: NX_Q8TE12
    UniProt: Q8TE12

  • Chr Location
    1q23.3; chr1:165201867-165356715 (-)  GRCh38.p7

Human Diseases
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  • Mutations/Alleles
    1 with disease annotations
  • References
    1 with disease annotations
Mutations,
Alleles, and
Phenotypes
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  • Phenotype Summary
    83 phenotypes from 14 alleles in 16 genetic backgrounds
    20 phenotypes from multigenic genotypes
    4 images
    53 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
immune system
integument
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
neoplasm
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
vision/eye

Click cells to view annotations.
Mutations in the dreher locus produce neurological and skeletal abnormalities, inner ear defects, and belly spotting. Deafness and hypoplasia of Mullerian duct derivatives are also reported for some alleles. Homozygous null mice have fewer dopaminergic neurons.
Gene Ontology
(GO)
Classifications
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  • All GO Annotations
  • GO References
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell death
cell differentiation
cell proliferation
cellular component organization
establishment of localization
homeostatic process
immune system process
lipid metabolic process
nucleic acid-templated transcription
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
non-membrane-bounded organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
synapse
vacuole
Click cells to view annotations.
Expression
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Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
  • Tissues
  • cDNA Data
  • Literature Summary
  • Comparison Matrix
  • Interactions
    less
    Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000026686 Ensembl Gene Model | MGI Sequence Detail 159505 C57BL/6J ±  kb
    transcript ENSMUST00000111377 Ensembl | MGI Sequence Detail 3200 Not Applicable  
    polypeptide ENSMUSP00000107008 Ensembl | MGI Sequence Detail 382 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 30
      Genomic 3
      cDNA 18
      Primer pair 3
      Other 6

      Microarray probesets 2
    Other
    Accession IDs
    less
    MGD-MRK-14613, MGD-MRK-8891, MGI:94923
    References
    more
    • Summaries
      All 196
      Developmental Gene Expression 141
      Diseases 1
      Gene Ontology 11
      Phenotypes 53
    • Earliest
      J:15346 FALCONER DS, et al., [Dreher, a new gene of the waltzer-shaker group in the house mouse.]. Z Indukt Abstamm Vererbungsl. 1951;84(2):71-3
    • Latest
      J:262601 Huang Y, et al., Reciprocal Negative Regulation Between Lmx1a and Lmo4 Is Required for Inner Ear Formation. J Neurosci. 2018 Jun 6;38(23):5429-5440

    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
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    last database update
    11/13/2018
    MGI 6.13
    The Jackson Laboratory