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 |
|---|---|---|---|---|---|---|---|---|
| 2573-YDL127W | YDL127W | PCL2 | cyclin PCL2|CLN4 | Cyclin, interacts with cyclin-dependent kinase Pho85p; member of the Pcl1,2-like subfamily, involved in the regulation of polarized growth and morphogenesis and progression through the cell cycle; localizes to sites of polarized cell growth; PCL2 has a paralog, PCL9, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2574-YDL128W | YDL128W | VCX1 | MNR1|HUM1 | Vacuolar membrane antiporter with Ca2+/H+ and K+/H+ exchange activity; involved in control of cytosolic Ca2+ and K+ concentrations; has similarity to sodium/calcium exchangers, including the bovine Na+/Ca2+,K+ antiporter | Core | NA | NA | NA |
| 2575-YDL129W | YDL129W | NA | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and the nucleus; YDL129W is not an essential gene; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 2576-YDL130W | YDL130W | RPP1B | ribosomal protein P1B|YP1beta|P1B|L44'|Ax|RPLA3|RPL44' | Ribosomal protein P1 beta; component of the ribosomal stalk, which is involved in interaction of translational elongation factors with ribosome; free (non-ribosomal) P1 stimulates the phosphorylation of the eIF2 alpha subunit (Sui2p) by Gcn2p; accumulation is regulated by phosphorylation and interaction with the P2 stalk component | Core | NA | NA | NA |
| 2577-YDL130W-A | YDL130W-A | STF1 | ATPase-binding protein|AIS2 | Protein involved in regulation of the mitochondrial F1F0-ATP synthase; Stf1p and Stf2p act as stabilizing factors that enhance inhibitory action of the Inh1p protein; protein abundance increases in response to DNA replication stress; STF1 has a paralog, INH1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2578-YDL132W | YDL132W | CDC53 | cullin CDC53 | Cullin; structural protein of SCF complexes (which also contain Skp1p, Cdc34p, Hrt1p and an F-box protein) involved in ubiquitination; SCF promotes the G1-S transition by targeting G1 cyclins and the Cln-CDK inhibitor Sic1p for degradation; human homolog CUL1 can complement yeast cdc53 null mutant | Core | NA | NA | NA |
| 2579-YDL133W | YDL133W | SRF1 | NA | Regulator of phospholipase D (Spo14p); interacts with Spo14p and regulates its catalytic activity; capable of buffering the toxicity of C16:0 platelet activating factor, a lipid that accumulates intraneuronally in Alzheimer's patients | Core | NA | NA | NA |
| 2580-YDL134C | YDL134C | PPH21 | phosphoprotein phosphatase 2A catalytic subunit PPH21 | Catalytic subunit of protein phosphatase 2A (PP2A); functionally redundant with Pph22p; methylated at C terminus; forms alternate complexes with several regulatory subunits; involved in signal transduction and regulation of mitosis; forms nuclear foci upon DNA replication stress; PPH21 has a paralog, PPH22, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2581-YDL135C | YDL135C | RDI1 | NA | Rho GDP dissociation inhibitor; involved in the localization and regulation of Cdc42p and Rho1p; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2582-YDL136W | YDL136W | RPL35B | uL29|ribosomal 60S subunit protein L35B|L35B|L29|SOS2 | Ribosomal 60S subunit protein L35B; homologous to mammalian ribosomal protein L35 and bacterial L29; RPL35B has a paralog, RPL35A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2583-YDL137W | YDL137W | ARF2 | Arf family GTPase ARF2 | ADP-ribosylation factor; GTPase of the Ras superfamily involved in regulation of coated formation vesicles in intracellular trafficking within the Golgi; ARF2 has a paralog, ARF1, that arose from the whole genome duplication; arf1 arf2 double null mutation is complemented by human ARF1, ARF4, ARF5, or ARF6 | Core | NA | NA | NA |
| 2584-YDL138W | YDL138W | RGT2 | glucose sensor | Plasma membrane high glucose sensor that regulates glucose transport; low affinity sesnor that contains 12 predicted transmembrane segments and a long C-terminal tail required for hexose transporter induction; phosphorylation of the tail by Yck1p/Yck2p facilitates binding to the HXT co-repressors, Mth1p and Std1p; RGT2 has a paralog, SNF3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2585-YDL139C | YDL139C | SCM3 | NA | Nonhistone component of centromeric chromatin; binds to histone H3 variant, Cse4p, and recruits it to centromeres; involved in the assembly and maintenance of Cse4-H4 at centromeres; required for kinetochore assembly and G2/M progression; may protect Cse4p from ubiquitination; homolog of mammalian HJURP | Core | NA | NA | NA |
| 2586-YDL140C_NumOfGenes_2 | YDL140C | RPO21 | DNA-directed RNA polymerase II core subunit RPO21|B220|SUA8|RPB220|RPB1 | RNA polymerase II largest subunit B220; part of central core; phosphorylation of C-terminal heptapeptide repeat domain regulates association with transcription and splicing factors; similar to bacterial beta-prime | Core | NA | NA | NA |
| 2587-YDL141W | YDL141W | BPL1 | biotin--[acetyl-CoA-carboxylase] ligase BPL1|ACC2 | Biotin:apoprotein ligase; covalently modifies proteins with the addition of biotin, required for acetyl-CoA carboxylase (Acc1p) holoenzyme formation; comparative analysis suggests that a mitochondrially targeted form may result from translation starting at a non-canonical codon upstream of the annotated start codon; human homolog HLCS can complement yeast BPL1 mutant | Core | NA | NA | NA |