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 |
|---|---|---|---|---|---|---|---|---|
| 4013-YGR114C | YGR114C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; open reading frame overlaps 5' end of the essential gene SPT6 | Accessory | Ancestral | NA | NA |
| 4014-YGR116W_NumOfGenes_2 | YGR116W | SPT6 | chromatin-remodeling histone chaperone SPT6|SSN20|CRE2 | Nucleosome remodeling protein; functions in various aspects of transcription, chromatin maintenance, and RNA processing; required for the maintenance of chromatin structure during transcription in order to inhibit transcription from promoters within the coding region; required for H3K36 trimethylation but not dimethylation by Set2p | Core | NA | NA | NA |
| 4015-YGR117C | YGR117C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm | Core | NA | NA | NA |
| 4016-YGR118W | YGR118W | RPS23A | uS12|ribosomal 40S subunit protein S23A|rp37|YS14|S28A|S23A|S12 | Ribosomal protein 28 (rp28) of the small (40S) ribosomal subunit; required for translational accuracy; homologous to mammalian ribosomal protein S23 and bacterial S12; RPS23A has a paralog, RPS23B, that arose from the whole genome duplication; deletion of both RPS23A and RPS23B is lethal | Core | NA | NA | NA |
| 4017-YGR119C | YGR119C | NUP57 | FG-nucleoporin NUP57 | FG-nucleoporin component of central core of the nuclear pore complex; contributes directly to nucleocytoplasmic transport and maintenance of the nuclear pore complex (NPC) permeability barrier; found in stable complex with Nic96p and two other FG-nucleoproteins (Nsp1p and Nup49p) | Core | NA | NA | NA |
| 4018-YGR120C | YGR120C | COG2 | Golgi transport complex subunit COG2|SEC35 | Essential component of the conserved oligomeric Golgi complex; a cytosolic tethering complex that functions in protein trafficking to mediate fusion of transport vesicles to Golgi compartments; the components of the Golgi complex are Gog1p through Cog8p | Core | NA | NA | NA |
| 4019-YGR121C | YGR121C | MEP1 | ammonium permease MEP1|AMT1 | Ammonium permease; belongs to a ubiquitous family of cytoplasmic membrane proteins that transport only ammonium (NH4+); expression is under the nitrogen catabolite repression regulation; human homolog RHCG complements yeast null mutant; mutations in human homolog RHCG implicated in metabolic acidosis; MEP1 has a paralog, MEP3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4020-YGR121W-A | YGR121W-A | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 4021-YGR122W | YGR122W | NA | NA | Protein that may be involved in pH regulation; probable ortholog of A. nidulans PalC, which is involved in pH regulation and binds to the ESCRT-III complex; null mutant does not properly process Rim101p and has decreased resistance to rapamycin; GFP-fusion protein is cytoplasmic; relative distribution to cytoplasm increases upon DNA replication stress | Core | NA | NA | NA |
| 4022-YGR123C | YGR123C | PPT1 | protein serine/threonine phosphatase | Protein serine/threonine phosphatase; regulates Hsp90 chaperone by affecting its ATPase and cochaperone binding activities; has similarity to human phosphatase PP5; present in both the nucleus and cytoplasm; expressed during logarithmic growth | Accessory | Ancestral | NA | NA |
| 4023-YGR124W | YGR124W | ASN2 | asparagine synthase (glutamine-hydrolyzing) 2 | Asparagine synthetase; catalyzes the synthesis of L-asparagine from L-aspartate in the asparagine biosynthetic pathway; ASN2 has a paralog, ASN1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4024-YGR125W | YGR125W | NA | NA | Putative protein of unknown function; deletion mutant has decreased rapamycin resistance but normal wormannin resistance; green fluorescent protein (GFP)-fusion protein localizes to the vacuole | Core | NA | NA | NA |
| 4025-YGR126W | YGR126W | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus and is induced in response to the DNA-damaging agent MMS | Core | NA | NA | NA |
| 4026-YGR127W | YGR127W | NA | NA | Putative protein of unknown function; expression is regulated by Msn2p/Msn4p, indicating a possible role in stress response | Core | NA | NA | NA |
| 4027-YGR128C | YGR128C | UTP8 | NA | Nucleolar protein required for export of tRNAs from the nucleus; also copurifies with the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA | Core | NA | NA | NA |