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 |
|---|---|---|---|---|---|---|---|---|
| 4343-YHR087W | YHR087W | RTC3 | HGI1 | Protein of unknown function involved in RNA metabolism; has structural similarity to SBDS, the human protein mutated in Shwachman-Diamond Syndrome (the yeast SBDS ortholog = SDO1); null mutation suppresses cdc13-1 temperature sensitivity; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4344-YHR088W | YHR088W | RPF1 | rRNA-binding ribosome biosynthesis protein RPF1 | Protein involved in assembly and export of the large ribosomal subunit; nucleolar protein; constituent of 66S pre-ribosomal particles; contains a sigma(70)-like motif, which is thought to bind RNA | Core | NA | NA | NA |
| 4345-YHR089C | YHR089C | GAR1 | H/ACA snoRNP pseudouridylase subunit GAR1 | Protein component of the H/ACA snoRNP pseudouridylase complex; involved in the modification and cleavage of the 18S pre-rRNA | Core | NA | NA | NA |
| 4346-YHR090C | YHR090C | YNG2 | histone acetyltransferase YNG2|EAF4|NBN1 | Subunit of NuA4, an essential histone acetyltransferase complex; positions Piccolo NuA4 for efficient acetylation of histone H4 or histone H2A; relocalizes to the cytosol in response to hypoxia; similar to human tumor suppressor ING1 and its isoforms ING4 and ING5 | Core | NA | NA | NA |
| 4347-YHR091C | YHR091C | MSR1 | arginine--tRNA ligase MSR1 | Mitochondrial arginyl-tRNA synthetase; mutations in human ortholog are associated with pontocerebellar hypoplasia type 6; MSR1 has a paralog, YDR341C, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4348-YHR092C_NumOfGenes_2 | YHR092C | HXT4 | hexose transporter HXT4|RAG1|LGT1 | High-affinity glucose transporter; member of the major facilitator superfamily, expression is induced by low levels of glucose and repressed by high levels of glucose; HXT4 has a paralog, HXT7, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4349-YHR093W | YHR093W | AHT1 | 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; multicopy suppressor of glucose transport defects, likely due to the presence of an HXT4 regulatory element in the region | Accessory | Ancestral | NA | NA |
| 4350-YHR094C | YHR094C | HXT1 | hexose transporter HXT1|HOR4 | Low-affinity glucose transporter of the major facilitator superfamily; expression is induced by Hxk2p in the presence of glucose and repressed by Rgt1p when glucose is limiting; HXT1 has a paralog, HXT6, what arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4351-YHR095W | YHR095W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 4352-YHR096C_NumOfGenes_2 | YHR096C | HXT5 | hexose transporter HXT5 | Hexose transporter with moderate affinity for glucose; induced in the presence of non-fermentable carbon sources, induced by a decrease in growth rate, contains an extended N-terminal domain relative to other HXTs; HXT5 has a paralog, HXT3, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4353-YHR097C_NumOfGenes_2 | YHR097C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and the nucleus; YHR097C has a paralog, PAL1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4354-YHR098C | YHR098C | SFB3 | LST1 | Component of the Sec23p-Sfb3p heterodimer of the COPII vesicle coat; COPII coat is required for cargo selection during vesicle formation in ER to Golgi transport; scaffolding function of Lst1p required to generate vesicles that can accommodate difficult cargo proteins that include large oligomeric assemblies and asymmetrically distributed membrane proteins; homologous to Sec24p and Sfb2p | Accessory | Ancestral | NA | NA |
| 4355-YHR099W | YHR099W | TRA1 | histone acetyltransferase TRA1 | Subunit of SAGA and NuA4 histone acetyltransferase complexes; interacts with acidic activators (e.g., Gal4p) which leads to transcription activation; similar to human TRRAP, which is a cofactor for c-Myc mediated oncogenic transformation | Core | NA | NA | NA |
| 4356-YHR100C | YHR100C | GEP4 | phosphatidylglycerophosphatase | Mitochondrial phosphatidylglycerophosphatase (PGP phosphatase); dephosphorylates phosphatidylglycerolphosphate to generate phosphatidylglycerol, an essential step during cardiolipin biosynthesis; null mutant is sensitive to tunicamycin, DTT | Core | NA | NA | NA |
| 4357-YHR101C | YHR101C | BIG1 | NA | Integral membrane protein of the endoplasmic reticulum; required for normal content of cell wall beta-1,6-glucan | Core | NA | NA | NA |