Gene name: CAF40
Reference locus (S288C): YNL288W
Gene biotype: protein_coding
Description: Protein CAF40; Component of the CCR4-NOT transcriptional complex; evolutionarily conserved; involved in controlling mRNA initiation, elongation, and degradation; binds Cdc39p
Top 10 interactors (score): CDC39 (0.999); CCR4 (0.999); MOT2 (0.999); NOT3 (0.999); CDC36 (0.999); POP2 (0.999); CAF130 (0.999); NOT5 (0.999); CAF16 (0.97); BTT1 (0.964); MTR4 (0.949); DHH1 (0.929); PAP2 (0.919); XRN1 (0.888); NGL1 (0.882); CAF4 (0.873); MPT5 (0.839); PHO92 (0.748); SCD6 (0.694); EGD1 (0.688)
Homologues (species, bitscore): RQCD1 (Homo sapiens, 335.9); Rqcd1 (Mus musculus, 337.0); rqcd1 (Danio rerio, 328.9); rqcd1 (Xenopus tropicalis, 337.4); Rcd-1 (Drosophila melanogaster, 311.2); ntl-9 (Caenorhabditis elegans, 285.0); AT3G20800 (Arabidopsis thaliana, 311.2)
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 | CM005308.1:84121-85233:+ | gene-YNL288W_AKU4011 | rna-NM_001183126.1_AKU4011 | cds-NP_014111.1_AKU4011 | 98.4 | 99.1 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| BG1 | GCA_001932575.1 | Bioethanol | South America | MSHP01000074.1:5410-6531:- | gene-YNL288W_BG1 | rna-NM_001183126.1_BG1 | cds-NP_014111.1_BG1 | 99.7 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| Bruggeman | GCA_001738585.1 | Bread | Not Applicable | CM005516.1:93462-94583:+ | gene-YNL288W_Bruggeman | rna-NM_001183126.1_Bruggeman | cds-NP_014111.1_Bruggeman | 99.4 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| CAT1 | GCA_001738705.1 | Bioethanol | South America | CM005532.1:96067-97188:+ | gene-YNL288W_CAT1 | rna-NM_001183126.1_CAT1 | cds-NP_014111.1_CAT1 | 99.5 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| CBS1585 | GCA_001738375.1 | Sake | Asia | CM005372.1:84451-85563:+ | gene-YNL288W_CBS1585 | rna-NM_001183126.1_CBS1585 | cds-NP_014111.1_CBS1585 | 98.5 | 99.1 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| CBS436 | GCA_001738355.1 | Sake | Asia | CM005356.1:84934-86055:+ | gene-YNL288W_CBS436 | rna-NM_001183126.1_CBS436 | cds-NP_014111.1_CBS436 | 99.7 | 100.0 | Mismatch | 1 | 1 | 1 | False | True | False | False | False |
| CBS6412 | GCA_001738345.1 | Sake | Asia | CM005340.1:81108-82220:+ | gene-YNL288W_CBS6412 | rna-NM_001183126.1_CBS6412 | cds-NP_014111.1_CBS6412 | 98.5 | 99.1 | Mismatch | 1 | 1 | 1 | False | True | False | False | False |
| CBS6413 | GCA_001738265.1 | Sake | Asia | CM005324.1:81299-82411:+ | gene-YNL288W_CBS6413 | rna-NM_001183126.1_CBS6413 | cds-NP_014111.1_CBS6413 | 98.5 | 99.1 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| CENPK1137D | GCA_000269885.1 | Laboratory | Not Applicable | CM001535.1:84135-85256:+ | gene-YNL288W_CENPK1137D | rna-NM_001183126.1_CENPK1137D | cds-NP_014111.1_CENPK1137D | 100.0 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| EthanolRed | GCA_001738615.1 | Bioethanol | Asia | CM005484.1:81137-82267:+ | gene-YNL288W_EthanolRed | rna-NM_001183126.1_EthanolRed | cds-NP_014111.1_EthanolRed | 98.8 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| FaliES1 | GCA_001738715.1 | Bioethanol | Asia | CM005548.1:82036-83166:+ | gene-YNL288W_FaliES1 | rna-NM_001183126.1_FaliES1 | cds-NP_014111.1_FaliES1 | 98.8 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| JAY291 | GCA_000182315.2 | Bioethanol | South America | ACFL01000171.1:5066-6187:- | gene-YNL288W_JAY291 | rna-NM_001183126.1_JAY291 | cds-NP_014111.1_JAY291 | 99.7 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| MUCL30387 | GCA_001738515.1 | Bread | Europe | CM005420.1:93961-95091:+ | gene-YNL288W_MUCL30387 | rna-NM_001183126.1_MUCL30387 | cds-NP_014111.1_MUCL30387 | 98.8 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| MUCL30388 | GCA_001738495.1 | Bread | Europe | CM005452.1:86741-87862:+ | gene-YNL288W_MUCL30388 | rna-NM_001183126.1_MUCL30388 | cds-NP_014111.1_MUCL30388 | 99.6 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| MUCL39482 | GCA_001738235.1 | Sake | Asia | CM005292.1:82085-83197:+ | gene-YNL288W_MUCL39482 | rna-NM_001183126.1_MUCL39482 | cds-NP_014111.1_MUCL39482 | 98.5 | 99.1 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| MUCL42920 | GCA_001738485.1 | Bread | Europe | CM005436.1:83770-84891:+ | gene-YNL288W_MUCL42920 | rna-NM_001183126.1_MUCL42920 | cds-NP_014111.1_MUCL42920 | 99.7 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| NCIM3186 | GCA_001029075.1 | Bioethanol | Asia | CP011823.1:90272-91393:+ | gene-YNL288W_NCIM3186 | rna-NM_001183126.1_NCIM3186 | cds-NP_014111.1_NCIM3186 | 99.4 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| NCYC1407 | GCA_001738225.1 | Sake | Asia | CM005276.1:83417-84529:+ | gene-YNL288W_NCYC1407 | rna-NM_001183126.1_NCYC1407 | cds-NP_014111.1_NCYC1407 | 98.5 | 99.1 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| PE2H3 | GCA_905220325.1 | Bioethanol | South America | HG994153.1:80609-81730:+ | gene-YNL288W_PE2H3 | rna-NM_001183126.1_PE2H3 | cds-NP_014111.1_PE2H3 | 99.7 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| PE2H4 | GCA_905220315.1 | Bioethanol | South America | LR999885.1:79997-81118:+ | gene-YNL288W_PE2H4 | rna-NM_001183126.1_PE2H4 | cds-NP_014111.1_PE2H4 | 99.7 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| S288C | GCF_000146045.2 | Laboratory | Not applicable | NC_001146.8:90303-91424:+ | gene-YNL288W_S288C | rna-NM_001183126.1_S288C | cds-NP_014111.1_S288C | 100.0 | 100.0 | Verified | 1 | 1 | 1 | True | True | False | False | False |
| SA1 | GCA_004114265.1 | Bioethanol | South America | SDIA01000052.1:5805-6917:- | gene-YNL288W_SA1 | rna-NM_001183126.1_SA1 | cds-NP_014111.1_SA1 | 98.7 | 99.1 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| ThermosaccDry | GCA_001738605.1 | Bioethanol | Asia | CM005500.1:82893-84023:+ | gene-YNL288W_ThermosaccDry | rna-NM_001183126.1_ThermosaccDry | cds-NP_014111.1_ThermosaccDry | 98.8 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| VR1 | GCA_001738595.1 | Bioethanol | South America | CM005468.1:95429-96550:+ | gene-YNL288W_VR1 | rna-NM_001183126.1_VR1 | cds-NP_014111.1_VR1 | 99.7 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| ZTW1 | GCA_000308935.1 | Bioethanol | Asia | AMDD01000029.1:74103-75233:+ | gene-YNL288W_ZTW1 | rna-NM_001183126.1_ZTW1 | cds-NP_014111.1_ZTW1 | 98.7 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |
| Sparadoxus | GCF_002079055.1 | Not applicable | Not applicable | NC_047500.1:92155-93276:+ | gene-YNL288W_Sparadoxus | rna-NM_001183126.1_Sparadoxus | cds-NP_014111.1_Sparadoxus | 92.0 | 100.0 | Verified | 1 | 1 | 1 | False | True | False | False | False |