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 |
|---|---|---|---|---|---|---|---|---|
| 6413-YNL018C_NumOfGenes_2 | YNL018C | NA | NA | Putative protein of unknown function; YNL018C has a paralog, YNL034W, that arose from a segmental duplication | Core | NA | NA | NA |
| 6414-YNL020C | YNL020C | ARK1 | serine/threonine protein kinase ARK1 | Serine/threonine protein kinase; involved in regulation of the cortical actin cytoskeleton; involved in control of endocytosis; ARK1 has a paralog, PRK1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6415-YNL021W | YNL021W | HDA1 | histone deacetylase HDA1 | Putative catalytic subunit of a class II histone deacetylase complex; role in azole resistance via Hsp90p, and in the heat shock response; Hda1p interacts with the Hda2p-Hda3p subcomplex to form an active tetramer; deletion increases histone H2B, H3 and H4 acetylation; other members of the HDA1 histone deacetylase complex are Hda2p and Hda3p | Core | NA | NA | NA |
| 6416-YNL022C | YNL022C | RCM1 | rRNA (cytosine-C5-)-methyltransferase RCM1 | rRNA m5C methyltransferase; methylates cytosine at position 2278 of 25S rRNA while Nop2p methylates cytosine at position 2870; contains seven beta-strand methyltransferase motif; localized to the nucleolus; interacts with Trm112p; homolog of NSUN5A, a human gene which is deleted in Williams-Beuren Syndrome | Core | NA | NA | NA |
| 6417-YNL023C | YNL023C | FAP1 | NA | Protein that binds to Fpr1p; confers rapamycin resistance by competing with rapamycin for Fpr1p binding; accumulates in the nucleus upon treatment of cells with rapamycin; has similarity to D. melanogaster shuttle craft and human NFX1 | Core | NA | NA | NA |
| 6418-YNL024C | YNL024C | EFM6 | putative protein-lysine N-methyltransferase | Putative S-adenosylmethionine-dependent lysine methyltransferase; responsible for modifying Lys-390 in translational elongation factor EF-1 alpha (eEF1A); has seven beta-strand methyltransferase motif; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm | Core | NA | NA | NA |
| 6419-YNL024C-A | YNL024C-A | KSH1 | NA | Essential protein suggested to function early in the secretory pathway; inviability is suppressed by overexpression of Golgi protein Tvp23p; SWAT-GFP and mCherry fusion proteins localize to the endoplasmic reticulum and cytosol respectively; ortholog of human Kish | Core | NA | NA | NA |
| 6420-YNL025C | YNL025C | SSN8 | cyclin-dependent protein serine/threonine kinase regulator SSN8|CNC1|CycC|RYE2|UME3|SRB11|NUT9|GIG3 | Cyclin-like component of the RNA polymerase II holoenzyme; involved in phosphorylation of the RNA polymerase II C-terminal domain; forms a kinase-cyclin pair in the RNAPII holoenzyme with Ssn3p; required for both entry into and execution of the meiotic program; involved in glucose repression and telomere maintenance; cyclin homolog 35% identical to human cyclin C | Core | NA | NA | NA |
| 6421-YNL026W | YNL026W | SAM50 | SAM complex subunit SAM50|TOB55|OMP85 | Component of the Sorting and Assembly Machinery (SAM) complex; the SAM (or TOB) complex is located in the mitochondrial outer membrane; the complex binds precursors of beta-barrel proteins and facilitates their outer membrane insertion; homologous to bacterial Omp85 | Core | NA | NA | NA |
| 6422-YNL027W | YNL027W | CRZ1 | DNA-binding transcription factor CRZ1|TCN1|HAL8 | Transcription factor, activates transcription of stress response genes; nuclear localization is positively regulated by calcineurin-mediated dephosphorylation; rapidly localizes to the nucleus under blue light stress; can be activated in stochastic pulses of nuclear localization in response to calcium | Core | NA | NA | NA |
| 6423-YNL028W | YNL028W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 6424-YNL029C | YNL029C | KTR5 | putative mannosyltransferase | Putative mannosyltransferase involved in protein glycosylation; member of the KRE2/MNT1 mannosyltransferase family; KTR5 has a paralog, KTR7, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6425-YNL031C | YNL031C | HHT2 | histone H3 | Histone H3; core histone protein required for chromatin assembly, part of heterochromatin-mediated telomeric and HM silencing; one of two identical histone H3 proteins (see HHT1); regulated by acetylation, methylation, and phosphorylation; H3K14 acetylation plays an important role in the unfolding of strongly positioned nucleosomes during repair of UV damage | Core | NA | NA | NA |
| 6426-YNL032W | YNL032W | SIW14 | putative tyrosine protein phosphatase SIW14|OCA3 | Tyrosine phosphatase involved in actin organization and endocytosis; localized to the cytoplasm | Core | NA | NA | NA |
| 6427-YNL033W_NumOfGenes_2 | YNL033W | NA | NA | Putative protein of unknown function; YNL033W has a paralog, YNL019C, that arose from a segmental duplication | Core | NA | NA | NA |