Gene name: RAT1
Reference locus (S288C): YOR048C
Gene biotype: protein_coding
Description: 5'-3' exoribonuclease 2; Nuclear 5' to 3' single-stranded RNA exonuclease; involved in RNA metabolism, including rRNA and snoRNA processing, as well as poly (A+) dependent and independent mRNA transcription termination; required for cotranscriptional pre-rRNA cleavage; displaces Cdk1p from elongating transcripts, especially as RNAPII reaches the poly(A) site, negatively regulates phosphorylation of the CTD of RNAPII, and inhibits RNAPII transcriptional elongation
Top 10 interactors (score): RAI1 (0.999); XRN1 (0.999); RTT103 (0.998); RRP6 (0.998); TRM8 (0.993); PCF11 (0.992); NCL1 (0.991); SEN1 (0.991); DIS3 (0.99); RNT1 (0.986); SKI2 (0.983); MTR4 (0.974); NAB3 (0.974); DCP2 (0.974); GRC3 (0.958); RRP17 (0.942); RPO21 (0.94); DXO1 (0.922); NAM7 (0.915); STO1 (0.91)
Homologues (species, bitscore): XRN2 (Homo sapiens, 624.8); Xrn2 (Mus musculus, 622.1); xrn2 (Danio rerio, 622.1); xrn2 (Xenopus tropicalis, 619.4); Rat1 (Drosophila melanogaster, 592.4); xrn-2 (Caenorhabditis elegans, 612.5); XRN3 (Arabidopsis thaliana, 620.5)
External links:
Saccharomyces genome database (SGD)
STRING database
BioGRID
UniProt Knowledgebase
Kyoto encyclopedia of genes and genomes (KEGG)
Reactome
UCSC Genome Browser
| strain | assembly | application | macro_region | gene_coord | geneID | rnaID | protID | %id | %cov_exon | status | copyNumber | copyID | nORFs | match_ref_CDS | validORF | missing_startCodon | missing_stopCodon | outOfFrame_stopCodon |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AKU4011 | GCA_001738255.1 | Sake | Asia | CM005309.1:402973-405993:- | gene-YOR048C_AKU4011 | rna-NM_001183467.1_AKU4011 | cds-NP_014691.1_AKU4011 | 99.8 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| BG1 | GCA_001932575.1 | Bioethanol | South America | MSHP01000152.1:218572-221592:- | gene-YOR048C_BG1 | rna-NM_001183467.1_BG1 | cds-NP_014691.1_BG1 | 99.1 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| Bruggeman | GCA_001738585.1 | Bread | Not Applicable | CM005517.1:405709-408729:- | gene-YOR048C_Bruggeman | rna-NM_001183467.1_Bruggeman | cds-NP_014691.1_Bruggeman | 99.7 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| CAT1 | GCA_001738705.1 | Bioethanol | South America | CM005533.1:403891-406911:- | gene-YOR048C_CAT1 | rna-NM_001183467.1_CAT1 | cds-NP_014691.1_CAT1 | 99.1 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| CBS1585 | GCA_001738375.1 | Sake | Asia | CM005373.1:397664-400684:- | gene-YOR048C_CBS1585 | rna-NM_001183467.1_CBS1585 | cds-NP_014691.1_CBS1585 | 99.8 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| CBS436 | GCA_001738355.1 | Sake | Asia | CM005357.1:402032-405052:- | gene-YOR048C_CBS436 | rna-NM_001183467.1_CBS436 | cds-NP_014691.1_CBS436 | 99.1 | 100.0 | Mismatch | 1 | 1 | 1 | False | True | False | False | False |
| CBS6412 | GCA_001738345.1 | Sake | Asia | CM005341.1:397018-400038:- | gene-YOR048C_CBS6412 | rna-NM_001183467.1_CBS6412 | cds-NP_014691.1_CBS6412 | 99.9 | 100.0 | Mismatch | 1 | 1 | 1 | False | True | False | False | False |
