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 |
|---|---|---|---|---|---|---|---|---|
| 5888-YLR430W | YLR430W | SEN1 | putative DNA/RNA helicase SEN1|NRD2|CIK3 | ATP-dependent 5' to 3' RNA/DNA and DNA helicase; subunit of the exosome-associated Nrd1p complex that mediates 3' end formation of snRNAs, snoRNAs, CUTs and some mRNAs; helicase-independent role in transcription-coupled repair; coordinates replication with transcription, associating with moving forks and preventing errors that occur when forks encounter transcribed regions; homolog of Senataxin, implicated in Ataxia-Oculomotor Apraxia 2 and a dominant form of juvenile ALS | Core | NA | NA | NA |
| 5889-YLR431C | YLR431C | ATG23 | CVT23 | Peripheral membrane protein required for autophagy and CVT; required for cytoplasm-to-vacuole targeting (Cvt) pathway and efficient macroautophagy; cycles between the phagophore assembly site (PAS) and non-PAS locations; forms a complex with Atg9p and Atg27p | Core | NA | NA | NA |
| 5890-YLR432W | YLR432W | IMD3 | IMP dehydrogenase IMD3 | Inosine monophosphate dehydrogenase; catalyzes the rate-limiting step in the de novo synthesis of GTP; member of a four-gene family in S. cerevisiae, constitutively expressed; IMD3 has a paralog, IMD4, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5891-YLR433C | YLR433C | CNA1 | calcineurin catalytic subunit A|CMP1 | Calcineurin A; one isoform (the other is Cmp2p) of the catalytic subunit of calcineurin, a Ca++/calmodulin-regulated protein phosphatase which regulates Crz1p (a stress-response transcription factor), the other calcineurin subunit is CNB1; regulates the function of Aly1p alpha-arrestin; CNA1 has a paralog, CMP2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5892-YLR434C | YLR434C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF TSR2/YLR435W | Core | NA | NA | NA |
| 5893-YLR435W | YLR435W | TSR2 | NA | Protein with a potential role in pre-rRNA processing | Core | NA | NA | NA |
| 5894-YLR436C | YLR436C | ECM30 | NA | Protein of unknown function; may play a role in cell wall biosynthesis, mutants have abormal relative levels of mannose and glucose and have Gap1p sorting and transport defects; (GFP)-fusion protein localizes to the cytoplasm | Core | NA | NA | NA |
| 5895-YLR437C | YLR437C | DIF1 | NA | Protein that regulates nuclear localization of Rnr2p and Rnr4p; phosphorylated by Dun1p in response to DNA damage and degraded; N-terminal half shows similarity to S. pombe Spd1 protein; DIF1 has a paralog, SML1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5896-YLR438C-A | YLR438C-A | LSM3 | U4/U6-U5 snRNP complex subunit LSM3|USS2|SMX4 | Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA; protein increases in abundance and relocalizes from nucleus to cytoplasmic foci upon DNA replication stress | Accessory | Ancestral | NA | NA |
| 5897-YLR438W_NumOfGenes_2 | YLR438W | CAR2 | ornithine-oxo-acid transaminase|cargB | L-ornithine transaminase (OTAse); catalyzes the second step of arginine degradation, expression is dually-regulated by allophanate induction and a specific arginine induction process; not nitrogen catabolite repression sensitive; protein abundance increases in response to DNA replication stress; human homolog OAT complements yeast null mutant | Core | NA | NA | NA |
| 5898-YLR439W | YLR439W | MRPL4 | mitochondrial 54S ribosomal protein YmL4|YmL4 | Mitochondrial ribosomal protein of the large subunit; homolog of prokaryotic L29 ribosomal protein; located at the ribosomal tunnel exit | Core | NA | NA | NA |
| 5899-YLR440C | YLR440C | SEC39 | DSL3 | Component of the Dsl1p tethering complex; this complex interacts with ER SNAREs Sec20p and Use1p; mediates Sey1p-independent homotypic ER fusion; proposed to be involved in protein secretion; localizes to the ER and nuclear envelope | Core | NA | NA | NA |
| 5900-YLR441C | YLR441C | RPS1A | eS1|ribosomal 40S subunit protein S1A|S1e|rp10A|S1A|RP10A | Ribosomal protein 10 (rp10) of the small (40S) subunit; homologous to mammalian ribosomal protein S3A, no bacterial homolog; RPS1A has a paralog, RPS1B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5901-YLR442C | YLR442C | SIR3 | chromatin-silencing protein SIR3|STE8|MAR2|CMT1 | Silencing protein; interacts with Sir2p, Sir4p, and histone H3/H4 tails to establish transcriptionally silent chromatin; required for spreading of silenced chromatin; recruited to chromatin through interaction with Rap1p; C-terminus assumes variant winged helix-turn-helix (wH) fold that mediates homodimerization, which is critical for holo-SIR complex loading; required for telomere hypercluster formation in quiescent yeast cells; has paralog ORC1 from whole genome duplication | Core | NA | NA | NA |
| 5902-YLR443W_NumOfGenes_2 | YLR443W | ECM7 | ZRG15 | Putative integral membrane protein with a role in calcium uptake; non-essential protein; mutant has cell wall defects and Ca+ uptake deficiencies; transcription is induced under conditions of zinc deficiency | Core | NA | NA | NA |