Lmx1b LIM homeobox transcription factor 1 beta [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Lmx1bprovided by MGI
Official Full Name: LIM homeobox transcription factor 1 betaprovided by MGI
Primary source: MGI:MGI:1100513
See related: Ensembl:ENSMUSG00000038765 AllianceGenome:MGI:1100513
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Icst; LMX1.1; LMX1.2
Summary: Enables DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in several processes, including memory; olfactory behavior; and positive regulation of transcription by RNA polymerase II. Acts upstream of or within several processes, including collagen fibril organization; nervous system development; and trabecular meshwork development. Located in nucleus. Is expressed in several structures, including central nervous system; embryo mesenchyme; hemolymphoid system; limb; and limb bud. Used to study nail-patella syndrome. Human ortholog(s) of this gene implicated in focal segmental glomerulosclerosis and nail-patella syndrome. Orthologous to human LMX1B (LIM homeobox transcription factor 1 beta). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in limb E14.5 (RPKM 9.6), mammary gland adult (RPKM 5.0) and 4 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 B; 2 22.48 cM

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (33450977..33531219, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (33560965..33641208, complement)

Chromosome 2 - NC_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Failure of digit tip regeneration in the absence of Lmx1b suggests Lmx1b functions disparate from dorsoventral polarity.
Title: Failure of digit tip regeneration in the absence of Lmx1b suggests Lmx1b functions disparate from dorsoventral polarity.
Identification of limb-specific Lmx1b auto-regulatory modules with Nail-patella syndrome pathogenicity.
Title: Identification of limb-specific Lmx1b auto-regulatory modules with Nail-patella syndrome pathogenicity.
The authors report that LIM homeodomain factor 1b (Lmx1b)-deficient serotonin (5-HT) neurons fail to generate axonal projections to the forebrain and spinal cord. Stage-specific targeting demonstrates that Lmx1b is required at successive stages to control 5-HT axon primary outgrowth, selective routing, and terminal arborization.
Title: Lmx1b is required at multiple stages to build expansive serotonergic axon architectures.
identified a novel NPS-causing LMX1B mutation and expanded the spectrum of mutations in the LMX1B gene. The c.712_714delTTC mutation may affect the quaternary structure of LMX1B, which is essential for the specification of dorsal limb fate at both zeugopodal and autopodal levels, leading to typical NPS
Title: A novel small deletion of LMX1B in a large Chinese family with nail-patella syndrome.
Authors conclude that Lmx1b plays a key role as an anti-osteogenic factor in patterning the head mesenchyme into areas with different osteogenic competence. In turn, this patterning event is crucial to generating the proper organization of the bones and soft tissue joints of the calvaria.
Title: Anti-osteogenic function of a LIM-homeodomain transcription factor LMX1B is essential to early patterning of the calvaria.
Data show that sustained expression of Lmx1a and Lmx1b is required for the survival of adult midbrain dopaminergic neurons.
Title: Lmx1a and Lmx1b regulate mitochondrial functions and survival of adult midbrain dopaminergic neurons.
Lmx1b is required for the topographical organization of dopaminergic innervation in the striatum.Lmx1b regulates Plxnc1 expression.
Title: Transcriptional repression of Plxnc1 by Lmx1a and Lmx1b directs topographic dopaminergic circuit formation.
This is the first report to describe genome-wide Lmx1b binding during limb development.
Title: Lmx1b-targeted cis-regulatory modules involved in limb dorsalization.
Otx2 critically depends on Lmx1b for the formation of mdDA neurons.
Title: Otx2 Requires Lmx1b to Control the Development of Mesodiencephalic Dopaminergic Neurons.
results demonstrate an important role for the intersection of Lmx1b and Hoxb8::cre expression in the development of nociceptive dorsal horn circuits critical for mechanical and thermal pain processing.
Title: Hoxb8 intersection defines a role for Lmx1b in excitatory dorsal horn neuron development, spinofugal connectivity, and nociception.

Submit: New GeneRIF Correction See all GeneRIFs (46)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (8) 1 citation
Chemically induced (ENU) (1) 1 citation
Endonuclease-mediated (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:493854

Lmx1b (e-PCR), detects polymorphism
- UniSTS:527405

Lmx1b (e-PCR), detects polymorphism
- UniSTS:461897

09.MMHAP14FRC9.seq (e-PCR)
- UniSTS:122964

D2Dcr47 (e-PCR), detects polymorphism
- UniSTS:507606

D2Mit367 (e-PCR), detects polymorphism
- UniSTS:129263

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology 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	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
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	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within camera-type eye development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within central nervous system neuron development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cerebellum morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within collagen fibril organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in dopaminergic neuron differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within dopaminergic neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in dopaminergic neuron differentiation	TAS Traceable Author Statement more info	PubMed
involved_in dorsal/ventral pattern formation	IEP Inferred from Expression Pattern more info	PubMed
involved_in embryonic limb morphogenesis	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within limb morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in locomotory behavior	IGI Inferred from Genetic Interaction more info	PubMed
involved_in memory	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within midbrain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within multicellular organism development	IEA Inferred from Electronic Annotation more info
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in olfactory behavior	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within organ growth	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of autophagy	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of intracellular transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in synapse organization	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within trabecular meshwork development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: LIM homeobox transcription factor 1-beta

Names: GENA 191; LIM homeo box transcription factor 1B; LIM/homeobox protein 1.2; LIM/homeobox protein LMX1B; LMX-1.2

NCBI Reference Sequences (RefSeq)

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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)

NM_010725.3 → NP_034855.3 LIM homeobox transcription factor 1-beta

Status: VALIDATED

Source sequence(s)

AL929212

Consensus CDS

CCDS15944.1

UniProtKB/TrEMBL

A0A0R4J0I7, H3BJD7

Related

ENSMUSP00000043616.6, ENSMUST00000041730.12

Conserved Domains (3) summary

cd09371
Location:62 → 114

LIM1_Lmx1b; The first LIM domain of Lmx1b

cd09378
Location:121 → 175

LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b

pfam00046
Location:228 → 282

Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000068.8 Reference GRCm39 C57BL/6J

Range

33450977..33531219 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006497746.5 → XP_006497809.1 LIM homeobox transcription factor 1-beta isoform X1

UniProtKB/TrEMBL

H3BJD7

Related

ENSMUSP00000134944.3, ENSMUST00000176067.2

Conserved Domains (3) summary

cd09371
Location:62 → 114

LIM1_Lmx1b; The first LIM domain of Lmx1b

cd09378
Location:121 → 175

LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b

pfam00046
Location:228 → 282

Homeobox; Homeobox domain