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Ribosomes are highly conserved large ribonucleoprotein (RNP) particles, consisting in yeast of a large 60S subunit and a small 40S subunit, that perform protein synthesis. Yeast ribosomes contain one copy each of four ribosomal RNAs (5S, 5.8S, 18S, and 25S; produced in two separate transcripts encoded within the rDNA repeat present as hundreds of copies on Chromosome 12) and 79 different ribosomal proteins (r-proteins), which are encoded by 137 different genes scattered about the genome, 59 of which are duplicated (1, 2). The 60S subunit contains 46 proteins and three RNA molecules: 25S RNA of 3392 nt, hydrogen bonded to the 5.8S RNA of 158 nt and associated with the 5S RNA of 121 nt. The 40S subunit has a single 18S RNA of 1798 nt and 33 proteins (5, 2). All yeast ribosomal proteins have a mammalian homolog (6).

In a rapidly growing yeast cell, 60% of total transcription is devoted to ribosomal RNA, and 50% of RNA polymerase II transcription and 90% of mRNA splicing are devoted to the production of mRNAs for r-proteins. Coordinate regulation of the rRNA genes and 137 r-protein genes is affected by nutritional cues and a number of signal transduction pathways that can abruptly induce or silence the ribosomal genes, whose transcripts have naturally short lifetimes, leading to major implications for the expression of other genes as well (8, 10, 12). The expression of some r-protein genes is influenced by Abf1p (13), and most are directly induced by binding of Rap1p to their promoters, which excludes nucleosomes and recruits Fhl1p and Ifh1p to drive transcription (14).

Ribosome assembly is a complex process, with different steps occurring in different parts of the cell. Ribosomal protein genes are transcribed in the nucleus, and the mRNA is transported to the cytoplasm for translation. The newly synthesized r-proteins then enter the nucleus and associate in the nucleolus with the two rRNA transcripts, one of which is methylated and pseudouridylated (view sites of modifications), and then cleaved into three individual rRNAs (18S, 5.8S, and 25S) as part of the assembly process (1). Separate ribosomal subunits are then transported from the nucleolus to the cytoplasm where they assemble into mature ribosomes before functioning in translation (15, 16). Blockage of subunit assembly, such as due to inhibition of rRNA synthesis or processing, results in degradation of newly synthesized r-proteins (17, 16). (For more information on the early steps of rRNA processing and small ribosomal subunit assembly, see the summary paragraph for the U3 snoRNA, encoded by snR17A and snR17B.)", "date_edited": "2007-02-14"}, "literature_overview": {"primary_count": 24, "additional_count": 78, "review_count": 24, "go_count": 0, "phenotype_count": 0, "disease_count": 0, "interaction_count": 11, "regulation_count": 0, "ptm_count": 0, "funComplement_count": 0, "htp_count": 0, "total_count": 135}, "disease_overview": {"manual_disease_terms": [], "htp_disease_terms": [], "computational_annotation_count": 0, "date_last_reviewed": null}, "ecnumbers": [], "URS_ID": "URS00004BEF81", "main_strain": "S288C", "regulation_overview": {"regulator_count": 0, "target_count": 0}, "reference_mapping": {"592595": 1, "397935": 2, "626936": 3, "596957": 4, "517471": 5, "556638": 6, "545514": 7, "631529": 8, "589235": 9, "554134": 10, "544893": 11, "585697": 12, "608664": 13, "518051": 14, "592541": 15, "508692": 16, "508689": 17}, "history": [{"category": "Name", "history_type": "LSP", "note": "Name: RDN37", "date_created": "2010-02-16", "references": []}, {"category": "Name", "history_type": "LSP", "note": "Name: RDN37-2", "date_created": "2000-05-19", "references": []}, {"category": "Mapping", "history_type": "SEQUENCE", "note": "Mapping: There are 2 copies of RDN37 in the systematic sequence.", "date_created": "2003-12-09", "references": []}], "complexes": []}, tabs: {"id": 1286889, "protein_tab": false, "interaction_tab": true, "summary_tab": true, "go_tab": true, "sequence_section": true, "expression_tab": false, "phenotype_tab": true, "literature_tab": true, "wiki_tab": false, "regulation_tab": true, "sequence_tab": true, "history_tab": true, "homology_tab": false, "disease_tab": false} }; RDN37-2 | SGD

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RDN37-2 / YNCL0020C Overview

Standard Name
RDN37-2
Systematic Name
YNCL0020C
SGD ID
SGD:S000006487
Aliases
RDN37
Feature Type
rRNA gene
Description
35S ribosomal RNA (35S rRNA) transcript; encoded by the RDN1 locus; processed into the 25S, 18S and 5.8S rRNAs (represented by the RDN25, RDN18, and RDN58 loci) 1
RNAcentral ID
URS00004BEF81
Secondary Structure
Comparative Info
Sequence Details

Sequence

The S. cerevisiae Reference Genome sequence is derived from laboratory strain S288C. Download DNA or protein sequence, view genomic context and coordinates. Click "Sequence Details" to view all sequence information for this locus, including that for other strains.

Analyze Sequence

S288C only

BLASTN | Design Primers | Restriction Fragment Map | Restriction Fragment Sizes

S288C vs. other species

BLASTN vs. fungi

Gene Ontology Details

Gene Ontology

GO Annotations consist of four mandatory components: a gene product, a term from one of the three Gene Ontology (GO) controlled vocabularies (Molecular Function, Biological Process, and Cellular Component), a reference, and an evidence code. SGD has manually curated and high-throughput GO Annotations, both derived from the literature, as well as computational, or predicted, annotations. Click "Gene Ontology Details" to view all GO information and evidence for this locus as well as biological processes it shares with other genes.

No Gene Ontology data available.

Phenotype Details

Phenotype

Phenotype annotations for a gene are curated single mutant phenotypes that require an observable (e.g., "cell shape"), a qualifier (e.g., "abnormal"), a mutant type (e.g., null), strain background, and a reference. In addition, annotations are classified as classical genetics or high-throughput (e.g., large scale survey, systematic mutation set). Whenever possible, allele information and additional details are provided. Click "Phenotype Details" to view all phenotype annotations and evidence for this locus as well as phenotypes it shares with other genes.

No phenotype data available.

Interaction Details

Interaction

Interaction annotations are curated by BioGRID and include physical or genetic interactions observed between at least two genes. An interaction annotation is composed of the interaction type, name of the interactor, assay type (e.g., Two-Hybrid), annotation type (e.g., manual or high-throughput), and a reference, as well as other experimental details. Click "Interaction Details" to view all interaction annotations and evidence for this locus, including an interaction visualization.

26 total interactions for 26 unique genes

Physical Interactions

  • Affinity Capture-RNA: 20
  • Co-fractionation: 1
  • Protein-RNA: 5
Regulation Details

Regulation

The number of putative Regulators (genes that regulate it) and Targets (genes it regulates) for the given locus, based on experimental evidence. This evidence includes data generated through high-throughput techniques. Click "Regulation Details" to view all regulation annotations, shared GO enrichment among regulation Targets, and a regulator/target diagram for the locus.

No regulation data available.

Summary Paragraph

A summary of the locus, written by SGD Biocurators following a thorough review of the literature. Links to gene names and curated GO terms are included within the Summary Paragraphs.

Last Updated: 2007-02-14

Literature Details

Literature

All manually curated literature for the specified gene, organized into topics according to their relevance to the gene (Primary Literature, Additional Literature, or Review). Click "Literature Details" to view all literature information for this locus, including shared literature between genes.

Primary
24
Additional
78
Reviews
24

Resources

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