RTR1 RNA polymerase II subunit B1 CTD phosphatase RTR1 [Saccharomyces cerevisiae S288C] - Gene

Summary

Go to the top of the page Help

Gene symbol: RTR1
Gene description: RNA polymerase II subunit B1 CTD phosphatase RTR1
Primary source: FungiDB:YER139C
Locus tag: YER139C
See related: SGD:S000000941; AllianceGenome:SGD:S000000941; VEuPathDB:YER139C
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Summary: Enables RNA polymerase II CTD heptapeptide repeat phosphatase activity. Involved in dephosphorylation of RNA polymerase II C-terminal domain and transcription by RNA polymerase II. Located in cytoplasm and nucleus. Orthologous to human RPAP2 (RNA polymerase II associated protein 2). [provided by Alliance of Genome Resources, Apr 2022]
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help

See RTR1 in Genome Data Viewer

Location:: chromosome: V

Exon count:: 1

Sequence:: Chromosome: V; NC_001137.3 (450563..451243, complement)

Chromosome V - NC_001137.3 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:: NC_001137.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Rtr1 is required for Rpb1-Rpb2 assembly of RNAPII and prevents their cytoplasmic clump formation.
Title: Rtr1 is required for Rpb1-Rpb2 assembly of RNAPII and prevents their cytoplasmic clump formation.
Findings show that Rtr1 is a global regulator of the C-terminal domain (CTD) code with deletion of RTR1 causing genome-wide changes in Ser5-P CTD phosphorylation and cotranscriptional histone H3 lysine 36 trimethylation.
Title: Phosphatase Rtr1 Regulates Global Levels of Serine 5 RNA Polymerase II C-Terminal Domain Phosphorylation and Cotranscriptional Histone Methylation.
Data indicate that the structure of the phosphoryl transfer domain and reaction mechanism for the phosphoryl transfer activity of regulator of transcription 1 (Rtr1) is distinct from those of other phosphatase families.
Title: Structure of Saccharomyces cerevisiae Rtr1 reveals an active site for an atypical phosphatase.
Rtr1p may imprint its RNA targets cotranscriptionally and determine their downstream degradation mechanism by directing these transcripts to a novel turnover pathway that involves Rtr1p, Dhh1p, and the REX family of exonucleases.
Title: The Rtr1p CTD phosphatase autoregulates its mRNA through a degradation pathway involving the REX exonucleases.
Studies revealed that hyperphosphorylated RNAPII is the primary interacting partner for Rtr1.
Title: The interactome of the atypical phosphatase Rtr1 in Saccharomyces cerevisiae.
Rtr1 functions as a CTD phosphatase essential for the Serine5-to-Serine2-Phosphorylation transition.
Title: Rtr1 is a CTD phosphatase that regulates RNA polymerase II during the transition from serine 5 to serine 2 phosphorylation.
YER139C encodes the closest yeast homolog of the human RPAP2 protein, recently identified as a novel RNA polymerase II (RNAPII)-associated factor.
Title: Rtr1 is the Saccharomyces cerevisiae homolog of a novel family of RNA polymerase II-binding proteins.

Submit: New GeneRIF Correction

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables RNA polymerase II CTD heptapeptide repeat phosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II CTD heptapeptide repeat phosphatase activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II CTD heptapeptide repeat phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase core enzyme binding	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables myosin phosphatase activity	IEA Inferred from Electronic Annotation more info
enables phosphoprotein phosphatase activity	IEA Inferred from Electronic Annotation more info
enables protein serine/threonine phosphatase activity	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	RCA inferred from Reviewed Computational Analysis more info	PubMed

Process	Evidence Code	Pubs
involved_in regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
involved_in transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transcription by RNA polymerase II	IPI Inferred from Physical Interaction more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	HDA more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

Go to the top of the page Help

Preferred Names: RNA polymerase II subunit B1 CTD phosphatase RTR1

NP_011066.3

EC 3.1.3.16

Dual specificity protein phosphatase; dephosphorylates T1 and S5 in C-terminal domain (CTD) of RNA polymerase II largest subunit, Rpo21p; autoregulates turnover of its mRNA; has a cysteine-rich motif required for function and conserved in eukaryotes; shuttles between the nucleus and cytoplasm; RTR1 has a paralog, RTR2, that arose from the whole genome duplication