Gene name: RTR1
Reference locus (S288C): YER139C
Gene biotype: protein_coding
Description: RNA polymerase II subunit B1 CTD phosphatase RTR1; CTD phosphatase; dephosphorylates S5-P in the C-terminal domain of Rpo21p; has a cysteine-rich motif required for function and conserved in eukaryotes; shuttles between the nucleus and cytoplasm; RTR1 has a paralog, RTR2, that arose from the whole genome duplication
Top 10 interactors (score): RPB4 (0.999); RPB9 (0.999); RPO21 (0.999); RPB10 (0.999); RPB8 (0.999); RPC10 (0.999); RPB5 (0.999); RPO26 (0.999); RPB11 (0.999); RPB3 (0.999); RPB2 (0.999); RPB7 (0.999); FCP1 (0.985); SSU72 (0.978); RTT103 (0.974); KIN28 (0.96); TYR1 (0.918); NPA3 (0.915); SUA7 (0.907); SSN3 (0.902)
Homologues (species, bitscore): RPAP2 (Homo sapiens, 57.4); Rpap2 (Mus musculus, 58.9)
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 | CM005299.1:438050-438730:- | gene-YER139C_AKU4011 | rna-NM_001179029.3_AKU4011 | cds-NP_011066.3_AKU4011 | 99.5 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| BG1 | GCA_001932575.1 | Bioethanol | South America | MSHP01000176.1:105879-106559:+ | gene-YER139C_BG1 | rna-NM_001179029.3_BG1 | cds-NP_011066.3_BG1 | 99.8 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| Bruggeman | GCA_001738585.1 | Bread | Not Applicable | CM005507.1:449335-450015:- | gene-YER139C_Bruggeman | rna-NM_001179029.3_Bruggeman | cds-NP_011066.3_Bruggeman | 99.7 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| CAT1 | GCA_001738705.1 | Bioethanol | South America | CM005523.1:437175-437855:- | gene-YER139C_CAT1 | rna-NM_001179029.3_CAT1 | cds-NP_011066.3_CAT1 | 99.8 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| CBS1585 | GCA_001738375.1 | Sake | Asia | CM005363.1:437850-438530:- | gene-YER139C_CBS1585 | rna-NM_001179029.3_CBS1585 | cds-NP_011066.3_CBS1585 | 99.5 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| CBS436 | GCA_001738355.1 | Sake | Asia | CM005347.1:441675-442355:- | gene-YER139C_CBS436 | rna-NM_001179029.3_CBS436 | cds-NP_011066.3_CBS436 | 99.7 | 100.0 | Mismatch | 1 | 1 | 1 | False | True | False | False | False |
| CBS6412 | GCA_001738345.1 | Sake | Asia | CM005331.1:436371-437051:- | gene-YER139C_CBS6412 | rna-NM_001179029.3_CBS6412 | cds-NP_011066.3_CBS6412 | 99.5 | 100.0 | Mismatch | 1 | 1 | 1 | True | True | False | False | False |
| CBS6413 | GCA_001738265.1 | Sake | Asia | CM005315.1:443915-444595:- | gene-YER139C_CBS6413 | rna-NM_001179029.3_CBS6413 | cds-NP_011066.3_CBS6413 | 99.5 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| CENPK1137D | GCA_000269885.1 | Laboratory | Not Applicable | CM001526.1:448336-449016:- | gene-YER139C_CENPK1137D | rna-NM_001179029.3_CENPK1137D | cds-NP_011066.3_CENPK1137D | 100.0 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| EthanolRed | GCA_001738615.1 | Bioethanol | Asia | CM005475.1:444331-445011:- | gene-YER139C_EthanolRed | rna-NM_001179029.3_EthanolRed | cds-NP_011066.3_EthanolRed | 99.1 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| FaliES1 | GCA_001738715.1 | Bioethanol | Asia | CM005539.1:444917-445597:- | gene-YER139C_FaliES1 | rna-NM_001179029.3_FaliES1 | cds-NP_011066.3_FaliES1 | 99.1 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| JAY291 | GCA_000182315.2 | Bioethanol | South America | ACFL01000111.1:40883-41563:+ | gene-YER139C_JAY291 | rna-NM_001179029.3_JAY291 | cds-NP_011066.3_JAY291 | 99.8 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| MUCL30387 | GCA_001738515.1 | Bread | Europe | CM005411.1:438079-438759:- | gene-YER139C_MUCL30387 | rna-NM_001179029.3_MUCL30387 | cds-NP_011066.3_MUCL30387 | 99.8 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| MUCL30388 | GCA_001738495.1 | Bread | Europe | CM005443.1:440970-441650:- | gene-YER139C_MUCL30388 | rna-NM_001179029.3_MUCL30388 | cds-NP_011066.3_MUCL30388 | 99.7 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| MUCL39482 | GCA_001738235.1 | Sake | Asia | CM005283.1:433821-434501:- | gene-YER139C_MUCL39482 | rna-NM_001179029.3_MUCL39482 | cds-NP_011066.3_MUCL39482 | 99.5 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| MUCL42920 | GCA_001738485.1 | Bread | Europe | CM005427.1:445896-446576:- | gene-YER139C_MUCL42920 | rna-NM_001179029.3_MUCL42920 | cds-NP_011066.3_MUCL42920 | 99.7 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| NCIM3186 | GCA_001029075.1 | Bioethanol | Asia | CP011814.1:450562-451242:- | gene-YER139C_NCIM3186 | rna-NM_001179029.3_NCIM3186 | cds-NP_011066.3_NCIM3186 | 99.7 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| NCYC1407 | GCA_001738225.1 | Sake | Asia | CM005267.1:443279-443959:- | gene-YER139C_NCYC1407 | rna-NM_001179029.3_NCYC1407 | cds-NP_011066.3_NCYC1407 | 99.5 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| PE2H3 | GCA_905220325.1 | Bioethanol | South America | HG994144.1:458973-459653:- | gene-YER139C_PE2H3 | rna-NM_001179029.3_PE2H3 | cds-NP_011066.3_PE2H3 | 99.8 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| PE2H4 | GCA_905220315.1 | Bioethanol | South America | LR999876.1:448914-449594:- | gene-YER139C_PE2H4 | rna-NM_001179029.3_PE2H4 | cds-NP_011066.3_PE2H4 | 99.8 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| S288C | GCF_000146045.2 | Laboratory | Not applicable | NC_001137.3:450563-451243:- | gene-YER139C_S288C | rna-NM_001179029.3_S288C | cds-NP_011066.3_S288C | 100.0 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| SA1 | GCA_004114265.1 | Bioethanol | South America | SDIA01000030.1:8444-9124:- | gene-YER139C_SA1 | rna-NM_001179029.3_SA1 | cds-NP_011066.3_SA1 | 99.8 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| ThermosaccDry | GCA_001738605.1 | Bioethanol | Asia | CM005491.1:445715-446395:- | gene-YER139C_ThermosaccDry | rna-NM_001179029.3_ThermosaccDry | cds-NP_011066.3_ThermosaccDry | 99.1 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| VR1 | GCA_001738595.1 | Bioethanol | South America | CM005459.1:438837-439517:- | gene-YER139C_VR1 | rna-NM_001179029.3_VR1 | cds-NP_011066.3_VR1 | 99.8 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| ZTW1 | GCA_000308935.1 | Bioethanol | Asia | AMDD01000010.1:679-1359:- | gene-YER139C_ZTW1 | rna-NM_001179029.3_ZTW1 | cds-NP_011066.3_ZTW1 | 99.7 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| Sparadoxus | GCF_002079055.1 | Not applicable | Not applicable | NC_047491.1:446560-447240:- | gene-YER139C_Sparadoxus | rna-NM_001179029.3_Sparadoxus | cds-NP_011066.3_Sparadoxus | 92.5 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |