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 |
|---|---|---|---|---|---|---|---|---|
| 3893-YGL254W | YGL254W | FZF1 | SUL1|RSU1|NRC299 | Transcription factor involved in sulfite metabolism; sole identified regulatory target is SSU1; overexpression suppresses sulfite-sensitivity of many unrelated mutants due to hyperactivation of SSU1, contains five zinc fingers; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 3894-YGL255W | YGL255W | ZRT1 | high-affinity Zn(2+) transporter ZRT1 | High-affinity zinc transporter of the plasma membrane; responsible for the majority of zinc uptake; transcription is induced under low-zinc conditions by the Zap1p transcription factor | Accessory | Ancestral | NA | NA |
| 3895-YGL256W_NumOfGenes_2 | YGL256W | ADH4 | alcohol dehydrogenase ADH4|ZRG5|NRC465 | Alcohol dehydrogenase isoenzyme type IV; dimeric enzyme demonstrated to be zinc-dependent despite sequence similarity to iron-activated alcohol dehydrogenases; transcription is induced in response to zinc deficiency | Core | NA | NA | NA |
| 3896-YGL257C_NumOfGenes_2 | YGL257C | MNT2 | alpha-1,3-mannosyltransferase MNT2 | Mannosyltransferase; involved in adding the 4th and 5th mannose residues of O-linked glycans | Accessory | Ancestral | NA | NA |
| 3897-YGL258W_NumOfGenes_2 | YGL258W | VEL1 | NA | Protein of unknown function; highly induced in zinc-depleted conditions and has increased expression in NAP1 deletion mutants; VEL1 has a paralog, YOR387C, that arose from a single-locus duplication | Accessory | Ancestral | NA | NA |
| 3898-YGL258W-A_NumOfGenes_2 | YGL258W-A | NA | NA | Putative protein of unknown function | Accessory | Unknown | NA | NA |
| 3899-YGL259W | YGL259W | YPS5 | NA | Protein with similarity to GPI-anchored aspartic proteases; such proteases are Yap1p and Yap3p; mCherry fusion protein localizes to the vacuole | Accessory | Unknown | NA | NA |
| 3900-YGL262W | YGL262W | NA | NA | Putative protein of unknown function; null mutant displays elevated sensitivity to expression of a mutant huntingtin fragment or of alpha-synuclein; YGL262W is not an essential gene | Accessory | Ancestral | NA | NA |
| 3901-YGL263W | YGL263W | COS12 | NA | Endosomal protein involved in turnover of plasma membrane proteins; member of the DUP380 subfamily of conserved, often subtelomeric COS genes; required for the multivesicular vesicle body sorting pathway that internalizes plasma membrane proteins for degradation; Cos proteins provide ubiquitin in trans for nonubiquitinated cargo proteins | Accessory | Unknown | S. mikatae | NA |
| 3902-YGR001C | YGR001C | EFM5 | protein-lysine N-methyltransferase|AML1 | S-adenosylmethionine-dependent lysine methyltransferase; involved in the trimethylation of eEF1A (Tef1p/Tef2p) at lysine 79; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; required for replication of Brome mosaic virus in budding yeast; expresses a circular RNA; originally misclassified as a N-6-adenine specific DNA methyltransferase based on sequence similarity; both Efm5p and human ortholog N6AMT2 can methylate eEF1a from either species in vitro | Core | NA | NA | NA |
| 3903-YGR002C | YGR002C | SWC4 | GOD1|EAF2 | Component of the Swr1p complex that incorporates Htz1p into chromatin; component of the NuA4 histone acetyltransferase complex | Core | NA | NA | NA |
| 3904-YGR003W | YGR003W | CUL3 | cullin CUL3|CULLIN B|CULB | Ubiquitin-protein ligase; forms a complex with Elc1p that polyubiquitylates monoubiquitylated RNA polymerase II to trigger its proteolysis; cullin family member with similarity to Cdc53p and human CUL3 | Core | NA | NA | NA |
| 3905-YGR004W | YGR004W | PEX31 | peroxisome biogenesis protein | Peroxisomal integral membrane protein; involved in negative regulation of peroxisome size; partially functionally redundant with Pex30p and Pex32p; probably acts at a step downstream of steps mediated by Pex28p and Pex29p; PEX31 has a paralog, PEX30, that arose from the whole genome duplication | Core | NA | NA | NA |
| 3906-YGR005C | YGR005C | TFG2 | transcription factor IIF subunit TFG2 | TFIIF (Transcription Factor II) middle subunit; involved in both transcription initiation and elongation of RNA polymerase II; homologous to human RAP30 | Core | NA | NA | NA |
| 3907-YGR006W | YGR006W | PRP18 | mRNA splicing protein PRP18 | Splicing factor and component of snRNP U5; factor involved in the positioning of the 3' splice site during the second catalytic step of splicing; interacts with Slu7p | Core | NA | NA | NA |