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 |
|---|---|---|---|---|---|---|---|---|
| 6233-YMR170C | YMR170C | ALD2 | aldehyde dehydrogenase (NAD(+)) ALD2 | Cytoplasmic aldehyde dehydrogenase; involved in ethanol oxidation and beta-alanine biosynthesis; uses NAD+ as the preferred coenzyme; expression is stress induced and glucose repressed; very similar to Ald3p | Accessory | Ancestral | NA | NA |
| 6234-YMR171C | YMR171C | EAR1 | NA | Specificity factor required for Rsp5p-dependent ubiquitination; also required for sorting of specific cargo proteins at the multivesicular body; mRNA is targeted to the bud via the mRNA transport system involving She2p | Core | NA | NA | NA |
| 6235-YMR172W_NumOfGenes_2 | YMR172W | HOT1 | NA | Transcription factor for glycerol biosynthetic genes; required for the transient induction of glycerol biosynthetic genes GPD1 and GPP2 in response to high osmolarity; targets Hog1p to osmostress responsive promoters; has similarity to Msn1p and Gcr1p | Core | NA | NA | NA |
| 6236-YMR173W_NumOfGenes_3 | YMR173W | DDR48 | DNA damage-responsive protein 48|FSP | DNA damage-responsive protein; expression is increased in response to heat-shock stress or treatments that produce DNA lesions; contains multiple repeats of the amino acid sequence NNNDSYGS; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 6237-YMR174C_NumOfGenes_2 | YMR174C | PAI3 | IA3 | Cytoplasmic proteinase A (Pep4p) inhibitor; dependent on Pbs2p and Hog1p protein kinases for osmotic induction; intrinsically unstructured, N-terminal half becomes ordered in the active site of proteinase A upon contact | Core | NA | NA | NA |
| 6238-YMR175W_NumOfGenes_2 | YMR175W | SIP18 | NA | Phospholipid-binding hydrophilin; essential to overcome desiccation-rehydration process; expression is induced by osmotic stress; SIP18 has a paralog, GRE1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6239-YMR175W-A_NumOfGenes_2 | YMR175W-A | NA | NA | Putative protein of unknown function | Core | NA | NA | NA |
| 6240-YMR176W | YMR176W | ECM5 | NA | Subunit of the Snt2C complex; physically associates with Snt2p and Rpd3p; along with Snt2p, recruits Rpd3p to a small number of promoters; also colocalizes with Snt2p, independently of Rpd3p, to promoters of stress response genes in response to oxidative stress; contains ATP/GTP-binding site motif A; null mutant exhibits increased cellular volume, large drooping buds with elongated necks; relative distribution to the nucleus increases upon DNA replication stress | Accessory | Ancestral | NA | NA |
| 6241-YMR177W | YMR177W | MMT1 | MFT1 | Putative metal transporter involved in mitochondrial iron accumulation; MMT1 has a paralog, MMT2, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 6242-YMR178W | YMR178W | NA | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and nucleus; YMR178W is not an essential gene; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 6243-YMR179W | YMR179W | SPT21 | NA | Protein with a role in transcriptional silencing; required for normal transcription at several loci including HTA2-HTB2 and HHF2-HHT2, but not required at the other histone loci; functionally related to Spt10p; localizes to nuclear foci that become diffuse upon DNA replication stress | Accessory | Ancestral | NA | NA |
| 6244-YMR180C | YMR180C | CTL1 | polynucleotide 5'-phosphatase|CTH1 | RNA 5'-triphosphatase, localizes to both the nucleus and cytoplasm; CTL1 has a paralog, CET1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 6245-YMR181C | YMR181C | NA | NA | Protein of unknown function; mRNA transcribed as part of a bicistronic transcript with a predicted transcriptional repressor RGM1/YMR182C; mRNA is destroyed by nonsense-mediated decay (NMD); not an essential gene; YMR181C has a paralog, YPL229W, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 6246-YMR182C | YMR182C | RGM1 | NA | Putative zinc finger DNA binding transcription factor; contains two N-terminal C2H2 zinc fingers and C-terminal proline rich domain; overproduction impairs cell growth and induces expression of genes involved in monosaccharide catabolism and aldehyde metabolism; regulates expression of of Y' telomeric elements and subtelomeric COS genes; relocalizes to the cytosol in response to hypoxia; RGM1 has a paralog, USV1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 6247-YMR182W-A | YMR182W-A | NA | NA | Putative protein of unknown function | Accessory | Ancestral | NA | NA |