Gene name: TDP1
Reference locus (S288C): YBR223C
Gene biotype: protein_coding
Description: Tyrosyl-DNA phosphodiesterase I; hydrolyzes 3' and 5'-phosphotyrosyl bonds; involved in the repair of DNA lesions created by topo I and topo II; mutations in the human homolog, TDP1, result in the a neurodegenerative disease, spinocerebellar ataxia with axonal neuropathy (SCAN1); yeast cells and human rhabdomyosarcoma lines that overexpress TDP1 both exhibit elevated dosage chromosomal instability (dCIN)
Top 10 interactors (score): TOP1 (0.998); TPP1 (0.993); APN2 (0.988); TOP2 (0.979); MUS81 (0.96); WSS1 (0.96); APN1 (0.94); HNT3 (0.928); YKU70 (0.92); EXO1 (0.917); RAD10 (0.915); RAD27 (0.915); DNL4 (0.914); RAD1 (0.913); RAD52 (0.908); POL4 (0.898); CDC9 (0.885); SMT3 (0.877); MRE11 (0.788); SPO11 (0.786)
Homologues (species, bitscore): TDP1 (Homo sapiens, 82.8); Tdp1 (Mus musculus, 75.1); tdp1 (Danio rerio, 85.1); tdp1 (Xenopus tropicalis, 67.8); gkt (Drosophila melanogaster, 59.7); F52C12.1 (Caenorhabditis elegans, 55.5)
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 | CM005296.1:652969-654603:- | gene-YBR223C_AKU4011 | rna-NM_001178571.3_AKU4011 | cds-NP_009782.3_AKU4011 | 99.8 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| BG1 | GCA_001932575.1 | Bioethanol | South America | MSHP01000066.1:23890-25524:- | gene-YBR223C_BG1 | rna-NM_001178571.3_BG1 | cds-NP_009782.3_BG1 | 99.5 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| Bruggeman | GCA_001738585.1 | Bread | Not Applicable | CM005504.1:654124-655758:- | gene-YBR223C_Bruggeman | rna-NM_001178571.3_Bruggeman | cds-NP_009782.3_Bruggeman | 99.5 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| CAT1 | GCA_001738705.1 | Bioethanol | South America | CM005520.1:657329-658963:- | gene-YBR223C_CAT1 | rna-NM_001178571.3_CAT1 | cds-NP_009782.3_CAT1 | 99.5 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| CBS1585 | GCA_001738375.1 | Sake | Asia | CM005360.1:644501-646135:- | gene-YBR223C_CBS1585 | rna-NM_001178571.3_CBS1585 | cds-NP_009782.3_CBS1585 | 99.8 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| CBS436 | GCA_001738355.1 | Sake | Asia | CM005344.1:650926-652560:- | gene-YBR223C_CBS436 | rna-NM_001178571.3_CBS436 | cds-NP_009782.3_CBS436 | 99.5 | 100.0 | Mismatch | 1 | 1 | 1 | False | True | False | False | False |
| CBS6412 | GCA_001738345.1 | Sake | Asia | CM005328.1:739478-741112:- | gene-YBR223C_CBS6412 | rna-NM_001178571.3_CBS6412 | cds-NP_009782.3_CBS6412 | 99.8 | 100.0 | Mismatch | 1 | 1 | 1 | False | True | False | False | False |
| CBS6413 | GCA_001738265.1 | Sake | Asia | CM005312.1:650539-652173:- | gene-YBR223C_CBS6413 | rna-NM_001178571.3_CBS6413 | cds-NP_009782.3_CBS6413 | 99.8 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| CENPK1137D | GCA_000269885.1 | Laboratory | Not Applicable | CM001523.1:662443-664077:- | gene-YBR223C_CENPK1137D | rna-NM_001178571.3_CENPK1137D | cds-NP_009782.3_CENPK1137D | 99.5 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| EthanolRed | GCA_001738615.1 | Bioethanol | Asia | CM005472.1:776214-777848:- | gene-YBR223C_EthanolRed | rna-NM_001178571.3_EthanolRed | cds-NP_009782.3_EthanolRed | 99.8 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| FaliES1 | GCA_001738715.1 | Bioethanol | Asia | CM005536.1:669321-670955:- | gene-YBR223C_FaliES1 | rna-NM_001178571.3_FaliES1 | cds-NP_009782.3_FaliES1 | 99.8 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| JAY291 | GCA_000182315.2 | Bioethanol | South America | ACFL01000067.1:131400-133034:+ | gene-YBR223C_JAY291 | rna-NM_001178571.3_JAY291 | cds-NP_009782.3_JAY291 | 99.5 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| MUCL30387 | GCA_001738515.1 | Bread | Europe | CM005408.1:656137-657771:- | gene-YBR223C_MUCL30387 | rna-NM_001178571.3_MUCL30387 | cds-NP_009782.3_MUCL30387 | 99.5 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| MUCL30388 | GCA_001738495.1 | Bread | Europe | CM005440.1:673217-674851:- | gene-YBR223C_MUCL30388 | rna-NM_001178571.3_MUCL30388 | cds-NP_009782.3_MUCL30388 | 99.5 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| MUCL39482 | GCA_001738235.1 | Sake | Asia | CM005280.1:642853-644487:- | gene-YBR223C_MUCL39482 | rna-NM_001178571.3_MUCL39482 | cds-NP_009782.3_MUCL39482 | 99.8 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| MUCL42920 | GCA_001738485.1 | Bread | Europe | CM005424.1:652696-654330:- | gene-YBR223C_MUCL42920 | rna-NM_001178571.3_MUCL42920 | cds-NP_009782.3_MUCL42920 | 99.5 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| NCIM3186 | GCA_001029075.1 | Bioethanol | Asia | CP011811.1:668460-670094:- | gene-YBR223C_NCIM3186 | rna-NM_001178571.3_NCIM3186 | cds-NP_009782.3_NCIM3186 | 99.5 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| NCYC1407 | GCA_001738225.1 | Sake | Asia | CM005264.1:644715-646349:- | gene-YBR223C_NCYC1407 | rna-NM_001178571.3_NCYC1407 | cds-NP_009782.3_NCYC1407 | 99.8 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| PE2H3 | GCA_905220325.1 | Bioethanol | South America | HG994141.1:667831-669465:- | gene-YBR223C_PE2H3 | rna-NM_001178571.3_PE2H3 | cds-NP_009782.3_PE2H3 | 99.5 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| PE2H4 | GCA_905220315.1 | Bioethanol | South America | LR999873.1:665507-667141:- | gene-YBR223C_PE2H4 | rna-NM_001178571.3_PE2H4 | cds-NP_009782.3_PE2H4 | 99.5 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| S288C | GCF_000146045.2 | Laboratory | Not applicable | NC_001134.8:668663-670297:- | gene-YBR223C_S288C | rna-NM_001178571.3_S288C | cds-NP_009782.3_S288C | 100.0 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| SA1 | GCA_004114265.1 | Bioethanol | South America | SDIA01000019.1:23788-25422:- | gene-YBR223C_SA1 | rna-NM_001178571.3_SA1 | cds-NP_009782.3_SA1 | 99.5 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| ThermosaccDry | GCA_001738605.1 | Bioethanol | Asia | CM005488.1:668331-669965:- | gene-YBR223C_ThermosaccDry | rna-NM_001178571.3_ThermosaccDry | cds-NP_009782.3_ThermosaccDry | 99.8 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| VR1 | GCA_001738595.1 | Bioethanol | South America | CM005456.1:648504-650138:- | gene-YBR223C_VR1 | rna-NM_001178571.3_VR1 | cds-NP_009782.3_VR1 | 99.4 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| ZTW1 | GCA_000308935.1 | Bioethanol | Asia | AMDD01000003.1:641196-642830:- | gene-YBR223C_ZTW1 | rna-NM_001178571.3_ZTW1 | cds-NP_009782.3_ZTW1 | 99.6 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| Sparadoxus | GCF_002079055.1 | Not applicable | Not applicable | NC_047488.1:685160-686794:- | gene-YBR223C_Sparadoxus | rna-NM_001178571.3_Sparadoxus | cds-NP_009782.3_Sparadoxus | 84.8 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |