Lmx1a MGI Mouse Gene Detail - MGI:1888519 - LIM homeobox transcription factor 1 alpha

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
Alliance

gene page
Transcription Start Sites

6 TSS

Sequence Map

Chr1:167516806-167676310 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 1, 75.08 cM
Mapping Data

14 experiments

SNPs within 2kb

4709 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1888519	protein coding gene	Chr1:167515864-167676310 (+)
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 (+)

Human Ortholog

LMX1A, LIM homeobox transcription factor 1 alpha

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

LMX1A, LIM homeobox transcription factor 1 alpha
Synonyms

DFNA7, LMX1, LMX1.1
Links

HGNC:6653

NCBI Gene ID: 4009

neXtProt AC: NX_Q8TE12

UniProt: Q8TE12
Chr Location

1q23.3; chr1:165201867-165356715 (-) GRCh38

MGI Vertebrate Homology

Lmx1a stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: LMX1A
Gene Tree

Lmx1a

Diseases

1 with human LMX1A associations

				Human Disease	Mouse Models
				autosomal dominant nonsyndromic deafness 7 IDs autosomal dominant nonsyndromic deafness 7 DOID:0110591 ICD10CM:H90.3 OMIM:601412

Click on a disease name to see all genes associated with that disease.

Mutations/Alleles

1 with disease annotations

References

1 with disease annotations

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Phenotype Summary

83 phenotypes from 14 alleles in 16 genetic backgrounds
20 phenotypes from multigenic genotypes
4 images
65 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

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	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

26
Chemically induced (other)

2
Endonuclease-mediated

2
Spontaneous

16
Targeted

6
Genomic Mutations

2 involving Lmx1a
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

21 strains or lines available
Comparison Matrix

Gene Expression + Phenotype
Recombinase Activity

Comparison Matrix Gene Expression + Recombinase Activity

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.

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All GO Annotations

29
GO References

12

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 differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	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	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

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

1256
Tissues

256
cDNA Data

21
Literature Summary

185

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase lmx1a

ZFIN lmx1a

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All Sequences

39
RefSeq

8
UniProt

2
CCDS

CCDS15460.1

Ensembl

ENSMUSG00000026686 (Evidence)
NCBI Gene

110648

			Length	Strain/Species	Flank
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

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UniProt

2 Sequences
Protein Ontology

PR:000009870 LIM homeobox transcription factor 1-alpha

(term hierarchy)
InterPro Domains

IPR017970 Homeobox, conserved site

IPR001356 Homeobox domain

IPR009057 Homeobox-like domain superfamily

IPR050453 LIM/homeobox transcription factors

IPR042688 Lmx1a, first LIM domain

IPR001781 Zinc finger, LIM-type

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All nucleic 42

Genomic 3

cDNA 21

Primer pair 6

Other 12

Microarray probesets 2

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MGD-MRK-14613, MGD-MRK-8891, MGI:94923

Summaries

All 250

Developmental Gene Expression 185

Diseases 1

Gene Ontology 12

Phenotypes 65
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:353281 Rybiczka-Tesulov M, et al., Circular RNAs regulate neuron size and migration of midbrain dopamine neurons during development. Nat Commun. 2024 Aug 8;15(1):6773

TSS for Lmx1a:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr9906	Chr1:167516189-167516202 (+)	-610 bp
Tssr9907	Chr1:167516677-167516695 (+)	-120 bp
Tssr9908	Chr1:167516771-167516786 (+)	-27 bp
Tssr9909	Chr1:167517094-167517103 (+)	293 bp
Tssr9910	Chr1:167517121-167517132 (+)	321 bp
Tssr9911	Chr1:167517203-167517231 (+)	411 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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