SWN SET domain-containing protein [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: SWN
Official Full Name: SET domain-containing protein
Primary source: TAIR:AT4G02020
Locus tag: AT4G02020
See related: Araport:AT4G02020
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Arabidopsis thaliana (ecotype: Columbia)
Lineage: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Also known as: EZA1; SDG10; SET DOMAIN-CONTAINING PROTEIN 10; SWINGER; T10M13.3; T10M13_3
Summary: Encodes a polycomb group protein. Forms part of a large protein complex that can include VRN2 (VERNALIZATION 2), VIN3 (VERNALIZATION INSENSITIVE 3) and polycomb group proteins FERTILIZATION INDEPENDENT ENDOSPERM (FIE) and CURLY LEAF (CLF). The complex has a role in establishing FLC (FLOWERING LOCUS C) repression during vernalization. Performs a partially redundant role to MEA in controlling seed initiation by helping to suppress central cell nucleus#endosperm proliferation within the FG.
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Genomic context

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See SWN in Genome Data Viewer

Location:: chromosome: 4

Exon count:: 17

Sequence:: Chromosome: 4; NC_003075.7 (886580..891987)

Chromosome 4 - NC_003075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003075.7

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The complexity of PRC2 catalysts CLF and SWN in plants.
Title: The complexity of PRC2 catalysts CLF and SWN in plants.
expression of embryo development genes is repressed by PRC1-catalytic core subunits AtBMI1 and AtRING1 in common with PRC2-catalytic enzymes CLF or SWINGER (SWN).
Title: Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements.
MEA and SWN are SET-domain partners of FIS2 and perform partially redundant functions in controlling the initiation of endosperm development before fertilization in Arabidopsis. [SWINGER] [SWN]
Title: Partially redundant functions of two SET-domain polycomb-group proteins in controlling initiation of seed development in Arabidopsis.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

NM_001340355.1

Supported by ESTs:

NM_001340356.1

Supported by ESTs:

NM_001340357.1

Supported by ESTs:

NM_116433.3

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables histone H3 acetyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables histone H3K27 trimethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables single-stranded RNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within callus formation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within endosperm development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within epigenetic programming in the endosperm	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of gene expression, epigenetic	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of leaf senescence	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within response to abscisic acid	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within vernalization response	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of PcG protein complex	IEA Inferred from Electronic Annotation more info
part_of chromatin silencing complex	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISM Inferred from Sequence Model more info
located_in plasmodesma	HDA more info	PubMed

General protein information

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Preferred Names: SET domain-containing protein

NP_567221.1

SWINGER (SWN); CONTAINS InterPro DOMAIN/s: SANT, DNA-binding (InterPro:IPR001005), SET domain (InterPro:IPR001214); BEST Arabidopsis thaliana protein match is: SET domain-containing protein (TAIR:AT2G23380.1); Has 5041 Blast hits to 4734 proteins in 465 species: Archae - 0; Bacteria - 399; Metazoa - 2132; Fungi - 472; Plants - 1030; Viruses - 0; Other Eukaryotes - 1008 (source: NCBI BLink).

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_003075.7 Reference assembly

Range

886580..891987

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_116433.3 → NP_567221.1 SET domain-containing protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_567221.1

Status: REVIEWED

UniProtKB/Swiss-Prot

O04246, Q9ZSM8

UniProtKB/TrEMBL

A0A5S9XQX2, A0A654FL26, A0A7G2EXT4

Conserved Domains (3) summary

cd00167
Location:492 → 536

SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...

cd10519
Location:707 → 823

SET_EZH; SET domain found in enhancer of zeste homolog 1 (EZH1), zeste homolog 2 (EZH2) and similar proteins

pfam18264
Location:646 → 677

preSET_CXC; CXC domain
NM_001340355.1 → NP_001328437.1 SET domain-containing protein [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A1P8B4N3, A0A7G2EXT4

Conserved Domains (3) summary

cd00167
Location:492 → 536

SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...

cl40432
Location:707 → 768

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

pfam18264
Location:646 → 677

preSET_CXC; CXC domain
NM_001340356.1 → NP_001328436.1 SET domain-containing protein [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A1P8B4N3, A0A7G2EXT4

Conserved Domains (3) summary

cd00167
Location:492 → 536

SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...

cl40432
Location:707 → 768

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

pfam18264
Location:646 → 677

preSET_CXC; CXC domain
NM_001340357.1 → NP_001328435.1 SET domain-containing protein [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A1P8B4N2, A0A7G2EXT4