PRP16 / YKR086W Overview


Standard Name
PRP16 1
Systematic Name
YKR086W
SGD ID
SGD:S000001794
Aliases
PRP23 4 8 , RNA16 9
Feature Type
ORF , Verified
Description
DEAH-box RNA helicase; involved in the second catalytic step of splicing and in exon ligation; exhibits ATP-dependent RNA unwinding activity; mediates the release of Yju2p and Cwc25p in the second step; in the absence of ATP, stabilizes the binding of Cwc25p to the spliceosome in the first catalytic step; missense mutation in human ortholog DHX38 associated with early-onset retinitis pigmentosa 2 3 5 6 7
Name Description
Pre-mRNA Processing 4
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.


Summary
PRP16 is located on the right arm of chromosome XI between MRPL20 mitochondrial ribosomal protein and OMA1 mitochondrial metalloendopeptidase; coding sequence is 3216 nucleotides long with 24 SNPs, 6 of which cause amino acid polymorphisms
Protein Details

Protein

Basic sequence-derived (length, molecular weight, isoelectric point) and experimentally-determined (median abundance, median absolute deviation) protein information. Click "Protein Details" for further information about the protein such as half-life, abundance, domains, domains shared with other proteins, protein sequence retrieval for various strains, physico-chemical properties, protein modification sites, and external identifiers for the protein.


Summary
Prp16p is 1071 amino acids long, low in abundance; contains DEAD/DEAH box helicase domain and DEAD-box helicase OB fold; phosphorylated on S108 and S143
Length (a.a.)
1071
Mol. Weight (Da)
121660.8
Isoelectric Point
8.37
Median Abundance (molecules/cell)
810 +/- 172

Alleles

Curated mutant alleles for the specified gene, listed alphabetically. Click on the allele name to open the allele page. Click "SGD search" to view all alleles in search results. Click "YeastMine" to view all alleles in YeastMine.


View all PRP16 alleles in SGD search | YeastMine

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.


Summary
Subunit of the U2-type catalytic step 2 spliceosome; ATP-dependent RNA helicase that contributes to generation of catalytic spliceosome for the second transesterification step of mRNA splicing; also involved in small nuclear RNA (snRNA) metabolism

View computational annotations

Molecular Function

Manually Curated

Biological Process

Manually Curated

Cellular Component

Manually Curated
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.


Summary
Essential gene; mutants have extremely short or undetectable spindles, accumulate unspliced pre-mRNA; heterozygous null is haploinsufficient, shows decreased starvation resistance; conditional alleles grow poorly, are sensitive to cold
Disease Details

Disease

Disease Annotations consist of three mandatory components: a gene product, a term from the Disease Ontology (DO) controlled vocabulary and an evidence code. SGD provides manually curated DO Annotations derived from the literature. Click "Disease Details" to view all Disease information and evidence for this locus as well as diseases it shares with other genes.


Summary
PRP16 is orthologous to human DHX38 and has been used to study retinitis pigmentosa

Manually Curated

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.


Summary
Prp16p interacts physically with proteins involved in mRNA processing; PRP16 interacts genetically with genes involved mitotic cell cycle

442 total interactions for 341 unique genes

Physical Interactions

  • Affinity Capture-MS: 46
  • Affinity Capture-RNA: 4
  • Affinity Capture-Western: 4
  • Co-fractionation: 1
  • Co-localization: 1
  • Reconstituted Complex: 1
  • Two-hybrid: 4

Genetic Interactions

  • Dosage Lethality: 2
  • Dosage Rescue: 2
  • Negative Genetic: 294
  • Phenotypic Enhancement: 1
  • Positive Genetic: 49
  • Synthetic Growth Defect: 8
  • Synthetic Lethality: 22
  • Synthetic Rescue: 3
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.


Summary
PRP16 promoter is bound by Yap1p in response to heat
Regulators
1
Targets
0
Expression Details

Expression

Expression data are derived from records contained in the Gene Expression Omnibus (GEO), and are first log2 transformed and normalized. Referenced datasets may contain one or more condition(s), and as a result there may be a greater number of conditions than datasets represented in a single clickable histogram bar. The histogram division at 0.0 separates the down-regulated (green) conditions and datasets from those that are up-regulated (red). Click "Expression Details" to view all expression annotations and details for this locus, including a visualization of genes that share a similar expression pattern.


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
38
Additional
69
Reviews
19

Resources