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 |
|---|---|---|---|---|---|---|---|---|
| 6908-YOL110W | YOL110W | SHR5 | ERF4 | Palmitoyltransferase subunit; this complex adds a palmitoyl lipid moiety to heterolipidated substrates such as Ras1p and Ras2p through a thioester linkage; palmitoylation is required for Ras2p membrane localization; Palmitoyltransferase is composed of Shr5p and Erf2 | Core | NA | NA | NA |
| 6909-YOL111C | YOL111C | MDY2 | GET5|TMA24 | Protein involved in inserting tail-anchored proteins into ER membranes; forms a complex with Get4p; required for efficient mating; involved in shmoo formation and nuclear migration in the pre-zygote; associates with ribosomes | Core | NA | NA | NA |
| 6910-YOL112W | YOL112W | MSB4 | Rab GTPase-activating protein MSB4 | GTPase-activating protein of the Ras superfamily; acts primarily on Sec4p, localizes to the bud site and bud tip; msb3 msb4 double mutation causes defects in secretion and actin organization; similar to the TBC-domain Tre2 oncogene; MSB4 has a paralog, MSB3, that arose from the whole genome duplication; human homolog USP6NL can complement yeast msb3 msb4 double null mutant | Core | NA | NA | NA |
| 6911-YOL113W | YOL113W | SKM1 | putative serine/threonine protein kinase SKM1 | Member of the PAK family of serine/threonine protein kinases; similar to Ste20p; involved in down-regulation of sterol uptake; proposed to be a downstream effector of Cdc42p during polarized growth; SKM1 has a paralog, CLA4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6912-YOL114C | YOL114C | PTH4 | NA | Protein similar to the human peptidyl-tRNA hydrolase gene ICT1; associates with mitochondrial large subunit; may function in translation termination; YOL114C is not an essential gene | Core | NA | NA | NA |
| 6913-YOL115W | YOL115W | PAP2 | non-canonical poly(A) polymerase PAP2|TRF4 | Non-canonical poly(A) polymerase; involved in nuclear RNA degradation as a component of TRAMP; catalyzes polyadenylation of hypomodified tRNAs, and snoRNA and rRNA precursors; required for mRNA surveillance and maintenance of genome integrity, serving as a link between RNA and DNA metabolism; overlapping but non-redundant functions with Trf5p; relocalizes to cytosol in response to hypoxia | Core | NA | NA | NA |
| 6914-YOL116W | YOL116W | MSN1 | PHD2|MSS10|HRB382|FUP1 | Transcriptional activator; involved in regulation of invertase and glucoamylase expression, invasive growth and pseudohyphal differentiation, iron uptake, chromium accumulation, and response to osmotic stress; localizes to the nucleus; relative distribution to the nucleus increases upon DNA replication stress | Core | NA | NA | NA |
| 6915-YOL117W | YOL117W | RRI2 | CSN10 | Subunit of the COP9 signalosome (CSN) complex; this complex cleaves the ubiquitin-like protein Nedd8 from SCF ubiquitin ligases; plays a role in the mating pheromone response | Core | NA | NA | NA |
| 6916-YOL118C | YOL118C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data | Core | NA | NA | NA |
| 6917-YOL119C | YOL119C | MCH4 | NA | Protein with similarity to mammalian monocarboxylate permeases; monocarboxylate permeases are involved in transport of monocarboxylic acids across the plasma membrane but mutant is not deficient in monocarboxylate transport | Core | NA | NA | NA |
| 6918-YOL120C | YOL120C | RPL18A | eL18|ribosomal 60S subunit protein L18A|L18e|rp28A|L18A|RP28A | Ribosomal 60S subunit protein L18A; intron of RPL18A pre-mRNA forms stem-loop structures that are a target for Rnt1p cleavage leading to degradation; homologous to mammalian ribosomal protein L18, no bacterial homolog; RPL18A has a paralog, RPL18B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6919-YOL121C | YOL121C | RPS19A | eS19|ribosomal 40S subunit protein S19A|S19e|rp55a|YS16A|S19A|S16aA | Protein component of the small (40S) ribosomal subunit; required for assembly and maturation of pre-40 S particles; homologous to mammalian ribosomal protein S19, no bacterial homolog; mutations in human RPS19 are associated with Diamond Blackfan anemia; RPS19A has a paralog, RPS19B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 6920-YOL122C | YOL122C | SMF1 | divalent metal ion transporter SMF1|SBS1 | Divalent metal ion transporter; broad specificity for di-valent and tri-valent metals; post-translationally regulated by levels of metal ions; member of the Nramp family of metal transport proteins | Accessory | Ancestral | NA | NA |
| 6921-YOL123W | YOL123W | HRP1 | NAB5|NAB4 | Subunit of cleavage factor I; cleavage factor I is a five-subunit complex required for the cleavage and polyadenylation of pre-mRNA 3' ends; RRM-containing heteronuclear RNA binding protein and hnRNPA/B family member that binds to poly (A) signal sequences; required for genome stability | Accessory | Ancestral | NA | NA |
| 6922-YOL124C | YOL124C | TRM11 | tRNA (guanine-N2-)-methyltransferase | Catalytic subunit of adoMet-dependent tRNA methyltransferase complex; required for the methylation of the guanosine nucleotide at position 10 (m2G10) in tRNAs; contains a THUMP domain and a methyltransferase domain; another complex member is Trm112p | Core | NA | NA | NA |