Lhx5 LIM homeobox 5 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Lhx5provided by RGD
Official Full Name: LIM homeobox 5provided by RGD
Primary source: RGD:71079
See related: EnsemblRapid:ENSRNOG00000001392 AllianceGenome:RGD:71079
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 positive regulation of DNA-templated transcription; regulation of transcription by RNA polymerase II; and spinal cord association neuron differentiation. Predicted to act upstream of or within nervous system development and regulation of neural precursor cell proliferation. Predicted to be active in nucleus. Orthologous to human LHX5 (LIM homeobox 5). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Brain (RPKM 8.4) and Testes (RPKM 2.2) See more
Orthologs: human mouse all
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Genomic context

Location:: 12q16

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	12	NC_086030.1 (41786746..41795183, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	12	NC_051347.1 (36126186..36134625, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	12	NC_005111.4 (41663000..41671437, complement)

Chromosome 12 - NC_086030.1 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
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?

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General gene information

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Markers

D12Rat97 (e-PCR), detects polymorphism
- UniSTS:226489

Gene Ontology Provided by RGD

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

Process	Evidence Code	Pubs
acts_upstream_of_or_within cell proliferation in forebrain	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell-cell signaling	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cerebellar Purkinje cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cerebellar Purkinje cell-granule cell precursor cell signaling	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 forebrain neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within hippocampus development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuroblast proliferation	ISO Inferred from Sequence Orthology more info
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of neuroblast proliferation	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 spinal cord association neuron differentiation	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 protein Lhx5

Names: LIM homeobox protein 5; homeobox protein LIM-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_139036.2 → NP_620605.1 LIM/homeobox protein Lhx5

See identical proteins and their annotated locations for NP_620605.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000012

UniProtKB/Swiss-Prot

P61376

UniProtKB/TrEMBL

A6J1J7

Related

ENSRNOP00000001883.2, ENSRNOT00000001883.5

Conserved Domains (4) summary

cd09367
Location:5 → 56

LIM1_Lhx1_Lhx5; The first LIM domain of Lhx1 (also known as Lim1) and Lhx5

cd09375
Location:64 → 119

LIM2_Lhx1_Lhx5; The second LIM domain of Lhx1 (also known as Lim1) and Lhx5

PHA03378
Location:247 → 392

PHA03378; EBNA-3B; Provisional

pfam00046
Location:183 → 237

Homeobox; Homeobox domain