chd-3 Chromodomain-helicase-DNA-binding protein 3 homolog [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: chd-3
Official Full Name: Chromodomain-helicase-DNA-binding protein 3 homolog
Primary source: WormBase:WBGene00000482
Locus tag: CELE_T14G8.1
See related: AllianceGenome:WB:WBGene00000482
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 several functions, including ATP hydrolysis activity; ATP-dependent activity, acting on DNA; and histone binding activity. Involved in cell fate determination; negative regulation of Ras protein signal transduction; and negative regulation of vulval development. Predicted to be located in chromatin. Predicted to be part of NuRD complex. Predicted to be active in nucleus. Is expressed in several structures, including distal tip cell; pharynx; ventral nerve cord; vulva; and vulval precursor cell. Human ortholog(s) of this gene implicated in Sifrim-Hitz-Weiss syndrome; colorectal cancer (multiple); lung cancer (multiple); and lymphoma. Orthologous to several human genes including CHD3 (chromodomain helicase DNA binding protein 3). [provided by Alliance of Genome Resources, Nov 2024]
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Genomic context

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See chd-3 in Genome Data Viewer

Location:: chromosome: X

Exon count:: 8

Sequence:: Chromosome: X; NC_003284.9 (12846439..12852601, 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?

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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

T14G8.1 (e-PCR)
- UniSTS:308035

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	ISS Inferred from Sequence or Structural Similarity more info
enables ATP-dependent chromatin remodeler activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATP-dependent chromatin remodeler activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent chromatin remodeler activity	ISS Inferred from Sequence or Structural Similarity more info
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	TAS Traceable Author Statement more info	PubMed
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA duplex unwinding	IEA Inferred from Electronic Annotation more info
involved_in cell fate determination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of Ras protein signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of vulval development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of NuRD complex	ISS Inferred from Sequence or Structural Similarity more info
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
part_of histone deacetylase complex	ISS Inferred from Sequence or Structural Similarity more info	PubMed
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

General protein information

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Preferred Names: Chromodomain-helicase-DNA-binding protein 3 homolog

NP_510140.1

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

12846439..12852601 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_077739.8 → NP_510140.1 Chromodomain-helicase-DNA-binding protein 3 homolog [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_510140.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q18794, Q22516

Conserved Domains (12) summary

smart00298
Location:501 → 555

CHROMO; Chromatin organization modifier domain

COG5034
Location:180 → 311

TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]

cd00024
Location:381 → 461

CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...

cd00046
Location:636 → 794

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd15531
Location:268 → 309

PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins

cd15532
Location:330 → 372

PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins

pfam00176
Location:619 → 915

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:940 → 1054

Helicase_C; Helicase conserved C-terminal domain

pfam06461
Location:1299 → 1418

DUF1086; Domain of Unknown Function (DUF1086)

pfam06465
Location:1199 → 1252

DUF1087; Domain of Unknown Function (DUF1087)

pfam08073
Location:97 → 149

CHDNT; CHDNT (NUC034) domain

pfam08074
Location:1511 → 1687

CHDCT2; CHDCT2 (NUC038) domain