ncl-1 B box-type domain-containing protein;B-box type zinc finger protein ncl-1;RING-type E3 ubiquitin transferase [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: ncl-1
Official Full Name: B box-type domain-containing protein;B-box type zinc finger protein ncl-1;RING-type E3 ubiquitin transferase
Primary source: WormBase:WBGene00003559
Locus tag: CELE_ZK112.2
See related: AllianceGenome:WB:WBGene00003559
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 translation repressor activity. Involved in several processes, including negative regulation of DNA-templated transcription; negative regulation of ribosome biogenesis; and nucleologenesis. Located in cytoplasm. Is expressed in several structures, including anal depressor muscle; head; intestine; pharynx; and tail. Orthologous to human TRIM3 (tripartite motif containing 3). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See ncl-1 in Genome Data Viewer

Location:: chromosome: III

Exon count:: 12

Sequence:: Chromosome: III; NC_003281.10 (7719729..7738105)

Chromosome III - NC_003281.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003281.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

NCL-1 extends lifespan and limits nucleolar size in the major C. elegans longevity pathways, as part of a convergent mechanism focused on the nucleolus.
Title: Small nucleoli are a cellular hallmark of longevity.
NCL-1 suppressed the translation of FIB-1/fibrillarin, while let-7 targeted the 3'UTR of ncl-1 and inhibited its expression. Consequently, the abundance of FIB-1 is tightly controlled and correlated with the nucleolar size
Title: A Genetic Cascade of let-7-ncl-1-fib-1 Modulates Nucleolar Size and rRNA Pool in Caenorhabditis 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

ZK112.4 (e-PCR)
- UniSTS:316267

ZK112.2 (e-PCR)
- UniSTS:310410

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables transferase activity	IEA Inferred from Electronic Annotation more info
enables translation repressor activity	IBA Inferred from Biological aspect of Ancestor more info
enables translation repressor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in negative regulation of ribosome biogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase I	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase III	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of translation	IBA Inferred from Biological aspect of Ancestor more info
involved_in nucleologenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein localization to cell cortex	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of establishment of cell polarity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of translation	IEA Inferred from Electronic Annotation more info
involved_in ribosome biogenesis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: B box-type domain-containing protein;B-box type zinc finger protein ncl-1;RING-type E3 ubiquitin transferase

NP_001299852.1

Confirmed by transcript evidence

NP_001299853.1

Confirmed by transcript evidence

NP_001299924.1

Confirmed by transcript evidence

NP_001299926.1

Confirmed by transcript evidence

NP_001299927.1

Confirmed by transcript evidence

NP_001299928.1

Confirmed by transcript evidence

NP_001368538.1

Confirmed by transcript evidence

NP_001379611.1

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_003281.10 Reference assembly

Range

7719729..7738105

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001312923.3 → NP_001299852.1 RING-type E3 ubiquitin transferase [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A0K3AX41

Conserved Domains (4) summary

smart00502
Location:396 → 522

BBC; B-Box C-terminal domain

smart00336
Location:346 → 389

BBOX; B-Box-type zinc finger

cd00162
Location:87 → 131

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

cd14959
Location:694 → 964

NHL_brat_like; NHL repeat domain of the Drosophila brain-tumor protein (brat) and similar proteins
NM_001312924.2 → NP_001299853.1 RING-type E3 ubiquitin transferase [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A0K3ARS2

Conserved Domains (4) summary

smart00502
Location:399 → 525

BBC; B-Box C-terminal domain

smart00336
Location:349 → 392

BBOX; B-Box-type zinc finger

cd00162
Location:87 → 131

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

cd14959
Location:697 → 967

NHL_brat_like; NHL repeat domain of the Drosophila brain-tumor protein (brat) and similar proteins
NM_001312995.3 → NP_001299924.1 RING-type E3 ubiquitin transferase [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A0K3AUA6

Conserved Domains (4) summary

smart00502
Location:387 → 513

BBC; B-Box C-terminal domain

smart00336
Location:337 → 380

BBOX; B-Box-type zinc finger

cd00162
Location:75 → 119

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

cd14959
Location:685 → 955

NHL_brat_like; NHL repeat domain of the Drosophila brain-tumor protein (brat) and similar proteins
NM_001379801.1 → NP_001368538.1 RING-type E3 ubiquitin transferase [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A0K3ARF3

Conserved Domains (6) summary

smart00502
Location:384 → 510

BBC; B-Box C-terminal domain

cd14959
Location:682 → 952

NHL_brat_like; NHL repeat domain of the Drosophila brain-tumor protein (brat) and similar proteins

TIGR00599
Location:75 → 181

rad18; DNA repair protein rad18

cd19798
Location:334 → 377

Bbox2_BRAT-like; B-box-type 2 zinc finger found in Drosophila melanogaster brain tumor protein (BRAT) and similar proteins

cd19813
Location:247 → 290

Bbox1_BRAT-like; B-box-type 1 zinc finger found in Drosophila melanogaster brain tumor protein (BRAT) and similar proteins

cl17238
Location:75 → 119

RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
NM_001392143.1 → NP_001379611.1 B-box type zinc finger protein ncl-1 [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/Swiss-Prot

P34611

Conserved Domains (4) summary

smart00502
Location:268 → 394

BBC; B-Box C-terminal domain

cd14959
Location:566 → 836

NHL_brat_like; NHL repeat domain of the Drosophila brain-tumor protein (brat) and similar proteins

cd19798
Location:218 → 261

Bbox2_BRAT-like; B-box-type 2 zinc finger found in Drosophila melanogaster brain tumor protein (BRAT) and similar proteins

cd19813
Location:131 → 174

Bbox1_BRAT-like; B-box-type 1 zinc finger found in Drosophila melanogaster brain tumor protein (BRAT) and similar proteins
NM_001312997.3 → NP_001299926.1 RING-type E3 ubiquitin transferase [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A0K3AUY6

Conserved Domains (4) summary

smart00502
Location:333 → 459

BBC; B-Box C-terminal domain

smart00336
Location:283 → 326

BBOX; B-Box-type zinc finger

cd00162
Location:21 → 65

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

cd14959
Location:631 → 901

NHL_brat_like; NHL repeat domain of the Drosophila brain-tumor protein (brat) and similar proteins
NM_001312998.3 → NP_001299927.1 RING-type E3 ubiquitin transferase [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A0K3AXB1

Conserved Domains (4) summary

smart00502
Location:330 → 456

BBC; B-Box C-terminal domain

smart00336
Location:280 → 323

BBOX; B-Box-type zinc finger

cd00162
Location:21 → 65

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

cd14959
Location:628 → 898

NHL_brat_like; NHL repeat domain of the Drosophila brain-tumor protein (brat) and similar proteins
NM_001312999.3 → NP_001299928.1 B box-type domain-containing protein [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A0K3AS01

Conserved Domains (3) summary

smart00502
Location:271 → 397

BBC; B-Box C-terminal domain

smart00336
Location:221 → 264

BBOX; B-Box-type zinc finger

cd14959
Location:569 → 839

NHL_brat_like; NHL repeat domain of the Drosophila brain-tumor protein (brat) and similar proteins