lhx5 LIM homeobox 5 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: lhx5provided by ZNC
Official Full Name: LIM homeobox 5provided by ZNC
Primary source: ZFIN:ZDB-GENE-980526-484
See related: Ensembl:ENSDARG00000057936 AllianceGenome:ZFIN:ZDB-GENE-980526-484
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: lim5
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 eye development and forebrain development. Predicted to be active in nucleus. Is expressed in several structures, including CiA; cranial neural crest; forebrain; neural keel; and presumptive ectoderm. Orthologous to human LHX5 (LIM homeobox 5). [provided by Alliance of Genome Resources, Jul 2025]
Orthologs: human mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: chromosome: 21

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2025_04	current	GRCz12tu (GCF_049306965.1)	21	NC_133196.1 (17321875..17337990, complement)
RS_2024_08	previous assembly	GRCz11 (GCF_000002035.6)	21	NC_007132.7 (15913130..15929011, complement)

Chromosome 21 - NC_133196.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

discrete enhancer elements control lhx5 expression in different regions of the forebrain.
Title: Conserved Noncoding Sequences Regulate lhx5 Expression in the Zebrafish Forebrain.
Lhx5 is a required factor that promotes forebrain development and inhibits Wnt signaling by activating the transcription of secreted Wnt antagonists.
Title: Lhx5 promotes forebrain development and activates transcription of secreted Wnt antagonists.

Submit: New GeneRIF Correction

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

lim5 (e-PCR)
- UniSTS:205576

G41734 (e-PCR)
- UniSTS:70760

lim5 (e-PCR)
- UniSTS:186986

Z6089 (e-PCR)
- UniSTS:204735

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
acts_upstream_of_or_within eye development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within forebrain development	IDA Inferred from Direct Assay 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 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

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

Go to the top of the page Help

Preferred Names: LIM/homeobox protein Lhx5

Names: LIM homeobox protein 5; homeobox protein LIM-5

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_131218.1 → NP_571293.1 LIM/homeobox protein Lhx5

See identical proteins and their annotated locations for NP_571293.1

Status: PROVISIONAL

Source sequence(s)

L42547

UniProtKB/Swiss-Prot

P52889, Q4KMK6

Related

ENSDARP00000075139.4, ENSDART00000080693.5

Conserved Domains (5) 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

COG5576
Location:126 → 242

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam00046
Location:183 → 236

Homeobox; Homeobox domain

pfam05349
Location:298 → 390

GATA-N; GATA-type transcription activator, N-terminal