YRA1 RNA-binding protein YRA1 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: YRA1
Official Full Name: RNA-binding protein YRA1
Primary source: SGD:S000002789
Locus tag: YDR381W
See related: AllianceGenome:SGD:S000002789; FungiDB:YDR381W; VEuPathDB:YDR381W
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Also known as: SHE11
Summary: Enables DNA/RNA hybrid binding activity; RNA binding activity; and RNA helicase inhibitor activity. Involved in mRNA export from nucleus and transcription-coupled nucleotide-excision repair. Part of transcription export complex. Orthologous to human ALYREF (Aly/REF export factor). [provided by Alliance of Genome Resources, Jan 2025]
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Genomic context

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See YRA1 in Genome Data Viewer

Location:: chromosome: IV

Exon count:: 2

Sequence:: Chromosome: IV; NC_001136.10 (1236558..1238004)

Chromosome IV - NC_001136.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001136.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Single-molecule quantitation of RNA-binding protein occupancy and stoichiometry defines a role for Yra1 (Aly/REF) in nuclear mRNP organization.
Title: Single-molecule quantitation of RNA-binding protein occupancy and stoichiometry defines a role for Yra1 (Aly/REF) in nuclear mRNP organization.
the data provide evidence that Yra1 plays a crucial role in DSB repair via homologous recombination. While Yra1 sumoylation and/or ubiquitination are dispensable, the Yra1 C-box region is essential in this process.
Title: The mRNA export adaptor Yra1 contributes to DNA double-strand break repair through its C-box domain.
Yra1 binds RNA-DNA hybrids in vitro and, when artificially overexpressed, can be recruited to chromatin in an RNA-DNA hybrid-dependent manner, stabilizing R loops and converting them into replication obstacles in vivo
Title: Yra1-bound RNA-DNA hybrids cause orientation-independent transcription-replication collisions and telomere instability.
Both THO and Yra1-C stimulated Sub2's intrinsic ATPase activity. The authors propose that THO surveys common landmarks in each nuclear mRNP to localize Sub2 for targeted loading of Yra1.
Title: Structural and biochemical analyses of the DEAD-box ATPase Sub2 in association with THO or Yra1.
YRA1 overexpression causes a cell senescence-like phenotype and telomere shortening
Title: Excess of Yra1 RNA-Binding Factor Causes Transcription-Dependent Genome Instability, Replication Impairment and Telomere Shortening.
These data show that Yra1 inhibits unwinding in a concentration-dependent manner by preventing the association of Dbp2 with single-stranded RNA.
Title: Recruitment, Duplex Unwinding and Protein-Mediated Inhibition of the Dead-Box RNA Helicase Dbp2 at Actively Transcribed Chromatin.
the phospho-CTD is likely involved directly in the cotranscriptional recruitment of Yra1.
Title: Cotranscriptional association of mRNA export factor Yra1 with C-terminal domain of RNA polymerase II.
Data indicate that Edc3p-mediated YRA1 pre-mRNA decay occurs independently of translation and also requires Mex67p.
Title: Degradation of YRA1 Pre-mRNA in the cytoplasm requires translational repression, multiple modular intronic elements, Edc3p, and Mex67p.
Yra1 binds directly to the Zn finger/Clp1 region of Pcf11, the pol II CTD-binding subunit of CF1A.
Title: Cotranscriptional recruitment of the mRNA export factor Yra1 by direct interaction with the 3' end processing factor Pcf11.
Nap1 interacts directly with Yra1. The recruitment of Nap1 to the coding region of actively transcribed genes is Yra1 dependent.
Title: Nap1 links transcription elongation, chromatin assembly, and messenger RNP complex biogenesis.

Submit: New GeneRIF Correction See all GeneRIFs (14)

Pathways from PubChem

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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

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables DNA/RNA hybrid binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA helicase inhibitor activity	IDA Inferred from Direct Assay more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in mRNA export from nucleus	IGI Inferred from Genetic Interaction more info	PubMed
involved_in transcription-coupled nucleotide-excision repair	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of transcription export complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: RNA-binding protein YRA1

NP_010669.1

Nuclear polyadenylated RNA-binding protein; required for export of poly(A)+ mRNA from the nucleus; proposed to couple mRNA export with 3' end processing via its interactions with Mex67p and Pcf11p; interacts with DBP2; inhibits the helicase activity of Dbp2; functionally redundant with Yra2p, another REF family member

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_001136.10 Reference assembly

Range

1236558..1238004

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001180689.1 → NP_010669.1 TPA: RNA-binding protein YRA1 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_010669.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VT14, Q12159

UniProtKB/TrEMBL

A6ZYY1, B3LFS0, C8Z5U5, G2WBC0

Conserved Domains (2) summary

COG0724
Location:1 → 226

RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

cd12267
Location:78 → 156

RRM_YRA1_MLO3; RNA recognition motif (RRM) found in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins