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

Summary

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Official Symbol: RTR1
Official Full Name: RNA polymerase II subunit B1 CTD phosphatase RTR1
Primary source: SGD:S000000941
Locus tag: YER139C
See related: AllianceGenome:SGD:S000000941; FungiDB:YER139C; 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 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, Dec 2024]
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Genomic context

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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

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Go to reference sequence details

Genomic Sequence:: NC_001137.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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.

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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 MAP kinase serine/threonine phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity	IEA Inferred from Electronic Annotation more info
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 calmodulin-dependent protein phosphatase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AXS140 phosphatase activity	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 chromatin remodeling	IEA Inferred from Electronic Annotation more info
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

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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

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_001137.3 Reference assembly

Range

450563..451243 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001179029.3 → NP_011066.3 TPA: RNA polymerase II subunit B1 CTD phosphatase RTR1 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_011066.3

Status: REVIEWED

UniProtKB/Swiss-Prot

D3DM46, P40084

UniProtKB/TrEMBL

A6ZR96, B3LRQ2, B5VHR4, C7GQ57, C8Z7F9, G2WD26, N1P3M0

Conserved Domains (1) summary

pfam04181
Location:53 → 128

RPAP2_Rtr1; Rtr1/RPAP2 family