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 |
|---|---|---|---|---|---|---|---|---|
| 4028-YGR129W | YGR129W | SYF2 | NTC31 | Member of the NineTeen Complex (NTC); NTC contains Prp19p and stabilizes U6 snRNA in catalytic forms of the spliceosome containing U2, U5, and U6 snRNAs; relocalizes to the cytosol in response to hypoxia; isy1 syf2 cells have defective spindles activiating cell cycle arrest | Core | NA | NA | NA |
| 4029-YGR130C | YGR130C | NA | NA | Component of the eisosome with unknown function; GFP-fusion protein localizes to the cytoplasm; specifically phosphorylated in vitro by mammalian diphosphoinositol pentakisphosphate (IP7) | Core | NA | NA | NA |
| 4030-YGR131W | YGR131W | FHN1 | NA | Protein of unknown function; induced by ketoconazole; promoter region contains sterol regulatory element motif, which has been identified as a Upc2p-binding site; overexpression complements function of Nce102p in NCE102 deletion strain; FHN1 has a paralog, NCE102, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4031-YGR132C | YGR132C | PHB1 | prohibitin subunit PHB1 | Subunit of the prohibitin complex (Phb1p-Phb2p); prohibitin is a 1.2 MDa ring-shaped inner mitochondrial membrane chaperone that stabilizes newly synthesized proteins; determinant of replicative life span; involved in mitochondrial segregation; prohibitin deficiency induces a mitochondrial unfolded protein response (mtUPR) | Core | NA | NA | NA |
| 4032-YGR133W | YGR133W | PEX4 | E2 ubiquitin-protein ligase peroxin 4|UBC10|PAS2 | Peroxisomal ubiquitin conjugating enzyme; required for peroxisomal matrix protein import and peroxisome biogenesis | Core | NA | NA | NA |
| 4033-YGR134W | YGR134W | CAF130 | CCR4-NOT core subunit CAF130 | Subunit of the CCR4-NOT transcriptional regulatory complex; CCR4-NOT complex is evolutionarily-conserved and involved in controlling mRNA initiation, elongation, and degradation | Core | NA | NA | NA |
| 4034-YGR135W | YGR135W | PRE9 | proteasome core particle subunit alpha 3 | Alpha 3 subunit of the 20S proteasome; the only nonessential 20S subunit; may be replaced by the alpha 4 subunit (Pre6p) under stress conditions to create a more active proteasomal isoform | Core | NA | NA | NA |
| 4035-YGR136W | YGR136W | LSB1 | NA | Negative regulator of actin nucleation-promoting factor activity; interacts with Las17p, a homolog of human Wiskott-Aldrich Syndrome protein (WASP), via an N-terminal SH3 domain, and along with PIN3 cooperatively inhibits the nucleation of actin filaments; overexpression blocks receptor-mediated endocytosis; protein increases in abundance and forms nuclear foci in response to DNA replication stress; LSB1 has a paralog, PIN3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4036-YGR137W | YGR137W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 4037-YGR138C_NumOfGenes_2 | YGR138C | TPO2 | spermine transporter | Polyamine transporter of the major facilitator superfamily; member of the 12-spanner drug:H(+) antiporter DHA1 family; specific for spermine; localizes to the plasma membrane; transcription of TPO2 is regulated by Haa1p; TPO2 has a paralog, TPO3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4038-YGR139W | YGR139W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 4039-YGR140W | YGR140W | CBF2 | CSL5|NDC10|CTF14|CEP2|CBF3A | Essential kinetochore protein; component of the CBF3 multisubunit complex that binds to the CDEIII region of the centromere; Cbf2p also binds to the CDEII region possibly forming a different multimeric complex, ubiquitinated in vivo; sumoylated in an Mms21p-dependent manner; relative distribution to the spindle pole body decreases upon DNA replication stress | Core | NA | NA | NA |
| 4040-YGR141W | YGR141W | VPS62 | NA | Vacuolar protein sorting (VPS) protein; required for cytoplasm to vacuole targeting of proteins; VPS62 has a paralog, TDA6, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4041-YGR142W | YGR142W | BTN2 | NA | v-SNARE binding protein; facilitates specific protein retrieval from a late endosome to the Golgi; modulates arginine uptake, possible role in mediating pH homeostasis between the vacuole and plasma membrane H(+)-ATPase; contributes to prion curing; preferentially expressed after severe ethanol stress | Core | NA | NA | NA |
| 4042-YGR143W | YGR143W | SKN1 | beta-glucan synthesis-associated protein SKN1 | Protein involved in sphingolipid biosynthesis; type II membrane protein; SKN1 has a paralog, KRE6, that arose from the whole genome duplication | Core | NA | NA | NA |