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 |
|---|---|---|---|---|---|---|---|---|
| 3458-YER128W | YER128W | VFA1 | NA | Protein that interacts with Vps4p and has a role in vacuolar sorting; stimulates the ATPase activity of Vps4; localizes to endosomes in a Vps4-dependent manner; overexpression causes canavanine sensitivity and confers a partial class D vacuole morphology | Core | NA | NA | NA |
| 3459-YER129W | YER129W | SAK1 | serine/threonine protein kinase SAK1|PAK1 | Upstream serine/threonine kinase for the SNF1 complex; plays a role in pseudohyphal groth; partially redundant with Elm1p and Tos3p; members of this family have functional orthology with LKB1, a mammalian kinase associated with Peutz-Jeghers cancer-susceptibility syndrome; SAK1 has a paralog, TOS3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3460-YER130C | YER130C | COM2 | NA | Transcription factor that binds IME1 Upstream Activation Signal (UAS)ru; COM2 transcription is regulated by Haa1p, Sok2p and Zap1p transcriptional activators; may bind the IME1 promoter under all growth conditions to negatively regulate its transcription in the absence of a positive regulator that binds more effectively; repressor activity may depend on phosphorylation by PKA; C. albicans homolog (MNL1) plays a role in adaptation to stress | Core | NA | NA | NA |
| 3461-YER131W | YER131W | RPS26B | eS26|ribosomal 40S subunit protein S26B|S26e|S26B | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S26, no bacterial homolog; RPS26B has a paralog, RPS26A, that arose from the whole genome duplication; human homolog can partially complement an RPS26A, RPS26B double null mutant; mutations in the human gene are associated with Diamond-Blackfan anemia | Core | NA | NA | NA |
| 3462-YER132C | YER132C | PMD1 | NA | Protein with an N-terminal kelch-like domain; putative negative regulator of early meiotic gene expression; required, with Mds3p, for growth under alkaline conditions; PMD1 has a paralog, MDS3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3463-YER133W | YER133W | GLC7 | type 1 serine/threonine-protein phosphatase catalytic subunit GLC7|DIS2S1|PP1|DIS2|CID1 | Type 1 S/T protein phosphatase (PP1) catalytic subunit; involved in glycogen metabolism, sporulation and mitotic progression; interacts with multiple regulatory subunits; regulates actomyosin ring formation; subunit of CPF; recruited to mating projections by Afr1p interaction; regulates nucleocytoplasmic shuttling of Hxk2p; import into the nucleus is inhibited during spindle assembly checkpoint arrest; involved in dephosphorylating Rps6a/b and Bnr1p | Core | NA | NA | NA |
| 3464-YER134C_NumOfGenes_2 | YER134C | NA | Mg-dependent acid phosphatase|MDP-1 | Magnesium-dependent acid phosphatase; member of the haloacid dehalogenase superfamily; non-essential gene | Accessory | Ancestral | NA | NA |
| 3465-YER135C | YER135C | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YER135C is not an essential gene | Accessory | Unknown | NA | NA |
| 3466-YER136W | YER136W | GDI1 | SEC19 | GDP dissociation inhibitor; regulates vesicle traffic in secretory pathways by regulating the dissociation of GDP from the Sec4/Ypt/rab family of GTP binding proteins | Core | NA | NA | NA |
| 3467-YER137C_NumOfGenes_2 | YER137C | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 3468-YER139C | YER139C | RTR1 | RNA polymerase II subunit B1 CTD phosphatase RTR1 | CTD phosphatase; dephosphorylates S5-P in the C-terminal domain of Rpo21p; has a cysteine-rich motif required for function and conserved in eukaryotes; shuttles between the nucleus and cytoplasm; RTR1 has a paralog, RTR2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3469-YER140W | YER140W | EMP65 | NA | Integral membrane protein of the ER; forms an ER-membrane associated protein complex with Slp1p; identified along with SLP1 in a screen for mutants defective in the unfolded protein response (UPR); proposed to function in the folding of integral membrane proteins; interacts genetically with MPS3; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Core | NA | NA | NA |
| 3470-YER141W | YER141W | COX15 | NA | Protein required for the hydroxylation of heme O to form heme A; heme A is an essential prosthetic group for cytochrome c oxidase | Core | NA | NA | NA |
| 3471-YER142C | YER142C | MAG1 | MMS5 | 3-methyl-adenine DNA glycosylase; involved in protecting DNA against alkylating agents; initiates base excision repair by removing damaged bases to create abasic sites that are subsequently repaired; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 3472-YER143W | YER143W | DDI1 | VSM1 | DNA damage-inducible v-SNARE binding protein; role in suppression of protein secretion; may play a role in S-phase checkpoint control; has ubiquitin-associated (UBA), ubiquitin-like (UBL), and retroviral-like proteinase (RVP) domains | Core | NA | NA | NA |