ham-3 SWI/SNF chromatin-remodeling accessory subunit 1 [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: ham-3
Official Full Name: SWI/SNF chromatin-remodeling accessory subunit 1
Primary source: WormBase:WBGene00044072
Locus tag: CELE_ZK1128.5
See related: AllianceGenome:WB:WBGene00044072
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 factor binding activity; transcription coactivator activity; and transcription corepressor activity. Involved in determination of adult lifespan; negative regulation of transcription by RNA polymerase II; and positive regulation of transcription by RNA polymerase II. Located in nucleus. Is expressed in several structures, including excretory cell; intestine; nervous system; pharynx; and reproductive system. Used to study alcohol use disorder. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 11. Orthologous to human SMARCD1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1); SMARCD2 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2); and SMARCD3 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See ham-3 in Genome Data Viewer

Location:: chromosome: III

Exon count:: 6

Sequence:: Chromosome: III; NC_003281.10 (10120781..10122925)

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?

ham-3 and swsn-2.2 have redundant functions in germline and vulva development; Number of postembryonic intestinal nuclei is controlled by ham-3 and swsn-2.2; ham-3 and swsn-2.2 cooperate in embryonic development, but only swsn-2.2 is essential in the early embryo
Title: Functional Interplay of Two Paralogs Encoding SWI/SNF Chromatin-Remodeling Accessory Subunits During Caenorhabditis elegans Development.

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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

ZK1128.4 (e-PCR)
- UniSTS:308255

ZK1128.5 (e-PCR)
- UniSTS:306105

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISS Inferred from Sequence or Structural Similarity more info
enables transcription coactivator activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables transcription coregulator activity	IBA Inferred from Biological aspect of Ancestor more info
enables transcription corepressor activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in determination of adult lifespan	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	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 transcription by RNA polymerase II	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 regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of SWI/SNF complex	IBA Inferred from Biological aspect of Ancestor more info
part_of SWI/SNF complex	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	HDA 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

General protein information

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Preferred Names: SWI/SNF chromatin-remodeling accessory subunit 1

NP_499250.1

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

10120781..10122925

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_066849.6 → NP_499250.1 SWI/SNF chromatin-remodeling accessory subunit 1 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_499250.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q09646

Conserved Domains (1) summary

cl38907
Location:224 → 300

SWIB-MDM2; SWIB/MDM2 domain family