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 |
|---|---|---|---|---|---|---|---|---|
| 4613-YIL132C | YIL132C | CSM2 | NA | Component of Shu complex (aka PCSS complex); Shu complex also includes Psy3, Shu1, Shu2, and promotes error-free DNA repair,; Shu complex mediates inhibition of Srs2p function; promotes formation of Rad51p filaments; Psy3p and Csm2p contain similar DNA-binding regions which work together to form a single DNA binding site; required for accurate chromosome segregation during meiosis | Core | NA | NA | NA |
| 4614-YIL133C | YIL133C | RPL16A | uL13|ribosomal 60S subunit protein L16A|L13|rp22|YL15|L21A|L16A|RPL13 | Ribosomal 60S subunit protein L16A; N-terminally acetylated, binds 5.8 S rRNA; transcriptionally regulated by Rap1p; homologous to mammalian ribosomal protein L13A and bacterial L13; RPL16A has a paralog, RPL16B, that arose from the whole genome duplication; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4615-YIL134C-A | YIL134C-A | NA | NA | Putative protein of unknown function; identified by fungal homology and RT-PCR | Core | NA | NA | NA |
| 4616-YIL134W | YIL134W | FLX1 | flavin adenine dinucleotide transporter FLX1 | Mitochondrial flavin adenine dinucleotide transporter; FAD is a synthesis product of riboflavin; human homolog SLC25A32 is implicated in multiple acyl-CoA dehydrogenase deficiency (MADD) or glutaric aciduria type II (GAII), and can complement yeast null mutant | Core | NA | NA | NA |
| 4617-YIL135C | YIL135C | VHS2 | NA | Regulator of septin dynamics; involved in the regulation of septin dynamics at bud neck after mitotic entry, likely by stabilizing septin structure; regulated at post-translational level by cell cycle dependent phosphorylation; likely phosphorylated by Cdc28p and dephosphorylated by Cdc14p before cytokinesis; high-copy suppressor of synthetic lethality of sis2 sit4 double mutant; VHS2 has a paralog, MLF3, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4618-YIL136W | YIL136W | OM45 | NA | Mitochondrial outer membrane protein of unknown function; major constituent of the outer membrane, extending into the intermembrane space; interacts with porin (Por1p) and with Om14p; imported via the presequence pathway involving the TOM and TIM23 complexes, then assembled in the outer membrane by Mim1p; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4619-YIL137C | YIL137C | TMA108 | TAE3|RBF108 | Ribosome-associated, nascent chain binding factor; binds N-terminal region of nascent peptides during translation; recognizes target proteins via its putative metallopeptidase peptide-binding pocket | Core | NA | NA | NA |
| 4620-YIL138C | YIL138C | TPM2 | tropomyosin TPM2 | Minor isoform of tropomyosin; binds to and stabilizes actin cables and filaments, which direct polarized cell growth and the distribution of several organelles; appears to have distinct and also overlapping functions with Tpm1p; TPM2 has a paralog, TPM1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4621-YIL139C | YIL139C | REV7 | NA | Accessory subunit of DNA polymerase zeta; involved in translesion synthesis during post-replication repair; required for mutagenesis induced by DNA damage; involved in double-strand break repair; forms a complex with Rev3p, Pol31p and Pol32p | Core | NA | NA | NA |
| 4622-YIL140W | YIL140W | AXL2 | SRO4|BUD10 | Integral plasma membrane protein; required for axial budding in haploid cells; localizes to the incipient bud site and bud neck; glycosylated by Pmt4p; potential Cdc28p substrate | Core | NA | NA | NA |
| 4623-YIL141W | YIL141W | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 4624-YIL142C-A | YIL142C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps ORF CCT2/YIL142W | Accessory | Ancestral | NA | NA |
| 4625-YIL142W | YIL142W | CCT2 | chaperonin-containing T-complex subunit CCT2|TCP2|BIN3 | Subunit beta of the cytosolic chaperonin Cct ring complex; related to Tcp1p, required for the assembly of actin and tubulins in vivo | Core | NA | NA | NA |
| 4626-YIL143C | YIL143C | SSL2 | TFIIH/NER complex ATPase/helicase subunit SSL2|RAD25|LOM3 | Component of RNA polymerase transcription factor TFIIH holoenzyme; acts as dsDNA-dependent translocase in context of TFIIH, unwinds DNA strands during initiation and promotes transcription start site (TSS) scanning; has DNA-dependent ATPase/helicase activity; interacts functionally with TFIIB, has roles in TSS selection and gene looping to juxtapose initiation and termination regions; involved in DNA repair; relocalizes to cytosol under hypoxia; homolog of human ERCC3 | Core | NA | NA | NA |
| 4627-YIL144W | YIL144W | NDC80 | kinetochore-associated Ndc80 complex subunit NDC80|TID3|HEC1 | Component of the kinetochore-associated Ndc80 complex; conserved coiled-coil protein involved in chromosome segregation, spindle checkpoint activity, and kinetochore assembly and clustering; evolutionarily conserved; complex members include Ndc80p, Nuf2p, Scp24p, and Spc25p; modified by sumoylation | Accessory | Ancestral | NA | NA |