UAP56a DEAD/DEAH box RNA helicase family protein [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: UAP56a
Official Full Name: DEAD/DEAH box RNA helicase family protein
Primary source: TAIR:AT5G11170
Locus tag: AT5G11170
See related: Araport:AT5G11170
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: F2I11.60; F2I11_60; homolog of human UAP56 a
Summary: One of two genes encoding an ATP-dependent RNA helicase that localizes predominantly to euchromatic regions of Arabidopsis nuclei, and associates with genes transcribed by RNA polymerase II independently from the presence of introns. It is not detected at non-transcribed loci. It interacts with ssRNA, dsRNA and dsDNA, but not with ssDNA. Its ATPase activity is stimulated by RNA and dsDNA and its ATP-dependent RNA helicase activity unwinds dsRNA but not dsDNA.
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Genomic context

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See UAP56a in Genome Data Viewer

Location:: chromosome: 5

Exon count:: 12

Sequence:: Chromosome: 5; NC_003076.8 (3553096..3557018)

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?

The authors identified DEAD box RNA helicases U2AF56 Associated Protein 56 (UAP56a/b) as new DRM2 partners. They have shown that, similar to DRM2 and other RdDM actors, UAP56 has chromatin-associated protein properties.
Title: UAP56 associates with DRM2 and is localized to chromatin in Arabidopsis.
The DEAD-box proteins UAP56a and UAP56b displays ATPase activity that is stimulated by RNA and dsDNA and it has ATP-dependent RNA helicase activity unwinding dsRNA, whereas it does not unwind dsDNA.
Title: Arabidopsis DEAD-box RNA helicase UAP56 interacts with both RNA and DNA as well as with mRNA export factors.

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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_001343160.1

Supported by ESTs:

NM_121155.4

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables ATP hydrolysis activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA helicase activity	IDA Inferred from Direct Assay more info	PubMed
enables double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables double-stranded RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
NOT enables single-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables single-stranded RNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in regulation of photomorphogenesis	IPI Inferred from Physical Interaction more info	PubMed
acts_upstream_of_or_within response to cadmium ion	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
located_in cytosol	HDA more info	PubMed
NOT located_in cytosol	RCA inferred from Reviewed Computational Analysis more info	PubMed
located_in nucleolus	HDA 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: DEAD/DEAH box RNA helicase family protein

NP_001318536.1

DEAD/DEAH box RNA helicase family protein; FUNCTIONS IN: helicase activity, ATP-dependent helicase activity, ATP binding, nucleic acid binding; INVOLVED IN: response to cadmium ion; LOCATED IN: nucleolus; EXPRESSED IN: guard cell, root, cultured cell; CONTAINS InterPro DOMAIN/s: DNA/RNA helicase, DEAD/DEAH box type, N-terminal (InterPro:IPR011545), DEAD-like helicase, N-terminal (InterPro:IPR014001), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021); BEST Arabidopsis thaliana protein match is: DEAD/DEAH box RNA helicase family protein (TAIR:AT5G11200.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink).

NP_568244.2

DEAD/DEAH box RNA helicase family protein; FUNCTIONS IN: helicase activity, ATP-dependent helicase activity, nucleic acid binding, ATP binding; INVOLVED IN: response to cadmium ion; LOCATED IN: nucleolus; EXPRESSED IN: guard cell, root, cultured cell; CONTAINS InterPro DOMAIN/s: DNA/RNA helicase, DEAD/DEAH box type, N-terminal (InterPro:IPR011545), RNA helicase, DEAD-box type, Q motif (InterPro:IPR014014), DEAD-like helicase, N-terminal (InterPro:IPR014001), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021); BEST Arabidopsis thaliana protein match is: DEAD/DEAH box RNA helicase family protein (TAIR:AT5G11200.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (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

3553096..3557018

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001343160.1 → NP_001318536.1 DEAD/DEAH box RNA helicase family protein [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

F4JWF3
NM_121155.4 → NP_568244.2 DEAD/DEAH box RNA helicase family protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_568244.2

Status: REVIEWED

UniProtKB/Swiss-Prot

C0Z3C4, Q0WWC6, Q3E9I7, Q56XG6, Q56YP8, Q93VJ8, Q9LFN6, Q9LFN9, Q9ZS06

UniProtKB/TrEMBL

A0A178UKF1, A0A5S9Y3I6, A0A7G2FDU7

Conserved Domains (2) summary

cd18787
Location:263 → 392

SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases

cd17950
Location:45 → 252

DEADc_DDX39; DEAD-box helicase domain of DEAD box protein 39