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 |
|---|---|---|---|---|---|---|---|---|
| 3173-YDR485C | YDR485C | VPS72 | SWC2 | Htz1p-binding component of the SWR1 complex; exchanges histone variant H2AZ (Htz1p) for chromatin-bound histone H2A; may function as a lock that prevents removal of H2AZ from nucleosomes; required for vacuolar protein sorting | Core | NA | NA | NA |
| 3174-YDR486C | YDR486C | VPS60 | CHM5|MOS10 | Protein involved in late endosome to vacuole transport; cytoplasmic and vacuolar membrane protein; required for normal filament maturation during pseudohyphal growth; may function in targeting cargo proteins for degradation; interacts with Vta1p | Core | NA | NA | NA |
| 3175-YDR487C | YDR487C | RIB3 | 3,4-dihydroxy-2-butanone-4-phosphate synthase RIB3 | 3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBP synthase); required for riboflavin biosynthesis from ribulose-5-phosphate, also has an unrelated function in mitochondrial respiration | Core | NA | NA | NA |
| 3176-YDR488C | YDR488C | PAC11 | dynein intermediate chain | Dynein intermediate chain, microtubule motor protein; required for intracellular transport and cell division; acts in cytoplasmic dynein pathway; forms complex with dynein light chain Dyn2p that promotes Dyn1p homodimerization and potentiates motor processivity; Dyn2p-Pac11p complex is also important for interaction of dynein motor complex with dynactin complex; forms cortical cytoplasmic microtubule capture site with Num1p; essential in the absence of CIN8 | Core | NA | NA | NA |
| 3177-YDR489W | YDR489W | SLD5 | DNA replication protein SLD5|CDC105 | Subunit of the GINS complex (Sld5p, Psf1p, Psf2p, Psf3p); complex is localized to DNA replication origins and implicated in assembly of the DNA replication machinery | Core | NA | NA | NA |
| 3178-YDR490C | YDR490C | PKH1 | serine/threonine protein kinase PKH1 | Serine/threonine protein kinase; involved in sphingolipid-mediated signaling pathway that controls endocytosis; activates Ypk1p and Ykr2p, components of signaling cascade required for maintenance of cell wall integrity; contains a PH-like domain; redundant with Pkh2p; PKH1 has a paralog, PKH2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3179-YDR491C | YDR491C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 3180-YDR492W | YDR492W | IZH1 | PAQR-type receptor | Membrane protein involved in zinc ion homeostasis; member of the four-protein IZH family; transcription is regulated directly by Zap1p, expression induced by zinc deficiency and fatty acids; deletion increases sensitivity to elevated zinc; IZH1 has a paralog, IZH4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3181-YDR493W | YDR493W | MZM1 | AIM8|FMP36 | Protein required for assembly of the cytochrome bc(1) complex; acts as a chaperone for Rip1p and facilitates its insertion into the complex at a late stage of assembly; localized to the mitochondrial matrix; null mutant exhibits a respiratory growth defect and reduced mitochondrial zinc levels, which is characteristic of mutations affecting bc(1) complex assembly; member of the LYR protein family; human LYRM7 is a functional ortholog | Core | NA | NA | NA |
| 3182-YDR494W | YDR494W | RSM28 | mitochondrial 37S ribosomal protein RSM28 | Mitochondrial ribosomal protein of the small subunit; genetic interactions suggest a possible role in promoting translation initiation | Core | NA | NA | NA |
| 3183-YDR495C | YDR495C | VPS3 | CORVET complex subunit VPS3|VPT17|VPL3|PEP6 | Component of CORVET membrane tethering complex; cytoplasmic protein required for the sorting and processing of soluble vacuolar proteins, acidification of the vacuolar lumen, and assembly of the vacuolar H+-ATPase | Core | NA | NA | NA |
| 3184-YDR496C | YDR496C | PUF6 | NA | Pumilio-homology domain protein; binds the 3' UTR of ASH1 mRNA and represses its translation, resulting in proper asymmetric localization of ASH1 mRNA; required at post-transcriptional step for efficient retrotransposition; absence results in decreased Ty1 Gag:GFP protein levels; co-sediments with the 60S ribosomal subunit and is required for its biogenesis | Core | NA | NA | NA |
| 3185-YDR497C | YDR497C | ITR1 | myo-inositol transporter ITR1 | Myo-inositol transporter; member of the sugar transporter superfamily; expression is repressed by inositol and choline via Opi1p and derepressed via Ino2p and Ino4p; relative distribution to the vacuole increases upon DNA replication stress; ITR1 has a paralog, ITR2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3186-YDR498C | YDR498C | SEC20 | NA | Membrane glycoprotein v-SNARE; involved in retrograde transport from the Golgi to the endoplasmic reticulum (ER); required for N- and O-glycosylation in the Golgi but not in the ER and for efficient nuclear fusion during mating; mediates Sey1p-independent homotypic ER fusion; interacts with the Dsl1p complex through Tip20p | Core | NA | NA | NA |
| 3187-YDR499W | YDR499W | LCD1 | PIE1|DDC2 | Essential protein required for the DNA integrity checkpoint pathways; interacts physically with Mec1p; putative homolog of S. pombe Rad26 and human ATRIP; forms nuclear foci upon DNA replication stress | Core | NA | NA | NA |