Lmx1b LIM homeobox transcription factor 1 beta [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Lmx1bprovided by RGD
Official Full Name: LIM homeobox transcription factor 1 betaprovided by RGD
Primary source: RGD:620843
See related: EnsemblRapid:ENSRNOG00000017019 AllianceGenome:RGD:620843
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including memory; olfactory behavior; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including collagen fibril organization; nervous system development; and trabecular meshwork development. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in nail-patella syndrome. Orthologous to human LMX1B (LIM homeobox transcription factor 1 beta). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Restricted expression toward (RPKM 13.6) See more
Orthologs: human mouse all
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Genomic context

Location:: 3p11

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (37257025..37338675, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (16862195..16940899, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (12608748..12686937, complement)

Chromosome 3 - NC_086021.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

LMX1B may be considered to be a negative regulator of the renal fibrosis index.
Title: LIM homeobox transcription factor 1B expression affects renal interstitial fibrosis and apoptosis in unilateral ureteral obstructed rats.

Submit: New GeneRIF Correction

General gene information

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Markers

D3Got11 (e-PCR)
- UniSTS:115225

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

AU049321 (e-PCR)
- UniSTS:145769

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
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	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within camera-type eye development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell population proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within central nervous system neuron development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cerebellum morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within collagen fibril organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within dopaminergic neuron differentiation	ISO Inferred from Sequence Orthology more info
involved_in dopaminergic neuron differentiation	ISO Inferred from Sequence Orthology more info
involved_in dorsal/ventral pattern formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within limb morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in locomotory behavior	ISO Inferred from Sequence Orthology more info
involved_in memory	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within midbrain development	ISO Inferred from Sequence Orthology more info
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron migration	ISO Inferred from Sequence Orthology more info
involved_in olfactory behavior	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within organ growth	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of autophagy	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in regulation of intracellular transport	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in synapse organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within trabecular meshwork development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
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

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_053709.1 → NP_446161.1 LIM homeobox transcription factor 1-beta

See identical proteins and their annotated locations for NP_446161.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000003

UniProtKB/TrEMBL

G3V877

Related

ENSRNOP00000022953.6, ENSRNOT00000022953.8

Conserved Domains (3) summary

cd09371
Location:56 → 108

LIM1_Lmx1b; The first LIM domain of Lmx1b

cd09378
Location:115 → 169

LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b

pfam00046
Location:222 → 276

Homeobox; Homeobox domain