Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
A searchable table of the S. cerevisiae pangenome ORFs defined in Peter et al. (2018) Nature (LINK) is provided below. The listed core/accessory classification and origin assignment are based on the original study. Click on the PanORF ID to find out the detailed presence/absence pattern of the corresponding pangenome ORF in both ScRAPdb and the 1002ScGP strain collections (which were recalculated by ScRAPdb).
| PanORF ID | SGD systematic Name | SGD standard name | Alias | Description | Type | Origin assignment | Mostly likely origin species | NCBI megablast hit |
|---|---|---|---|---|---|---|---|---|
| 6668-YNL281W | YNL281W | HCH1 | NA | Heat shock protein regulator; binds to Hsp90p and may stimulate ATPase activity; originally identified as a high-copy number suppressor of a HSP90 loss-of-function mutation; role in regulating Hsp90 inhibitor drug sensitivity; GFP-fusion protein localizes to the cytoplasm and nucleus; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 6669-YNL282W | YNL282W | POP3 | NA | Subunit of both RNase MRP and nuclear RNase P; RNase MRP cleaves pre-rRNA, while nuclear RNase P cleaves tRNA precursors to generate mature 5' ends and facilitates turnover of nuclear RNAs; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 6670-YNL283C | YNL283C | WSC2 | STA3 | Sensor-transducer of the stress-activated PKC1-MPK1 signaling pathway; involved in maintenance of cell wall integrity and recovery from heat shock; required for the arrest of secretion response; WSC2 has a paralog, WSC3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6671-YNL284C | YNL284C | MRPL10 | mitochondrial 54S ribosomal protein YmL10/YmL18|YmL10|YmL18|MRPL18 | Mitochondrial ribosomal protein of the large subunit; appears as two protein spots (YmL10 and YmL18) on two-dimensional SDS gels | Core | NA | NA | NA |
| 6672-YNL285W | YNL285W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 6673-YNL286W | YNL286W | CUS2 | U2 snRNP complex subunit CUS2 | Putative checkpoint factor in transcription; binds to U2 snRNA and Prp11p; regulates toggling of the U2 snRNA stem II region between different structures; contains two RNA recognition motifs (RRMs) | Core | NA | NA | NA |
| 6674-YNL287W | YNL287W | SEC21 | coatomer subunit gamma | Gamma subunit of coatomer; coatomer is a heptameric protein complex that together with Arf1p forms the COPI coat; involved in ER to Golgi transport of selective cargo | Core | NA | NA | NA |
| 6675-YNL288W | YNL288W | CAF40 | CCR4-NOT core subunit CAF40 | Component of the CCR4-NOT transcriptional complex; evolutionarily conserved; involved in controlling mRNA initiation, elongation, and degradation; binds Cdc39p | Core | NA | NA | NA |
| 6676-YNL289W | YNL289W | PCL1 | HCS26 | Cyclin, interacts with cyclin-dependent kinase Pho85p; member of the Pcl1,2-like subfamily, involved in the regulation of polarized growth and morphogenesis and progression through the cell cycle; is ubiquitinated by Dma1p; phosphorylation by Pho85p targets it for degradation; localizes to sites of polarized cell growth | Core | NA | NA | NA |
| 6677-YNL290W | YNL290W | RFC3 | replication factor C subunit 3 | Subunit of heteropentameric Replication factor C (RF-C); which is a DNA binding protein and ATPase that acts as a clamp loader of the proliferating cell nuclear antigen (PCNA) processivity factor for DNA polymerases delta and epsilon; relocalizes to the cytosol in response to hypoxia | Core | NA | NA | NA |
| 6678-YNL291C | YNL291C | MID1 | NA | N-glycosylated integral membrane protein of the ER and plasma membrane; functions as a stretch-activated Ca2+-permeable cation channel required for Ca2+ influx stimulated by pheromone; interacts with Cch1p; forms an oligomer | Core | NA | NA | NA |
| 6679-YNL292W | YNL292W | PUS4 | pseudouridine synthase PUS4 | Pseudouridine synthase; catalyzes only the formation of pseudouridine-55 (Psi55), a highly conserved tRNA modification, in mitochondrial and cytoplasmic tRNAs; also responsible for pseudouracil modification of some mRNAs; PUS4 overexpression leads to translational derepression of GCN4 (Gcd- phenotype) | Core | NA | NA | NA |
| 6680-YNL293W | YNL293W | MSB3 | Rab GTPase-activating protein MSB3|GYP3 | Rab GTPase-activating protein; regulates endocytosis via inactivation of Vps21p at endosomes and vacuole fusion via inactivation of Ypt7p at vacuoles; also acts on Ypt52p and Sec4p; localizes to plasma membrane, sites of polarized growth; relocalizes from bud neck to cytoplasm upon DNA replication stress; similar to TBC-domain Tre2 oncogene; MSB3 has a paralog, MSB4, that arose from the whole genome duplication; human homolog USP6NL can complement yeast msb3 msb4 double null | Core | NA | NA | NA |
| 6681-YNL294C | YNL294C | RIM21 | PAL2 | pH sensor molecule, component of the RIM101 pathway; has a role in cell wall construction and alkaline pH response; is glycosylated and phosphorylated; interacts with Dfg16p and Rim9p to form a pH-sensing complex; localization to the plasma membrane is dependent on Dfg16p and Rim9p; has similarity to A. nidulans PalH | Core | NA | NA | NA |
| 6682-YNL295W | YNL295W | MRX6 | NA | Protein that associates with mitochondrial ribosome | Core | NA | NA | NA |