lhx3 LIM homeobox 3 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: lhx3provided by ZNC
Official Full Name: LIM homeobox 3provided by ZNC
Primary source: ZFIN:ZDB-GENE-980526-131
See related: AllianceGenome:ZFIN:ZDB-GENE-980526-131
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: lim3
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 ventral spinal cord interneuron specification. Predicted to be active in nucleus. Is expressed in adenohypophyseal placode; nervous system; neural keel; and neural tube. Human ortholog(s) of this gene implicated in panhypopituitarism. Orthologous to human LHX3 (LIM homeobox 3). [provided by Alliance of Genome Resources, Dec 2024]
Annotation information: Annotation category: suggests misassembly; Annotation category: partial on reference assembly
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 5

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	5	NC_007116.7 (71801870..71819836)
105	previous assembly	GRCz10 (GCF_000002035.5)	5	NC_007116.6 (71028034..71046000)

Chromosome 5 - NC_007116.7 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: 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?

Lhx3 and Lhx4 have roles in suppressing Kolmer-Agduhr interneuron characteristics within zebrafish axial motoneurons
Title: Lhx3 and Lhx4 suppress Kolmer-Agduhr interneuron characteristics within zebrafish axial motoneurons.

Submit: New GeneRIF Correction

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
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within ventral spinal cord interneuron specification	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 Lhx3

Names: LIM homeobox protein 3; homeobox protein LIM-3

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_131208.1 → NP_571283.1 LIM/homeobox protein Lhx3

See identical proteins and their annotated locations for NP_571283.1

Status: PROVISIONAL

Source sequence(s)

U34590

UniProtKB/Swiss-Prot

Q90421

Conserved Domains (3) summary

cd09376
Location:87 → 142

LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family

cd09467
Location:25 → 79

LIM1_Lhx3b; The first LIM domain of Lhx3b

pfam00046
Location:157 → 210

Homeobox; Homeobox domain