Lhx4 LIM homeobox 4 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Lhx4provided by RGD
Official Full Name: LIM homeobox 4provided by RGD
Primary source: RGD:1308044
See related: EnsemblRapid:ENSRNOG00000003595 AllianceGenome:RGD:1308044
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; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and methyl-CpG binding activity. Predicted to be involved in neuron differentiation and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including negative regulation of apoptotic process; neuron differentiation; and placenta development. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in panhypopituitarism. Orthologous to human LHX4 (LIM homeobox 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Adrenal (RPKM 4.5), Thymus (RPKM 2.6) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 13q21

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (70423768..70477337, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (67877109..67917219, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (73348874..73400416, complement)

Chromosome 13 - NC_086031.1 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?

The current study was undertaken to clarify the mechanisms driving rhythmic LIM homeobox 4 (Lhx4) expression in the pineal gland and the possible regulatory impact of Lhx4 on gene transcripts involved in melatonin synthesis and other biological processes.
Title: The Lhx4 homeobox transcript in the rat pineal gland: Adrenergic regulation and impact on transcripts encoding melatonin-synthesizing enzymes.

Submit: New GeneRIF Correction

General gene information

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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 methyl-CpG binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology 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 animal organ morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within medial motor column neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within motor neuron axon guidance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of apoptotic process	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 placenta development	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 transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor 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 Lhx4

Names: LIM homeobox protein 4

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_001108348.2 → NP_001101818.2 LIM/homeobox protein Lhx4

Status: VALIDATED

Source sequence(s)

JAXUCZ010000013

UniProtKB/TrEMBL

A0A1W2Q6B2, A6ICZ1, F1LZ08

Related

ENSRNOP00000060479.4, ENSRNOT00000067253.5

Conserved Domains (3) summary

cd09376
Location:89 → 144

LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family

cd09468
Location:30 → 81

LIM1_Lhx4; The first LIM domain of Lhx4

pfam00046
Location:160 → 214

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

70423768..70477337 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063272478.1 → XP_063128548.1 LIM/homeobox protein Lhx4 isoform X1

UniProtKB/TrEMBL

A6ICZ0
XM_063272479.1 → XP_063128549.1 LIM/homeobox protein Lhx4 isoform X2