ref-2 Zinc finger transcription factor ref-2 [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: ref-2
Official Full Name: Zinc finger transcription factor ref-2
Primary source: WormBase:WBGene00004335
Locus tag: CELE_C47C12.3
See related: AllianceGenome:WB:WBGene00004335
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 RNA polymerase II transcription regulatory region sequence-specific DNA binding activity and RNA polymerase II-specific DNA-binding transcription factor binding activity. Involved in several processes, including neuron fate specification; positive regulation of transcription by RNA polymerase II; and regulation of cell division. Acts upstream of or within with a positive effect on nematode larval development. Located in nucleus. Is expressed in several structures, including IL1 neuron; P3.p hermaphrodite; neuroblasts; rectal epithelial cell; and ventral nerve cord. Used to study holoprosencephaly. Human ortholog(s) of this gene implicated in Dandy-Walker syndrome; X-linked VACTERL association; craniosynostosis; holoprosencephaly (multiple); and visceral heterotaxy (multiple). Orthologous to several human genes including ZIC1 (Zic family member 1); ZIC2 (Zic family member 2); and ZIC3 (Zic family member 3). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See ref-2 in Genome Data Viewer

Location:: chromosome: X

Exon count:: 8

Sequence:: Chromosome: X; NC_003284.9 (7744239..7750013)

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?

pop-1/TCF, ref-2/ZIC and T-box factors regulate the development of anterior cells in the C. elegans embryo.
Title: pop-1/TCF, ref-2/ZIC and T-box factors regulate the development of anterior cells in the C. elegans embryo.
Inhibition of export by NXF-1 depends upon the TRE, CeNXF-2, CeREF-1, and CeREF-2.
Title: NXF-2, REF-1, and REF-2 affect the choice of nuclear export pathway for tra-2 mRNA in C. elegans.

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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

C47C12.3 (e-PCR)
- UniSTS:321996

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
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	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 RNA polymerase II transcription regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in anterior/posterior pattern specification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in central nervous system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within_positive_effect nematode larval development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron fate specification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cell division	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
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: Zinc finger transcription factor ref-2

NP_001024477.1

Confirmed by transcript evidence

NP_001024478.1

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

7744239..7750013

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001029307.5 → NP_001024478.1 Zinc finger transcription factor ref-2 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001024478.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q7JNM3, Q8MTC7, Q94178

Conserved Domains (3) summary

COG5048
Location:150 → 227

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:154 → 174

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:139 → 163

zf-H2C2_2; Zinc-finger double domain
NM_001029306.4 → NP_001024477.1 Zinc finger transcription factor ref-2 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001024477.1

Status: REVIEWED

UniProtKB/TrEMBL

Q94178

Conserved Domains (3) summary

COG5048
Location:137 → 214

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:141 → 161

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:126 → 150

zf-H2C2_2; Zinc-finger double domain