Gene name: RKR1
Reference locus (S288C): YMR247C
Gene biotype: protein_coding
Description: RING domain E3 ubiquitin ligase; involved in ubiquitin-mediated degradation of non-stop proteins and translationally stalled ER membrane proteins; component of ribosome-bound RQC (ribosome quality control) complex; degrades products of mRNAs lacking a termination codon regardless of a poly(A) tail; functional connections to chromatin modification; homolog of mouse Listerin, mutations in which reported to cause neurodegeneration; Belongs to the LTN1 family
Top 10 interactors (score): RQC2 (0.999); RQC1 (0.999); CDC48 (0.998); NPL4 (0.983); UFD1 (0.983); DOM34 (0.977); HUL4 (0.974); MOT2 (0.965); HEL2 (0.964); UBR1 (0.962); HBS1 (0.947); SKI7 (0.94); UBR2 (0.915); HUL5 (0.895); MDM20 (0.889); VMS1 (0.887); RLI1 (0.877); RPL25 (0.853); RPS20 (0.85); SKI2 (0.835)
Homologues (species, bitscore): LTN1 (Homo sapiens, 180.6); Ltn1 (Mus musculus, 180.6); LTN1 (Danio rerio, 184.9); ltn1 (Xenopus tropicalis, 181.8); l(3)76BDr (Drosophila melanogaster, 132.5); Y54E10A.11 (Caenorhabditis elegans, 121.7); AT5G58410 (Arabidopsis thaliana, 164.1)
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 | CM005307.1:803215-807903:- | gene-YMR247C_AKU4011 | rna-NM_001182755.1_AKU4011 | cds-NP_013975.1_AKU4011 | 98.9 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| BG1 | GCA_001932575.1 | Bioethanol | South America | MSHP01000069.1:146648-151336:+ | gene-YMR247C_BG1 | rna-NM_001182755.1_BG1 | cds-NP_013975.1_BG1 | 99.3 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| Bruggeman | GCA_001738585.1 | Bread | Not Applicable | CM005515.1:747455-752143:- | gene-YMR247C_Bruggeman | rna-NM_001182755.1_Bruggeman | cds-NP_013975.1_Bruggeman | 99.7 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| CAT1 | GCA_001738705.1 | Bioethanol | South America | CM005531.1:751375-756063:- | gene-YMR247C_CAT1 | rna-NM_001182755.1_CAT1 | cds-NP_013975.1_CAT1 | 99.3 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| CBS1585 | GCA_001738375.1 | Sake | Asia | CM005371.1:735475-740163:- | gene-YMR247C_CBS1585 | rna-NM_001182755.1_CBS1585 | cds-NP_013975.1_CBS1585 | 98.9 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| CBS436 | GCA_001738355.1 | Sake | Asia | CM005355.1:739756-744444:- | gene-YMR247C_CBS436 | rna-NM_001182755.1_CBS436 | cds-NP_013975.1_CBS436 | 99.8 | 100.0 | Mismatch | 1 | 1 | 1 | False | True | False | False | False |
| CBS6412 | GCA_001738345.1 | Sake | Asia | CM005339.1:847032-851720:- | gene-YMR247C_CBS6412 | rna-NM_001182755.1_CBS6412 | cds-NP_013975.1_CBS6412 | 98.9 | 100.0 | Mismatch | 1 | 1 | 1 | False | True | False | False | False |
| CBS6413 | GCA_001738265.1 | Sake | Asia | CM005323.1:734626-739314:- | gene-YMR247C_CBS6413 | rna-NM_001182755.1_CBS6413 | cds-NP_013975.1_CBS6413 | 98.9 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| CENPK1137D | GCA_000269885.1 | Laboratory | Not Applicable | CM001534.1:758077-762765:- | gene-YMR247C_CENPK1137D | rna-NM_001182755.1_CENPK1137D | cds-NP_013975.1_CENPK1137D | 98.8 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| EthanolRed | GCA_001738615.1 | Bioethanol | Asia | CM005486.1:795875-800563:- | gene-YMR247C_EthanolRed | rna-NM_001182755.1_EthanolRed | cds-NP_013975.1_EthanolRed | 98.9 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| FaliES1 | GCA_001738715.1 | Bioethanol | Asia | CM005547.1:741900-746588:- | gene-YMR247C_FaliES1 | rna-NM_001182755.1_FaliES1 | cds-NP_013975.1_FaliES1 | 98.9 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| JAY291 | GCA_000182315.2 | Bioethanol | South America | ACFL01000141.1:39986-44674:+ | gene-YMR247C_JAY291 | rna-NM_001182755.1_JAY291 | cds-NP_013975.1_JAY291 | 99.3 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| MUCL30387 | GCA_001738515.1 | Bread | Europe | CM005419.1:741238-745926:- | gene-YMR247C_MUCL30387 | rna-NM_001182755.1_MUCL30387 | cds-NP_013975.1_MUCL30387 | 99.0 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| MUCL30388 | GCA_001738495.1 | Bread | Europe | CM005451.1:748456-754412:- | gene-YMR247C_MUCL30388 | rna-NM_001182755.1_MUCL30388 | cds-NP_013975.1_MUCL30388 | 78.5 | 100.0 | Unannotated | 1 | 1 | 0 | False | False | False | True | False |
| MUCL39482 | GCA_001738235.1 | Sake | Asia | CM005291.1:736545-741233:- | gene-YMR247C_MUCL39482 | rna-NM_001182755.1_MUCL39482 | cds-NP_013975.1_MUCL39482 | 98.9 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| MUCL42920 | GCA_001738485.1 | Bread | Europe | CM005435.1:743902-748590:- | gene-YMR247C_MUCL42920 | rna-NM_001182755.1_MUCL42920 | cds-NP_013975.1_MUCL42920 | 99.4 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| NCIM3186 | GCA_001029075.1 | Bioethanol | Asia | CP011822.1:763305-767993:- | gene-YMR247C_NCIM3186 | rna-NM_001182755.1_NCIM3186 | cds-NP_013975.1_NCIM3186 | 78.9 | 90.7 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| NCYC1407 | GCA_001738225.1 | Sake | Asia | CM005275.1:736200-740888:- | gene-YMR247C_NCYC1407 | rna-NM_001182755.1_NCYC1407 | cds-NP_013975.1_NCYC1407 | 98.9 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| PE2H3 | GCA_905220325.1 | Bioethanol | South America | HG994152.1:746094-750782:- | gene-YMR247C_PE2H3 | rna-NM_001182755.1_PE2H3 | cds-NP_013975.1_PE2H3 | 99.3 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| PE2H4 | GCA_905220315.1 | Bioethanol | South America | LR999884.1:747139-751827:- | gene-YMR247C_PE2H4 | rna-NM_001182755.1_PE2H4 | cds-NP_013975.1_PE2H4 | 99.3 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| S288C | GCF_000146045.2 | Laboratory | Not applicable | NC_001145.3:763351-768039:- | gene-YMR247C_S288C | rna-NM_001182755.1_S288C | cds-NP_013975.1_S288C | 100.0 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| SA1 | GCA_004114265.1 | Bioethanol | South America | SDIA01000002.1:40100-44788:+ | gene-YMR247C_SA1 | rna-NM_001182755.1_SA1 | cds-NP_013975.1_SA1 | 99.3 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| ThermosaccDry | GCA_001738605.1 | Bioethanol | Asia | CM005499.1:738072-742760:- | gene-YMR247C_ThermosaccDry | rna-NM_001182755.1_ThermosaccDry | cds-NP_013975.1_ThermosaccDry | 98.9 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| VR1 | GCA_001738595.1 | Bioethanol | South America | CM005467.1:750627-755315:- | gene-YMR247C_VR1 | rna-NM_001182755.1_VR1 | cds-NP_013975.1_VR1 | 99.3 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| ZTW1 | GCA_000308935.1 | Bioethanol | Asia | AMDD01000028.1:153212-157900:- | gene-YMR247C_ZTW1 | rna-NM_001182755.1_ZTW1 | cds-NP_013975.1_ZTW1 | 98.8 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| Sparadoxus | GCF_002079055.1 | Not applicable | Not applicable | NC_047499.1:755905-760590:- | gene-YMR247C_Sparadoxus | rna-NM_001182755.1_Sparadoxus | cds-NP_013975.1_Sparadoxus | 87.2 | 99.8 | Mismatch | 1 | 1 | 1 | False | True | False | False | False |