lhx1b LIM homeobox 1b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: lhx1bprovided by ZNC
Official Full Name: LIM homeobox 1bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-980526-116
See related: Ensembl:ENSDARG00000007944 AllianceGenome:ZFIN:ZDB-GENE-980526-116
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: lim6
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. Predicted to be involved in neuron differentiation and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of DNA-templated transcription. Predicted to be active in nucleus. Is expressed in blastoderm; central nervous system; margin; midbrain neural keel; and shield. Orthologous to human LHX1 (LIM homeobox 1). [provided by Alliance of Genome Resources, Apr 2025]
Orthologs: all
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Genomic context

Location:: chromosome: 5

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2025_04	current	GRCz12tu (GCF_049306965.1)	5	NC_133180.1 (61599111..61604441)
RS_2024_08	previous assembly	GRCz11 (GCF_000002035.6)	5	NC_007116.7 (56268844..56274174)

Chromosome 5 - NC_133180.1 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: 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?

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General gene information

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Markers

lim6 (e-PCR)
- UniSTS:205575

lim6 (e-PCR)
- UniSTS:186987

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 anatomical structure morphogenesis	IEA Inferred from Electronic Annotation more info
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
involved_in system development	IEA Inferred from Electronic Annotation 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

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Preferred Names: LIM/homeobox protein Lhx1b

Names: LIM homeobox protein 6

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_131207.1 → NP_571282.1 LIM/homeobox protein Lhx1b

See identical proteins and their annotated locations for NP_571282.1

Status: PROVISIONAL

Source sequence(s)

AF001299

UniProtKB/TrEMBL

A0A0R4IPG0, A0A8N7XJ14, B3DG56, O13106

Related

ENSDARP00000025458.6, ENSDART00000021159.9

Conserved Domains (3) summary

cd09367
Location:4 → 55

LIM1_Lhx1_Lhx5; The first LIM domain of Lhx1 (also known as Lim1) and Lhx5

cd09375
Location:63 → 118

LIM2_Lhx1_Lhx5; The second LIM domain of Lhx1 (also known as Lim1) and Lhx5

pfam00046
Location:181 → 234

Homeobox; Homeobox domain