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 |
|---|---|---|---|---|---|---|---|---|
| 4988-YJR083C | YJR083C | ACF4 | NA | Protein of unknown function; computational analysis of large-scale protein-protein interaction data suggests a possible role in actin cytoskeleton organization; potential Cdc28p substrate | Core | NA | NA | NA |
| 4989-YJR084W | YJR084W | NA | CSN12 | Protein that forms a complex with Thp3p; may have a role in transcription elongation and/or mRNA splicing; identified as a COP9 signalosome component but phenotype and interactions suggest it may not be involved with the signalosome | Core | NA | NA | NA |
| 4990-YJR085C | YJR085C | NA | NA | Protein of unknown function; GFP-fusion protein is induced in response to the DNA-damaging agent MMS; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4991-YJR086W | YJR086W | STE18 | NA | G protein gamma subunit; forms a dimer with Ste4p to activate the mating signaling pathway, forms a heterotrimer with Gpa1p and Ste4p to dampen signaling; C-terminus is palmitoylated and farnesylated, which are required for normal signaling | Core | NA | NA | NA |
| 4992-YJR087W | YJR087W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; not conserved in closely related Saccharomyces species; partially overlaps the verified genes STE18 and ECM2 | Accessory | Ancestral | NA | NA |
| 4993-YJR088C | YJR088C | EMC2 | NA | Member of conserved ER transmembrane complex; required for efficient folding of proteins in the ER; null mutant displays induction of the unfolded protein response; homologous to worm Y57G7A.10/EMC-2, fly CG17556, human TTC35 | Core | NA | NA | NA |
| 4994-YJR089W | YJR089W | BIR1 | NA | Subunit of chromosomal passenger complex (CPC); CPC is comprised of Ipl1p-Sli15p-Bir1p-Nbl1p and regulates chromosome segregation; required for chromosome bi-orientation and for spindle assembly checkpoint activation upon reduced sister kinetochore tension; relative distribution to shortened microtubules increases upon DNA replication stress; sumoylated in an Mms21p-dependent manner; human survivin homolog | Core | NA | NA | NA |
| 4995-YJR090C | YJR090C | GRR1 | SCF ubiquitin ligase complex subunit GRR1|SDC1|SSU2|COT2|CAT80 | F-box protein component of an SCF ubiquitin-ligase complex; modular substrate specificity factor which associates with core SCF (Cdc53p, Skp1p and Hrt1p/Rbx1p) to form the SCF(Grr1) complex; SCF(Grr1) acts as a ubiquitin-protein ligase directing ubiquitination of substrates such as: Gic2p, Mks1p, Mth1p, Cln1p, Cln2p and Cln3p; involved in carbon catabolite repression, glucose-dependent divalent cation transport, glucose transport, morphogenesis, and sulfite detoxification | Core | NA | NA | NA |
| 4996-YJR091C | YJR091C | JSN1 | PUF1 | Member of the Puf family of RNA-binding proteins; interacts with mRNAs encoding membrane-associated proteins; involved in localizing the Arp2/3 complex to mitochondria; overexpression causes increased sensitivity to benomyl; JSN1 has a paralog, PUF2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4997-YJR092W | YJR092W | BUD4 | NA | Anillin-like protein involved in bud-site selection; required for the axial budding pattern; required for the formation and disassembly of the double septin ring structure, and generally for septin organization; functions as a platform linking the cytokinesis tag septins to the axial landmark through its multiple domains; in vivo substrate of Cdc28p/Clb2p | Core | NA | NA | NA |
| 4998-YJR093C | YJR093C | FIP1 | cleavage polyadenylation factor subunit FIP1 | Subunit of cleavage polyadenylation factor (CPF); interacts directly with poly(A) polymerase (Pap1p) to regulate its activity; bridging factor that links Pap1p and the CPF complex via Yth1p | Core | NA | NA | NA |
| 4999-YJR094C | YJR094C | IME1 | transcription factor IME1 | Master regulator of meiosis that is active only during meiotic events; activates transcription of early meiotic genes through interaction with Ume6p; degraded by the 26S proteasome following phosphorylation by Ime2p; transcription is negatively regulated in cis by the IRT1 long noncoding antisense RNA | Core | NA | NA | NA |
| 5000-YJR094W-A | YJR094W-A | RPL43B | eL43|ribosomal 60S subunit protein L43B|L43e|L43B | Ribosomal 60S subunit protein L43B; homologous to mammalian ribosomal protein L37A, no bacterial homolog; RPL43B has a paralog, RPL43A, that arose from the whole genome duplication; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5001-YJR095W | YJR095W | SFC1 | ACR1 | Mitochondrial succinate-fumarate transporter; transports succinate into and fumarate out of the mitochondrion; required for ethanol and acetate utilization | Core | NA | NA | NA |
| 5002-YJR096W | YJR096W | NA | aldo-keto reductase superfamily protein | Xylose and arabinose reductase; member of the aldo-keto reductase (AKR) family; GFP-fusion protein is induced in response to the DNA-damaging agent MMS | Core | NA | NA | NA |