lim-4 LIM/homeobox protein lim-4 [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: lim-4
Official Full Name: LIM/homeobox protein lim-4
Primary source: WormBase:WBGene00002987
Locus tag: CELE_ZC64.4
See related: AllianceGenome:WB:WBGene00002987
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Caenorhabditis elegans (strain: Bristol N2)
Lineage: Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
Summary: Enables DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in several processes, including positive regulation of transcription by RNA polymerase II; regulation of neuron differentiation; and serotonin biosynthetic process. Located in nucleus. Is expressed in ABalpppppa; ABpraaappa; head muscle; intestine; and nervous system. Orthologous to human LHX6 (LIM homeobox 6) and LHX8 (LIM homeobox 8). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See lim-4 in Genome Data Viewer

Location:: chromosome: X

Exon count:: 8

Sequence:: Chromosome: X; NC_003284.9 (3869404..3873545, complement)

Chromosome X - NC_003284.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003284.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

the evolutionarily conserved LIM-4/LHX6 homeodomain proteins function in generation of precise neuronal subtypes.
Title: The Evolutionarily Conserved LIM Homeodomain Protein LIM-4/LHX6 Specifies the Terminal Identity of a Cholinergic and Peptidergic C. elegans Sensory/Inter/Motor Neuron-Type.
cis-element(s) within introns are necessary and sufficient to direct lim-4 to specify serotonergic phenotype, whereas its 5'-upstream sequence directs lim-4 function in olfactory neuron AWB
Title: Cell-type specific regulation of serotonergic identity by the C. elegans LIM-homeodomain factor LIM-4.
lim-4 Lhx gene is required for several but not all aspects of RID motor neuron differentiation.
Title: LIM homeobox gene-dependent expression of biogenic amine receptors in restricted regions of the C. elegans nervous system.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

ZC64.4 (e-PCR)
- UniSTS:322452

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
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	IMP Inferred from Mutant Phenotype more info	PubMed
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell fate specification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuron differentiation	IEA Inferred from Electronic Annotation more info
involved_in neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of neuron differentiation	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
involved_in regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in serotonin biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info	PubMed

General protein information

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Preferred Names: LIM/homeobox protein lim-4

NP_001338856.1

Confirmed by transcript evidence

NP_001338857.1

Confirmed by transcript evidence

NP_508669.1

Confirmed by transcript evidence

NCBI Reference Sequences (RefSeq)

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Genome Annotation

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

Reference assembly

Genomic

NC_003284.9 Reference assembly

Range

3869404..3873545 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001351879.2 → NP_001338856.1 LIM/homeobox protein lim-4 [Caenorhabditis elegans]

Status: REVIEWED

Conserved Domains (3) summary

cd09379
Location:159 → 213

LIM2_AWH; The second LIM domain of Arrowhead (AWH)

smart00389
Location:230 → 286

HOX; Homeodomain

pfam00412
Location:98 → 153

LIM; LIM domain
NM_076268.2 → NP_508669.1 LIM/homeobox protein lim-4 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_508669.1

Status: REVIEWED

UniProtKB/Swiss-Prot

A0A1X7RBW0, A0A1X7RC92, G5EEA1

Conserved Domains (3) summary

cd09379
Location:168 → 222

LIM2_AWH; The second LIM domain of Arrowhead (AWH)

pfam00046
Location:243 → 296

Homeobox; Homeobox domain

pfam00412
Location:98 → 153

LIM; LIM domain
NM_001351878.2 → NP_001338857.1 LIM/homeobox protein lim-4 [Caenorhabditis elegans]

Status: REVIEWED

Conserved Domains (3) summary

cd09379
Location:157 → 211

LIM2_AWH; The second LIM domain of Arrowhead (AWH)

smart00389
Location:228 → 284

HOX; Homeodomain

pfam00412
Location:98 → 151

LIM; LIM domain