| CBS6413 | GCA_001738265.1 | Sake | Asia | CM005325.1:404394-407414:- | gene-YOR048C_CBS6413 | rna-NM_001183467.1_CBS6413 | cds-NP_014691.1_CBS6413 | 99.8 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| CENPK1137D | GCA_000269885.1 | Laboratory | Not Applicable | CM001536.1:418628-421648:- | gene-YOR048C_CENPK1137D | rna-NM_001183467.1_CENPK1137D | cds-NP_014691.1_CENPK1137D | 99.9 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| EthanolRed | GCA_001738615.1 | Bioethanol | Asia | CM005485.1:399671-402691:- | gene-YOR048C_EthanolRed | rna-NM_001183467.1_EthanolRed | cds-NP_014691.1_EthanolRed | 99.9 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| FaliES1 | GCA_001738715.1 | Bioethanol | Asia | CM005549.1:403018-406038:- | gene-YOR048C_FaliES1 | rna-NM_001183467.1_FaliES1 | cds-NP_014691.1_FaliES1 | 99.9 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| JAY291 | GCA_000182315.2 | Bioethanol | South America | ACFL01000035.1:73687-76707:- | gene-YOR048C_JAY291 | rna-NM_001183467.1_JAY291 | cds-NP_014691.1_JAY291 | 99.4 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| MUCL30387 | GCA_001738515.1 | Bread | Europe | CM005421.1:410504-413524:- | gene-YOR048C_MUCL30387 | rna-NM_001183467.1_MUCL30387 | cds-NP_014691.1_MUCL30387 | 99.4 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| MUCL30388 | GCA_001738495.1 | Bread | Europe | CM005453.1:413801-416821:- | gene-YOR048C_MUCL30388 | rna-NM_001183467.1_MUCL30388 | cds-NP_014691.1_MUCL30388 | 99.5 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| MUCL39482 | GCA_001738235.1 | Sake | Asia | CM005293.1:405147-408167:- | gene-YOR048C_MUCL39482 | rna-NM_001183467.1_MUCL39482 | cds-NP_014691.1_MUCL39482 | 99.8 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| MUCL42920 | GCA_001738485.1 | Bread | Europe | CM005437.1:419985-423005:- | gene-YOR048C_MUCL42920 | rna-NM_001183467.1_MUCL42920 | cds-NP_014691.1_MUCL42920 | 99.1 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| NCIM3186 | GCA_001029075.1 | Bioethanol | Asia | CP011824.1:418519-421539:- | gene-YOR048C_NCIM3186 | rna-NM_001183467.1_NCIM3186 | cds-NP_014691.1_NCIM3186 | 99.2 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| NCYC1407 | GCA_001738225.1 | Sake | Asia | CM005277.1:411849-414869:- | gene-YOR048C_NCYC1407 | rna-NM_001183467.1_NCYC1407 | cds-NP_014691.1_NCYC1407 | 99.8 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| PE2H3 | GCA_905220325.1 | Bioethanol | South America | HG994154.1:410708-413728:- | gene-YOR048C_PE2H3 | rna-NM_001183467.1_PE2H3 | cds-NP_014691.1_PE2H3 | 99.1 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| PE2H4 | GCA_905220315.1 | Bioethanol | South America | LR999886.1:421089-424109:- | gene-YOR048C_PE2H4 | rna-NM_001183467.1_PE2H4 | cds-NP_014691.1_PE2H4 | 99.1 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| S288C | GCF_000146045.2 | Laboratory | Not applicable | NC_001147.6:418630-421650:- | gene-YOR048C_S288C | rna-NM_001183467.1_S288C | cds-NP_014691.1_S288C | 100.0 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| SA1 | GCA_004114265.1 | Bioethanol | South America | SDIA01000001.1:386574-389594:- | gene-YOR048C_SA1 | rna-NM_001183467.1_SA1 | cds-NP_014691.1_SA1 | 99.1 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| ThermosaccDry | GCA_001738605.1 | Bioethanol | Asia | CM005501.1:401558-404578:- | gene-YOR048C_ThermosaccDry | rna-NM_001183467.1_ThermosaccDry | cds-NP_014691.1_ThermosaccDry | 99.9 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| VR1 | GCA_001738595.1 | Bioethanol | South America | CM005469.1:403033-406053:- | gene-YOR048C_VR1 | rna-NM_001183467.1_VR1 | cds-NP_014691.1_VR1 | 99.1 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| ZTW1 | GCA_000308935.1 | Bioethanol | Asia | AMDD01000032.1:136201-139221:- | gene-YOR048C_ZTW1 | rna-NM_001183467.1_ZTW1 | cds-NP_014691.1_ZTW1 | 99.3 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| Sparadoxus | GCF_002079055.1 | Not applicable | Not applicable | NC_047501.1:409051-412074:- | gene-YOR048C_Sparadoxus | rna-NM_001183467.1_Sparadoxus | cds-NP_014691.1_Sparadoxus | 91.6 | 99.9 | Verified | 1 | 1 | 1 | False | True | False | False | False |