ttx-3 LIM/homeobox protein ttx-3 [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: ttx-3
Official Full Name: LIM/homeobox protein ttx-3
Primary source: WormBase:WBGene00006654
Locus tag: CELE_C40H5.5
See related: AllianceGenome:WB:WBGene00006654
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 activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including olfactory learning; positive regulation of dauer larval development; and thermosensory behavior. Predicted to be located in axon and perikaryon. Predicted to be active in nucleus. Is expressed in head muscle; head neurons; and pharyngeal neurons. Orthologous to several human genes including LHX9 (LIM homeobox 9). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See ttx-3 in Genome Data Viewer

Location:: chromosome: X

Exon count:: 10

Sequence:: Chromosome: X; NC_003284.9 (11764456..11769378, 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?

Imaging of native transcription and transcriptional dynamics in vivo using a tagged Argonaute protein.
Title: Imaging of native transcription and transcriptional dynamics in vivo using a tagged Argonaute protein.
the type of differentiation program that is controlled by ttx-3 in different neuron types is specified by a distinct set of collaborating transcription factors, including the POU homeobox gene unc-86
Title: The LIM and POU homeobox genes ttx-3 and unc-86 act as terminal selectors in distinct cholinergic and serotonergic neuron types.
Mutants in ttx-3 showed abnormal thermal responses, suggesting that these genes are involved in warm avoidance.
Title: Distribution and movement of Caenorhabditis elegans on a thermal gradient.

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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

C40H5.5 (e-PCR)
- UniSTS:313842

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 activator activity, RNA polymerase II-specific	IMP Inferred from Mutant Phenotype 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 cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay 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 associative learning	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in axonogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in behavior	IEA Inferred from Electronic Annotation more info
involved_in dauer larval development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative adaptation of signaling pathway	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 olfactory learning	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of dauer larval development	IGI Inferred from Genetic Interaction 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	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in regulation of axon extension	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of axon guidance	IMP Inferred from Mutant Phenotype 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 thermosensory behavior	IGI Inferred from Genetic Interaction more info	PubMed
involved_in thermosensory behavior	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in thermotaxis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in thermotaxis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in axon	IEA Inferred from Electronic Annotation more info
located_in cell projection	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in perikaryon	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: LIM/homeobox protein ttx-3

NP_001257168.1

Confirmed by transcript evidence

NP_001257169.1

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

11764456..11769378 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001270239.2 → NP_001257168.1 LIM/homeobox protein ttx-3 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001257168.1

Status: REVIEWED

UniProtKB/Swiss-Prot

B6VQ91, G5EE86

Conserved Domains (3) summary

cd08368
Location:110 → 163

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

pfam00046
Location:296 → 348

Homeobox; Homeobox domain

cl02475
Location:171 → 226

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
NM_001270240.3 → NP_001257169.1 LIM/homeobox protein ttx-3 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001257169.1

Status: REVIEWED

UniProtKB/Swiss-Prot

G5EE86

Conserved Domains (3) summary

cd08368
Location:82 → 135

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

pfam00046
Location:268 → 320

Homeobox; Homeobox domain

cl02475
Location:143 → 198

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