lhx2b LIM homeobox 2b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: lhx2bprovided by ZNC
Official Full Name: LIM homeobox 2bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-051220-1
See related: Ensembl:ENSDARG00000031222 AllianceGenome:ZFIN:ZDB-GENE-051220-1
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: bel; lhx2; zgc:152707
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. Acts upstream of or within several processes, including camera-type eye development; nervous system development; and optomotor response. Predicted to be active in nucleus. Is expressed in several structures, including brain; forebrain neural keel; forebrain neural rod; optic vesicle; and retina. Used to study congenital nystagmus and pathologic nystagmus. Orthologous to human LHX2 (LIM homeobox 2). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 8

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	8	NC_007119.7 (3085077..3101385)
105	previous assembly	GRCz10 (GCF_000002035.5)	8	NC_007119.6 (3026363..3042636)

Chromosome 8 - NC_007119.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Lack of Lhx2/Lhx9 function as well as increased Wnt signaling alter the expression of the thalamus specific cell adhesion factor pcdh10b and lead subsequently to a striking anterior-posterior disorganization of the caudal forebrain.
Title: Lhx2 and Lhx9 determine neuronal differentiation and compartition in the caudal forebrain by regulating Wnt signaling.
Lhx2 may mediate an alternative or parallel pathway for control of cellular proliferation in the developing forebrain via Six3.
Title: Lhx2 mediates the activity of Six3 in zebrafish forebrain growth.
required for patterning in the ventral forebrain and eye.
Title: belladonna/(Ihx2) is required for neural patterning and midline axon guidance in the zebrafish forebrain.

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General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within brain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within camera-type eye development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within forebrain development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within optic nerve development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within optokinetic behavior	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within optomotor response	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within response to light stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within retinal ganglion cell axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within telencephalon development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within thalamus development	IGI Inferred from Genetic Interaction more info	PubMed

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

General protein information

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Preferred Names: LIM/homeobox protein Lhx2; LIM/homeobox protein Lhx2b

Names: LIM homeobox 2; LIM homeodomain type transcription factor Lhx2; belladonna

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_001040010.3 → NP_001035099.3 LIM/homeobox protein Lhx2b

Status: PROVISIONAL

Source sequence(s)

AL929566, BX005074

UniProtKB/TrEMBL

A0A8M1N8T6, B0R107

Related

ENSDARP00000123264.1, ENSDART00000148020.3

Conserved Domains (4) summary

cd09377
Location:142 → 200

LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family

cd09469
Location:74 → 137

LIM1_Lhx2; The first LIM domain of Lhx2

COG5576
Location:267 → 389

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam00046
Location:290 → 342

Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007119.7 Reference GRCz11 Primary Assembly

Range

3085077..3101385

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005167367.4 → XP_005167424.1 LIM/homeobox protein Lhx2 isoform X1

UniProtKB/TrEMBL

A0A8M2BFE8

Conserved Domains (4) summary

cd09377
Location:141 → 199

LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family

cd09469
Location:74 → 137

LIM1_Lhx2; The first LIM domain of Lhx2

COG5576
Location:266 → 388

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam00046
Location:289 → 341

Homeobox; Homeobox domain
XM_005167369.4 → XP_005167426.1 LIM/homeobox protein Lhx2 isoform X2

UniProtKB/TrEMBL

A0A8M2BEV2

Conserved Domains (4) summary

cd09377
Location:70 → 128

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:195 → 317

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam00046
Location:218 → 270

Homeobox; Homeobox domain