Lhx2 LIM homeobox 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Lhx2provided by RGD
Official Full Name: LIM homeobox 2provided by RGD
Primary source: RGD:71076
See related: EnsemblRapid:ENSRNOG00000010551 AllianceGenome:RGD:71076
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: LH2A; Lh-2
Summary: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Involved in neuron differentiation. Predicted to be active in nucleus. Orthologous to human LHX2 (LIM homeobox 2). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Brain (RPKM 45.8), Liver (RPKM 16.9) and 3 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 3q12

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (42523345..42553646)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (22113619..22143909)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (22628674..22658447)

Chromosome 3 - NC_086021.1 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 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 combination of hair follicle-specific marker LHX2 and co-expressed marker can distinguish between sweat gland placodes and hair placodes in rat.
Title: The combination of hair follicle-specific marker LHX2 and co-expressed marker can distinguish between sweat gland placodes and hair placodes in rat.

Submit: New GeneRIF Correction

General gene information

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Markers

Lhx2 (e-PCR), detects polymorphism
- UniSTS:507020

D3Got17 (e-PCR)
- UniSTS:115361

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
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 cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	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 chromatin binding	IEA Inferred from Electronic Annotation more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within anatomical structure formation involved in morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in axon extension	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within axon extension	ISO Inferred from Sequence Orthology more info
involved_in axon guidance	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within axon guidance	ISO Inferred from Sequence Orthology more info
involved_in axon guidance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within brain development	ISO Inferred from Sequence Orthology more info
involved_in cerebral cortex development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cerebral cortex development	ISO Inferred from Sequence Orthology more info
involved_in cerebral cortex development	ISO Inferred from Sequence Orthology more info
involved_in dorsal/ventral pattern formation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within dorsal/ventral pattern formation	ISO Inferred from Sequence Orthology more info
involved_in hair follicle development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within hair follicle development	ISO Inferred from Sequence Orthology more info
involved_in maintenance of epithelial cell apical/basal polarity	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within maintenance of epithelial cell apical/basal polarity	ISO Inferred from Sequence Orthology more info
involved_in mesoderm development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mesoderm development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression, epigenetic	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of gene expression, epigenetic	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of neurogenesis	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of neurogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within nervous system development	ISO Inferred from Sequence Orthology more info
involved_in neural tube closure	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neural tube closure	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neurogenesis	ISO Inferred from Sequence Orthology more info
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuron differentiation	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within neuron differentiation	ISO Inferred from Sequence Orthology more info
involved_in olfactory bulb development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within olfactory bulb development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of neural precursor cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of neural precursor cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation 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 transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in retina development in camera-type eye	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within retina development in camera-type eye	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within telencephalon development	ISO Inferred from Sequence Orthology more info
involved_in telencephalon regionalization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within telencephalon regionalization	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	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: LIM/homeobox protein Lhx2

Names: LIM homeobox protein 2; homeobox protein LH-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_001106571.1 → NP_001100041.1 LIM/homeobox protein Lhx2

See identical proteins and their annotated locations for NP_001100041.1

Status: PROVISIONAL

Source sequence(s)

CH473983

UniProtKB/Swiss-Prot

P36198

UniProtKB/TrEMBL

A6JEU2

Conserved Domains (4) summary

cd09377
Location:111 → 169

LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family

cd09469
Location:43 → 106

LIM1_Lhx2; The first LIM domain of Lhx2

COG5576
Location:247 → 378

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam00046
Location:270 → 323

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_086021.1 Reference GRCr8

Range

42523345..42553646

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017591665.3 → XP_017447154.1 LIM/homeobox protein Lhx2 isoform X2

UniProtKB/Swiss-Prot

P36198

Conserved Domains (4) summary

cd09377
Location:78 → 136

LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family

cd09469
Location:2 → 65

LIM1_Lhx2; The first LIM domain of Lhx2

COG5576
Location:214 → 345

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam00046
Location:237 → 290

Homeobox; Homeobox domain
XM_006234072.5 → XP_006234134.1 LIM/homeobox protein Lhx2 isoform X1

See identical proteins and their annotated locations for XP_006234134.1

UniProtKB/Swiss-Prot

P36198

UniProtKB/TrEMBL

D4A380

Related

ENSRNOP00000061914.2, ENSRNOT00000064507.5

Conserved Domains (4) summary

cd09377
Location:119 → 177

LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family

cd09469
Location:43 → 106

LIM1_Lhx2; The first LIM domain of Lhx2

COG5576
Location:255 → 386

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam00046
Location:278 → 331

Homeobox; Homeobox domain
XM_008761742.4 → XP_008759964.1 LIM/homeobox protein Lhx2 isoform X2

See identical proteins and their annotated locations for XP_008759964.1

UniProtKB/Swiss-Prot

P36198

Conserved Domains (4) summary

cd09377
Location:78 → 136

LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family

cd09469
Location:2 → 65

LIM1_Lhx2; The first LIM domain of Lhx2

COG5576
Location:214 → 345

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam00046
Location:237 → 290

Homeobox; Homeobox domain
XM_006234073.1 → XP_006234135.1 LIM/homeobox protein Lhx2 isoform X3

Conserved Domains (3) summary

cd09377
Location:34 → 92

LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family

COG5576
Location:170 → 301

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam00046
Location:193 → 246

Homeobox; Homeobox domain
XM_063283527.1 → XP_063139597.1 LIM/homeobox protein Lhx2 isoform X4