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 |
|---|---|---|---|---|---|---|---|---|
| 1793-YAL025C | YAL025C | MAK16 | ribosome biosynthesis protein MAK16 | Essential nuclear protein; constituent of 66S pre-ribosomal particles; required for maturation of 25S and 5.8S rRNAs; required for maintenance of M1 satellite double-stranded RNA of the L-A virus | Core | NA | NA | NA |
| 1794-YAL026C | YAL026C | DRS2 | aminophospholipid-translocating P4-type ATPase DRS2|SWA3|FUN38 | Trans-golgi network aminophospholipid translocase (flippase); maintains membrane lipid asymmetry in post-Golgi secretory vesicles; contributes to clathrin-coated vesicle formation, endocytosis, protein trafficking between the Golgi and endosomal system and the cellular response to mating pheromone; autoinhibited by its C-terminal tail; localizes to the trans-Golgi network; mutations in human homolog ATP8B1 result in liver disease | Core | NA | NA | NA |
| 1795-YAL026C-A | YAL026C-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YAL027W and the verified gene DRS2 | Accessory | Ancestral | NA | NA |
| 1796-YAL027W | YAL027W | SAW1 | DNA-binding protein SAW1 | 5'- and 3'-flap DNA binding protein; recruits Rad1p-Rad10p to single-strand annealing intermediates with 3' non-homologous tails for removal during double-strand break repair; complexes with Rad1p-Rad10p and stimulates its endonuclease activity; green fluorescent protein (GFP)-fusion protein localizes to the nucleus | Core | NA | NA | NA |
| 1797-YAL028W | YAL028W | FRT2 | HPH2 | Tail-anchored ER membrane protein of unknown function; interacts with homolog Frt1p; promotes growth in conditions of high Na+, alkaline pH, or cell wall stress, possibly via a role in posttranslational translocation; potential Cdc28p substrate; FRT2 has a paralog, FRT1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1798-YAL029C | YAL029C | MYO4 | myosin 4|SHE1|FUN22 | Type V myosin motor involved in actin-based transport of cargos; required for mRNA transport, including ASH1 mRNA, and facilitating the growth and movement of ER tubules into the growing bud along with She3p; MYO4 has a paralog, MYO2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1799-YAL030W | YAL030W | SNC1 | SNAP receptor SNC1 | Vesicle membrane receptor protein (v-SNARE); involved in the fusion between Golgi-derived secretory vesicles with the plasma membrane; proposed to be involved in endocytosis; member of the synaptobrevin/VAMP family of R-type v-SNARE proteins; SNC1 has a paralog, SNC2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1800-YAL031C | YAL031C | GIP4 | protein phosphatase regulator GIP4|FUN21 | Cytoplasmic protein that regulates protein phosphatase 1 Glc7p; protein overexpression relocalizes Glc7p from the nucleus and prevents chromosome segregation; potential Cdc28p substrate | Core | NA | NA | NA |
| 1801-YAL031W-A | YAL031W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps ORF GIP4/YAL031C | Accessory | Ancestral | NA | NA |
| 1802-YAL032C | YAL032C | PRP45 | mRNA splicing protein PRP45|FUN20 | Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene | Core | NA | NA | NA |
| 1803-YAL033W | YAL033W | POP5 | RNA-binding protein POP5|FUN53 | Subunit of both RNase MRP and nuclear RNase P; RNase MRP cleaves pre-rRNA, while nuclear RNase P cleaves tRNA precursors to generate mature 5' ends and facilitates turnover of nuclear RNAs | Core | NA | NA | NA |
| 1804-YAL034C | YAL034C | FUN19 | NA | Non-essential protein of unknown function; expression induced in response to heat stress; FUN19 has a paralog, YOR338W, that arose from the whole genome duplication | Core | NA | NA | NA |
| 1805-YAL034C-B | YAL034C-B | NA | YAL035C-A | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Accessory | Ancestral | NA | NA |
| 1806-YAL034W-A | YAL034W-A | MTW1 | MIND complex subunit MTW1|NSL2|DSN3 | Essential component of the MIND kinetochore complex; joins kinetochore subunits contacting DNA to those contacting microtubules; critical to kinetochore assembly; complex consists of Mtw1p Including Nnf1p-Nsl1p-Dsn1p (MIND) | Accessory | Ancestral | NA | NA |
| 1807-YAL035W | YAL035W | FUN12 | translation initiation factor eIF5B|eIF5B|yIF2 | Translation initiation factor eIF5B; GTPase that promotes Met-tRNAiMet binding to ribosomes and ribosomal subunit joining; promotes GTP-dependent maturation of 18S rRNA by Nob1p; protein abundance increases in response to DNA replication stress; homolog of bacterial IF2 | Accessory | Ancestral | NA | NA |