lim-6 LIM/homeobox protein lim-6 [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: lim-6
Official Full Name: LIM/homeobox protein lim-6
Primary source: WormBase:WBGene00002988
Locus tag: CELE_K03E6.1
See related: AllianceGenome:WB:WBGene00002988
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: Predicted to enable 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 defecation; regulation of gene expression; and uterus morphogenesis. Located in nucleus. Is expressed in several structures, including amphid neurons; excretory system; hermaphrodite gonad; nerve ring neurons; and ventral nerve cord. Human ortholog(s) of this gene implicated in autosomal dominant nonsyndromic deafness 7 and nail-patella syndrome. Orthologous to several human genes including LMX1B (LIM homeobox transcription factor 1 beta). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See lim-6 in Genome Data Viewer

Location:: chromosome: X

Exon count:: 9

Sequence:: Chromosome: X; NC_003284.9 (1073908..1079452)

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?

Transciption factor lsy-27 is broadly and exclusively expressed in the embryo and acts during the initiation, but not during the maintenance phase of asymmetric neuronal differentiation program to assist in the initiation of lim-6 expression.
Title: A left/right asymmetric neuronal differentiation program is controlled by the Caenorhabditis elegans lsy-27 zinc-finger transcription factor.
lim-6 Lhx gene is required for specific aspects of RIS interneuron differentiation.
Title: LIM homeobox gene-dependent expression of biogenic amine receptors in restricted regions of the C. elegans nervous system.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

K03E6.1 (e-PCR)
- UniSTS:320100

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 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
involved_in axonogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in behavior	IEA Inferred from Electronic Annotation more info
involved_in defecation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in detection of chemical stimulus involved in sensory perception	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in foraging behavior	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron development	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 gene expression	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	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 uterus morphogenesis	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

General protein information

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Preferred Names: LIM/homeobox protein lim-6

NP_001256980.1

Confirmed by transcript evidence

NP_001256981.1

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

1073908..1079452

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001270051.2 → NP_001256980.1 LIM/homeobox protein lim-6 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001256980.1

Status: REVIEWED

UniProtKB/Swiss-Prot

G4RV72, Q21192, Q94157

Conserved Domains (2) summary

pfam00046
Location:189 → 242

Homeobox; Homeobox domain

cl02475
Location:42 → 95

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
NM_001270052.2 → NP_001256981.1 LIM/homeobox protein lim-6 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001256981.1

Status: REVIEWED

UniProtKB/TrEMBL

G4RV72

Conserved Domains (2) summary

pfam00046
Location:189 → 242

Homeobox; Homeobox domain

cl02475
Location:42 → 95

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers