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 |
|---|---|---|---|---|---|---|---|---|
| 4643-YIL159W | YIL159W | BNR1 | formin BNR1 | Formin; nucleates the formation of linear actin filaments; involved in processes such as budding and mitotic spindle orientation which require the formation of polarized actin cables; activity is regulated by Hof1p and by the Bud14p-Kel1p-Kel2p complex; dephosphorylated and delocalized from the division site in a Glc7p/Ref2p-dependent manner; functionally redundant with BNI1 | Accessory | Ancestral | NA | NA |
| 4644-YIL160C | YIL160C | POT1 | acetyl-CoA C-acyltransferase|POX3|FOX3 | 3-ketoacyl-CoA thiolase with broad chain length specificity; cleaves 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA during beta-oxidation of fatty acids | Accessory | Ancestral | NA | NA |
| 4645-YIL161W | YIL161W | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; mRNA is enriched in Scp160p-associated mRNPs; YIL161W is a non-essential gene | Accessory | Ancestral | NA | NA |
| 4646-YIL162W | YIL162W | SUC2 | beta-fructofuranosidase SUC2 | Invertase; sucrose hydrolyzing enzyme; a secreted, glycosylated form is regulated by glucose repression, and an intracellular, nonglycosylated enzyme is produced constitutively | Accessory | Ancestral | NA | NA |
| 4647-YIL163C | YIL163C | NA | NA | Protein of unknown function; mRNA identified as translated by ribosome profiling data | Accessory | Ancestral | NA | NA |
| 4648-YIL164C | YIL164C | NIT1 | NA | Nitrilase; member of the nitrilase branch of the nitrilase superfamily; in closely related species and other S. cerevisiae strain backgrounds YIL164C and adjacent ORF, YIL165C, likely constitute a single ORF encoding a nitrilase gene | Accessory | Ancestral | NA | NA |
| 4649-YIL165C | YIL165C | NA | NA | Putative protein of unknown function; mutant exhibits mitophagy defects; in closely related species and other S. cerevisiae strain backgrounds YIL165C and adjacent ORF, YIL164C, likely constitute a single ORF encoding a nitrilase gene | Accessory | Ancestral | NA | NA |
| 4650-YIL166C | YIL166C | NA | NA | Putative protein with similarity to allantoate permease; similar to the allantoate permease (Dal5p) subfamily of the major facilitator superfamily; mRNA expression is elevated by sulfur limitation; YIL166C is a non-essential gene | Accessory | Ancestral | NA | NA |
| 4651-YIL167W | YIL167W | SDL1 | YIL168W | Blocked reading frame otherwise encoding L-serine dehydratase | Accessory | Ancestral | NA | NA |
| 4652-YIL169C_NumOfGenes_2 | YIL169C | CSS1 | HPF1' | Protein of unknown function, secreted when constitutively expressed; SWAT-GFP, seamless-GFP and mCherry fusion proteins localize to the cell periphery, SWAT-GFP fusion also localizes to the extracellular region, and mCherry fusion also localizes to the vacuole; S/T rich and highly similar to YOL155C, a putative glucan alpha-1,4-glucosidase; transcript is induced in both high and low pH environments; non-essential gene | Accessory | Ancestral | NA | NA |
| 4653-YIL171W | YIL171W | NA | HXT12 | Possible pseudogene in strain S288C; YIL171W and the adjacent ORF, YIL170W/HXT12, together encode a non-functional member of the hexose transporter family | Accessory | Ancestral | NA | NA |
| 4654-YIL172C_NumOfGenes_6 | YIL172C | IMA3 | oligo-1,6-glucosidase IMA3 | Alpha-glucosidase; weak, but broad substrate specificity for alpha-1,4- and alpha-1,6-glucosides; member of IMA isomaltase family; not required for isomaltose utilization, but Ima3p overexpression allows the ima1 null mutant to grow on isomaltose; lower activitiy and thermostability in vitro than Ima2p despite sequence difference of only 3 amino acids; cleaves alpha-1,3 linkage of nigerose and turanose, but not alpha-1,5 of leucrose; identical to IMA4 | Accessory | Ancestral | NA | NA |
| 4655-YIR001C | YIR001C | SGN1 | RBP29|RBP1 | Cytoplasmic RNA-binding protein; contains an RNA recognition motif (RRM); may have a role in mRNA translation, as suggested by genetic interactions with genes encoding proteins involved in translational initiation | Core | NA | NA | NA |
| 4656-YIR002C | YIR002C | MPH1 | 3'-5' DNA helicase | 3'-5' DNA helicase involved in error-free bypass of DNA lesions; binds flap DNA, stimulates activity of Rad27p and Dna2p; prevents crossovers between ectopic sequences by removing substrates for Mus81-Mms4 or Rad1-Rad10 cleavage; homolog of human FANCM Fanconi anemia protein that is involved in stabilizing and remodeling blocked replication forks; member of SF2 DExD/H superfamily of helicases; nonsense or missense mutations in FANCM can make people more likely to get cancer | Core | NA | NA | NA |
| 4657-YIR003W | YIR003W | AIM21 | NA | Protein of unknown function; involved in mitochondrial migration along actin filament; may interact with ribosomes; GFP-fusion protein colocalizes with Sac1p to the actin cytoskeleton | Core | NA | NA | NA |