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 |
|---|---|---|---|---|---|---|---|---|
| 7553-YPL204W | YPL204W | HRR25 | serine/threonine protein kinase HRR25|KTI14 | Conserved casein kinase; regulates diverse events including: vesicular traffic, DNA repair, the CVT pathway, monopolar attachment of sister kinetochores at meiosis I, and ribosomal subunit biogenesis; monopolin subunit; binds the RNAPII CTD; phosphorylates COPII coat subunits; interacts with Sit4p phosphatase; antagonizes calcineurin signaling, reducing nuclear accumulation of Crz1p; phosphorylates Dsn1p, the kinetochore receptor for monopolin; homolog of mammalian CK1delta | Core | NA | NA | NA |
| 7554-YPL205C | YPL205C | NA | NA | Hypothetical protein; deletion of locus affects telomere length | Core | NA | NA | NA |
| 7555-YPL206C | YPL206C | PGC1 | phosphatidylglycerol phospholipase | Phosphatidylglycerol phospholipase C; regulates phosphatidylglycerol (PG) accumulation via a phospholipase C-type degradation mechanism; PG levels affect mitochondrial function; contains glycerophosphodiester phosphodiesterase motifs | Core | NA | NA | NA |
| 7556-YPL207W | YPL207W | TYW1 | putative tRNA 4-demethylwyosine synthase | Iron-sulfer protein required for synthesis of Wybutosine modified tRNA; Wybutosine is a modified guanosine found at the 3'-position adjacent to the anticodon of phenylalanine tRNA which supports reading frame maintenance by stabilizing codon-anticodon interactions; induction by Yap5p in response to iron provides protection from high iron toxicity; overexpression results in increased cellular iron | Core | NA | NA | NA |
| 7557-YPL208W | YPL208W | RKM1 | protein-lysine N-methyltransferase | SET-domain lysine-N-methyltransferase; catalyzes the formation of dimethyllysine residues on the large ribosomal subunit proteins L23 (Rpl23Ap and Rpl23Bp) and monomethyllysine residues on L18 (Rps18Ap and Rps18Bp) | Core | NA | NA | NA |
| 7558-YPL209C | YPL209C | IPL1 | aurora kinase|PAC15 | Aurora kinase of chromosomal passenger complex; mediates release of mono-oriented kinetochores from microtubules in meiosis I, and kinetochore release from SPB clusters at meiotic exit; helps maintain condensed chromosomes during anaphase; required for SPB cohesion and prevention of multipolar spindle formation; promotes telomerase release at G2/M; Iocalizes to nuclear foci that diffuse upon DNA replication stress; required for inhibition of karyopherin Pse1p upon SAC arrest | Core | NA | NA | NA |
| 7559-YPL210C | YPL210C | SRP72 | signal recognition particle subunit SRP72 | Core component of the signal recognition particle (SRP); the SRP is a ribonucleoprotein (RNP) complex that functions in targeting nascent secretory proteins to the endoplasmic reticulum (ER) membrane | Core | NA | NA | NA |
| 7560-YPL211W | YPL211W | NIP7 | ribosome biosynthesis protein NIP7 | Nucleolar protein required for 60S ribosome subunit biogenesis; constituent of 66S pre-ribosomal particles; physically interacts with Nop8p and the exosome subunit Rrp43p | Core | NA | NA | NA |
| 7561-YPL212C | YPL212C | PUS1 | pseudouridine synthase PUS1 | tRNA:pseudouridine synthase; introduces pseudouridines at positions 26-28, 34-36, 65, and 67 of tRNA; also acts on U2 snRNA; also pseudouridylates some mRNAs, and pseudouridylation level varies with growth phase; nuclear protein that appears to be involved in tRNA export; PUS1 has a paralog, PUS2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7562-YPL213W | YPL213W | LEA1 | U2 snRNP complex subunit LEA1 | Component of U2 snRNP complex; disruption causes reduced U2 snRNP levels; physically interacts with Msl1p; putative homolog of human U2A' snRNP protein | Core | NA | NA | NA |
| 7563-YPL214C | YPL214C | THI6 | bifunctional hydroxyethylthiazole kinase/thiamine-phosphate diphosphorylase | Thiamine-phosphate diphosphorylase and hydroxyethylthiazole kinase; required for thiamine biosynthesis; GFP-fusion protein localizes to the cytoplasm in a punctate pattern | Core | NA | NA | NA |
| 7564-YPL215W | YPL215W | CBP3 | NA | Mitochondrial protein required for assembly of cytochrome bc1 complex; forms a complex with Cbp6p that binds to mt ribosomes near the polypeptide tunnel exit and promotes efficient translation of the COB mRNA; Cbp3p-Cbp6p complex also interacts with newly synthesized cytochrome b (Cobp) and Cbp4p to promote assembly of Cobp into the cytochrome bc1 complex; Cbp3p-Cbp6p complex is sequestered if assembly of Complex III is blocked, downregulating COB mRNA translation | Core | NA | NA | NA |
| 7565-YPL216W | YPL216W | NA | NA | Putative protein of unknown function; not an essential gene; YPL216W has a paralog, ITC1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 7566-YPL217C | YPL217C | BMS1 | GTPase BMS1 | GTPase required for ribosomal subunit synthesis and rRNA processing; required for synthesis of 40S ribosomal subunits and for processing the 35S pre-rRNA at sites A0, A1, and A2; interacts with Rcl1p, which stimulates its GTPase and U3 snoRNA binding activities; has similarity to Tsr1p | Core | NA | NA | NA |
| 7567-YPL218W | YPL218W | SAR1 | Arf family GTPase SAR1 | ARF family GTPase; component of the COPII vesicle coat; required for transport vesicle formation during ER to Golgi protein transport; lowers membrane rigidity aiding vesicle formation; localizes to ER-mitochondrial contact sites where it enhances membrane curvature, thereby reducing contact size via its N-terminal amphipathic helix; regulates mitochondrial fission and fusion dynamics | Core | NA | NA | NA |