Lmx1a LIM homeobox transcription factor 1 alpha [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Lmx1aprovided by RGD
Official Full Name: LIM homeobox transcription factor 1 alphaprovided by RGD
Primary source: RGD:1304784
See related: EnsemblRapid:ENSRNOG00000004642 AllianceGenome:RGD:1304784
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 activator 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 midbrain dopaminergic neuron differentiation; olfactory behavior; and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including negative regulation of neuron differentiation; nervous system development; and regulation of cell growth. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in autosomal dominant nonsyndromic deafness 7. Orthologous to human LMX1A (LIM homeobox transcription factor 1 alpha). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Brain (RPKM 3.9), Muscle (RPKM 3.6) and 5 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 13q24

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (82367493..82511157)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (79834614..79978253)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (85916753..86061534)

Chromosome 13 - NC_086031.1 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: 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?

the qc mutation of Lmx1a is involved in development of the ventricular system and dorsal migration of neurons
Title: Mutation at the Lmx1a locus provokes aberrant brain development in the rat.

Submit: New GeneRIF Correction

General gene information

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Markers

D0M1Mit110 (e-PCR)
- UniSTS:116694

D1Mit110 (e-PCR), detects polymorphism
- UniSTS:116694

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	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 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
acts_upstream_of_or_within axon guidance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within central nervous system development	ISO Inferred from Sequence Orthology more info
acts_upstream_of central nervous system neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within central nervous system neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cerebellum development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within dentate gyrus development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within dopaminergic neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within hippocampus development	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 midbrain dopaminergic neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of neuron differentiation	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
involved_in olfactory behavior	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of cell growth	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 transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in synapse organization	ISO Inferred from Sequence Orthology more info

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

General protein information

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Preferred Names: LIM homeobox transcription factor 1-alpha

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_001105967.2 → NP_001099437.2 LIM homeobox transcription factor 1-alpha

See identical proteins and their annotated locations for NP_001099437.2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000013

UniProtKB/TrEMBL

F1LRJ8

Related

ENSRNOP00000006163.4, ENSRNOT00000006163.7

Conserved Domains (3) summary

cd09370
Location:35 → 86

LIM1_Lmx1a; The first LIM domain of Lmx1a

cd09378
Location:94 → 148

LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b

pfam00046
Location:198 → 252

Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086031.1 Reference GRCr8

Range

82367493..82511157

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017598709.3 → XP_017454198.1 LIM homeobox transcription factor 1-alpha isoform X1

UniProtKB/TrEMBL

F1LRJ8

Conserved Domains (3) summary

cd09370
Location:35 → 86

LIM1_Lmx1a; The first LIM domain of Lmx1a

cd09378
Location:94 → 148

LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b

pfam00046
Location:198 → 252

Homeobox; Homeobox domain