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

Gene ID: 180459, updated on 4-Jan-2025

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, Jan 2025]
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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_003284.9Genomic Context describing neighboring genes Neighboring gene Band 7 domain-containing protein;Protein unc-1 Neighboring gene B9 domain-containing protein 1 Neighboring gene Profilin-3 Neighboring gene Guanine nucleotide exchange factor rei-2 Neighboring gene tRNA-Arg Neighboring gene ncRNA

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_003284.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Sleep-active neuron specification and sleep induction require FLP-11 neuropeptides to systemically induce sleep. Turek M, et al. Elife, 2016 Mar 7. PMID 26949257, Free PMC Article
  2. An unusual Zn-finger/FH2 domain protein controls a left/right asymmetric neuronal fate decision in C. elegans. Johnston RJ Jr, et al. Development, 2006 Sep. PMID 16887832
  3. Vector-free DNA constructs improve transgene expression in C. elegans. Etchberger JF, et al. Nat Methods, 2008 Jan. PMID 18165801
  4. The homeobox gene lim-6 is required for distinct chemosensory representations in C. elegans. Pierce-Shimomura JT, et al. Nature, 2001 Apr 5. PMID 11287956
  5. Identification of spatial and temporal cues that regulate postembryonic expression of axon maintenance factors in the C. elegans ventral nerve cord. Aurelio O, et al. Development, 2003 Feb. PMID 12490565

See all (43) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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

Homology

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

  1. NC_003284.9 Reference assembly

    Range
    1073908..1079452
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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
Nucleotide Protein
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