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 |
|---|---|---|---|---|---|---|---|---|
| 5393-YKR100C | YKR100C | SKG1 | YKR099C-A | Transmembrane protein with a role in cell wall polymer composition; localizes on inner surface of plasma membrane at bud and in daughter cell; SKG1 has a paralog, AIM20, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5394-YKR101W | YKR101W | SIR1 | NA | Protein involved in silencing at mating-type loci HML and HMR; recruitment to silent chromatin requires interactions with Orc1p and with Sir4p, through a common Sir1p domain; binds to centromeric chromatin | Core | NA | NA | NA |
| 5395-YKR102W | YKR102W | FLO10 | NA | Member of the FLO family of cell wall flocculation proteins; not expressed in most lab strains; overproduction induces flocculation that can be inhibited by mannose, sucrose, or glucose; overproduction also promotes haploid invasive growth and diploid filamentous growth | Accessory | Ancestral | NA | NA |
| 5396-YKR103W | YKR103W | NFT1 | putative multidrug transporter NFT1 | Putative transporter of the MRP subfamily; adjacent ORFs YKR103W and YKR104W are merged in different strain backgrounds; MRP stands for multidrug resistance-associated protein | Accessory | Ancestral | NA | NA |
| 5397-YKR104W | YKR104W | NA | NFT1 | Putative transporter of the MRP subfamily; contains a stop codon in S288C; adjacent ORFs YKR103W and YKR104W are merged in different strain backgrounds; MRP stands for multidrug resistance-associated protein | Accessory | Ancestral | NA | NA |
| 5398-YKR105C_NumOfGenes_2 | YKR105C | VBA5 | basic amino acid transporter | Plasma membrane protein of the Major Facilitator Superfamily (MFS); involved in amino acid uptake and drug sensitivity; VBA5 has a paralog, VBA3, that arose from a segmental duplication | Accessory | Ancestral | NA | NA |
| 5399-YKR106W_NumOfGenes_2 | YKR106W | GEX2 | glutathione exchanger | Proton:glutathione antiporter; localized to the vacuolar and plasma membranes; expressed at a very low level; potential role in resistance to oxidative stress and modulation of the PKA pathway; GEX2 has a paralog, GEX1, that arose from a segmental duplication | Accessory | Ancestral | NA | NA |
| 5400-YLL001W | YLL001W | DNM1 | dynamin-related GTPase DNM1 | Dynamin-related GTPase involved in mitochondrial organization; required for mitochondrial fission and inheritance; self assembles on the cytoplasmic face of mitochondrial tubules at sites where division will occur; participates in endocytosis and regulates peroxisome fission along with Vps1p; mutants in the human ortholog DNM1L, which mediates mitochondrial fission, peroxisomal division, autophagy, and mitophagy, are associated with slowly progressive infantile encephalopathy | Core | NA | NA | NA |
| 5401-YLL002W | YLL002W | RTT109 | H3 histone acetyltransferase RTT109|KAT11|REM50|KIM2 | Histone acetyltransferase; critical for cell survival in presence of DNA damage during S phase, required for recovery after DSB repair; acetylates H3K56, H3K9; H3K56 acetylation activity required for expression homeostasis, buffering of mRNA synthesis rate against changes in gene dosage during S phase; involved in non-homologous end joining and regulation of Ty1 transposition; prevents hyper-amplification of rDNA; interacts physically with Vps75p | Core | NA | NA | NA |
| 5402-YLL003W | YLL003W | SFI1 | NA | Centrin (Cdc31p)-binding protein required for SPB duplication; localizes to the half-bridge of the spindle pole body (SPB); required for progression through G(2)-M transition; phosphorylated by Cdc28p-Clb2p and by Cdc5p; dephosphorylated by Cdc14p; has similarity to Xenopus laevis XCAP-C | Core | NA | NA | NA |
| 5403-YLL004W | YLL004W | ORC3 | origin recognition complex subunit 3 | Subunit of the origin recognition complex (ORC); ORC directs DNA replication by binding to replication origins and is also involved in transcriptional silencing | Core | NA | NA | NA |
| 5404-YLL005C | YLL005C | SPO75 | NA | Meiosis-specific protein of unknown function; required for spore wall formation during sporulation; dispensable for both nuclear divisions during meiosis | Core | NA | NA | NA |
| 5405-YLL006W | YLL006W | MMM1 | ERMES complex subunit MMM1|YME6 | ER integral membrane protein, ERMES complex subunit; ERMES links the ER to mitochondria and may promote inter-organellar calcium and phospholipid exchange as well as coordinating mitochondrial DNA replication and growth; required for mitophagy; ERMES complex is often co-localized with peroxisomes and with concentrated areas of pyruvate dehydrogenase | Core | NA | NA | NA |
| 5406-YLL006W-A | YLL006W-A | NA | NA | Putative protein of unknown function; identified by fungal homology and RT-PCR | Core | NA | NA | NA |
| 5407-YLL007C | YLL007C | LMO1 | NA | Homolog of mammalian ELMO (Engulfment and celL MOtility); upstream component for regulation through the small GTPase Rho5p; may form a complex with Dck1p that acts as a GEF for Rho5p; cytoplasmic protein that relocates to mitochondria under oxidative stress; implicated in mitophagy; not an essential protein | Core | NA | NA | NA |