CHC1 SWIB/MDM2 domain superfamily protein [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: CHC1
Official Full Name: SWIB/MDM2 domain superfamily protein
Primary source: TAIR:AT5G14170
Locus tag: AT5G14170
See related: Araport:AT5G14170
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: BAF60; MUA22.17; MUA22_17
Summary: CHC1 is predicted to encode a protein that belongs to the chromodomain remodeling complex. Two RNAi knock-down lines have a dwarf phenotype and reduced rates of Agrobacterium-mediated transformation. The low rate of root-mediated transformation rate may result from altered root morphology or reduced root growth rates.
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Genomic context

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See CHC1 in Genome Data Viewer

Location:: chromosome: 5

Exon count:: 3

Sequence:: Chromosome: 5; NC_003076.8 (4568480..4570994, complement)

Chromosome 5 - NC_003076.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003076.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

BAF60 binds nucleosome-free regions of multiple G box-containing genes, opposing in cis the promoting effect of the photomorphogenic and thermomorphogenic regulator Phytochrome Interacting Factor 4 (PIF4) on hypocotyl elongation. Furthermore, BAF60 expression level is regulated in response to light and daily rhythms.
Title: The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility.
BAF60 creates a repressive chromatin configuration at the FLC locus.[BAF60]
Title: The BAF60 subunit of the SWI/SNF chromatin-remodeling complex directly controls the formation of a gene loop at FLOWERING LOCUS C 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_121421.4

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA repair	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of flower development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of leaf development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to UV-B	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within root development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISM Inferred from Sequence Model more info

General protein information

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Preferred Names: SWIB/MDM2 domain superfamily protein

NP_196921.1

CHC1; CONTAINS InterPro DOMAIN/s: SWIB/MDM2 domain (InterPro:IPR003121); BEST Arabidopsis thaliana protein match is: SWIB/MDM2 domain superfamily protein (TAIR:AT3G01890.1); Has 1254 Blast hits to 1169 proteins in 258 species: Archae - 0; Bacteria - 112; Metazoa - 460; Fungi - 424; Plants - 177; Viruses - 4; Other Eukaryotes - 77 (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_003076.8 Reference assembly

Range

4568480..4570994 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_121421.4 → NP_196921.1 SWIB/MDM2 domain superfamily protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_196921.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q9FMT4

UniProtKB/TrEMBL

A0A178UDN5, A0A5S9Y4C4

Conserved Domains (1) summary

pfam02201
Location:317 → 389

SWIB; SWIB/MDM2 domain