RAT5 Histone superfamily protein [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: RAT5
Official Full Name: Histone superfamily protein
Primary source: TAIR:AT5G54640
Locus tag: AT5G54640
See related: Araport:AT5G54640
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: ATHTA1; histone H2A 1; HTA1; MRB17.14; MRB17_14; RESISTANT TO AGROBACTERIUM TRANSFORMATION 5
Summary: Isolated from T-DNA insertion line, the rat5 mutant is deficient in T-DNA integration. Encodes histone2A protein.
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Genomic context

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See RAT5 in Genome Data Viewer

Location:: chromosome: 5

Exon count:: 2

Sequence:: Chromosome: 5; NC_003076.8 (22196287..22197492)

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?

Clustered pathways are characterized by distinct chromatin signatures of H3K27me3 and H2A.Z, associated with cluster repression and activation, respectively, and represent discrete windows of co-regulation in the genome.
Title: Delineation of metabolic gene clusters in plant genomes by chromatin signatures.
Mutation of HTA1, the gene encoding histone H2A-1, results in decreased T-DNA integration into the genome of Arabidopsis roots, whereas overexpression of HTA1 increases transformation frequency.
Title: Overexpression of several Arabidopsis histone genes increases agrobacterium-mediated transformation and transgene expression in plants.
Data suggest that, with respect to Agrobacterium-mediated transformation, all Arabidopsis histone H2A proteins are functionally redundant.
Title: Constitutive expression exposes functional redundancy between the Arabidopsis histone H2A gene HTA1 and other H2A gene family members.

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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_124845.4

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	IEA Inferred from Electronic Annotation more info
enables structural constituent of chromatin	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA-mediated transformation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to bacterium	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within response to wounding	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
located_in nucleolus	HDA more info	PubMed
located_in nucleus	ISM Inferred from Sequence Model more info
located_in plastid	HDA more info	PubMed

General protein information

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Preferred Names: Histone superfamily protein

NP_200275.1

RESISTANT TO AGROBACTERIUM TRANSFORMATION 5 (RAT5); FUNCTIONS IN: DNA binding; INVOLVED IN: DNA mediated transformation, response to bacterium, response to wounding; LOCATED IN: nucleolus; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Histone H2A (InterPro:IPR002119), Histone-fold (InterPro:IPR009072), Histone core (InterPro:IPR007125); BEST Arabidopsis thaliana protein match is: histone H2A 2 (TAIR:AT4G27230.2); Has 1807 Blast hits to 1807 proteins in 277 species: Archae - 0; Bacteria - 0; Metazoa - 736; Fungi - 347; Plants - 385; Viruses - 0; Other Eukaryotes - 339 (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

22196287..22197492

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_124845.4 → NP_200275.1 Histone superfamily protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_200275.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q9LD28

UniProtKB/TrEMBL

A0A178UIB7, A0A5S9YE54

Conserved Domains (1) summary

PLN00157
Location:1 → 130

PLN00157; histone H2A; Provisional