CDC39/YCR093W Summary

CDC39/YCR093W Summary

Standard Name	CDC39 1, 2
Systematic Name	YCR093W
Alias	NOT1 3 , ROS1 , SMD6
Feature Type	ORF, Verified
Description	Component of the CCR4-NOT complex, which has multiple roles in regulating mRNA levels including regulation of transcription and destabilizing mRNAs by deadenylation; basal transcription factor (4, 5)
Name Description	Cell Division Cycle 6

Chromosomal Location	ChrIII:280117 to 286443 \| ORF Map \| GBrowse

	Genetic position: 91 cM

Gene Ontology Annotations All CDC39 GO evidence and references

	View Computational GO annotations for CDC39
Molecular Function
Manually curated	molecular_function unknown (ND)
Biological Process
Manually curated	negative regulation of transcription from RNA polymerase II promoter (TAS) nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (IDA, IGI, IMP) nuclear-transcribed mRNA poly(A) tail shortening (IDA) positive regulation of transcription elongation from RNA polymerase II promoter (IDA, IPI) pseudohyphal growth (IMP) regulation of cell cycle (IMP) regulation of transcription from RNA polymerase II promoter (IPI) response to pheromone involved in conjugation with cellular fusion (IMP) transcription elongation from RNA polymerase II promoter (IGI, IMP)
Cellular Component
Manually curated	CCR4-NOT core complex (IPI) cytoplasm (IDA) nucleus (IDA)

Mutant phenotypes All CDC39 Phenotype evidence and references

Classical genetics
conditional	cell cycle passage through START: arrested cell shape: abnormal heat sensitivity: increased
reduction of function	resistance to hydroxyurea: decreased viable
unspecified	pseudohyphal growth: absent transposable element transposition: decreased
Large-scale survey
conditional	colony sectoring: increased
null	inviable
overexpression	cell cycle progression: abnormal
reduction of function	competitive fitness: increased
Resources	PROPHECY \| PhenoM \| SCMD \| ScreenTroll \| Yeast Fitness Database

interactions All CDC39 Interaction evidence and references

	194 total interaction(s) for 77 unique genes/features.
Physical Interactions	Affinity Capture-MS: 63 Affinity Capture-RNA: 3 Affinity Capture-Western: 39 Co-crystal Structure: 1 Co-fractionation: 1 Co-purification: 11 PCA: 21 Reconstituted Complex: 1 Two-hybrid: 19
Genetic Interactions	Dosage Lethality: 1 Dosage Rescue: 8 Phenotypic Suppression: 3 Positive Genetic: 1 Synthetic Haploinsufficiency: 1 Synthetic Lethality: 10 Synthetic Rescue: 11
Resources	BioGRID \| BOND \| BioPIXIE \| CYC2008 (complexes) \| Complexome \| DIP \| DRYGIN \| GeneMANIA \| InterologFinder

Expression Summary


Resources	Expression Summary \| Cell cycle and metabolic oscillation \| Cell cycle transcript profile \| Cyclebase \| Genevestigator \| GermOnline \| SPELL \| YMGV \| YeastFunc

Protein Information All CDC39 Protein evidence and references

Localization	YeastRC \| Organelle DB (UMich) \| YPL+ \| YeastGFP
Phosphorylation	PhosphoGRID \| PhosphoPep Database
Structure	GPMDB \| SCOP \| YeastRC
Homologs	Ashbya (AGD) \| CGD Homologs \| CandidaDB Homologs \| Fungal Orthogroups Repository \| P-POD \| PDB Homologs \| PhylomeDB \| YGOB \| YOGY

sequence information

ChrIII:280117 to 286443 | |

This feature contains embedded feature(s): YCRX20C

SGD ORF map

: 91 cM

Last Update

Coordinates: 2011-02-03 | Sequence: 2000-09-13

Subfeature details

	Relative Coordinates	Chromosomal Coordinates	Most Recent Updates
	Relative Coordinates	Chromosomal Coordinates	Coordinates	Sequence
CDS	1..6327	280117..286443	2011-02-03	2000-09-13

Retrieve sequences

Analyze Sequence

S288C only	BLASTP \| ATCC/WashU Clones \| BLASTN \| Design Primers \| Restriction Fragment Map \| Restriction Fragment Sizes \| Six-Frame Translation
S288C vs. other species	Fungal Alignment \| BLASTN vs. fungi \| BLASTP at NCBI \| BLASTP vs. fungi \| Synteny Viewer
S288C vs. other strains	Strain Alignment

Resources

External Links	All Associated Seq \| Entrez Gene \| Entrez RefSeq Protein \| MIPS \| Search all NCBI (Entrez) \| UniProtKB

Primary SGDID	S000000689

References cited on this page View Complete Literature Guide for CDC39

1)	Reed SI (1980) The selection of S. cerevisiae mutants defective in the start event of cell division. Genetics 95(3):561-77
2)	Breter HJ, et al. (1983) Isolation and transcriptional characterization of three genes which function at start, the controlling event of the Saccharomyces cerevisiae cell division cycle: CDC36, CDC37, and CDC39. Mol Cell Biol 3(5):881-91
3)	Collart MA and Struhl K (1994) NOT1(CDC39), NOT2(CDC36), NOT3, and NOT4 encode a global-negative regulator of transcription that differentially affects TATA-element utilization. Genes Dev 8(5):525-37
4)	Liu HY, et al. (2001) Characterization of CAF4 and CAF16 reveals a functional connection between the CCR4-NOT complex and a subset of SRB proteins of the RNA polymerase II holoenzyme. J Biol Chem 276(10):7541-8
5)	Russell P, et al. (2002) Characterization of mutations in NOT2 indicates that it plays an important role in maintaining the integrity of the CCR4-NOT complex. J Mol Biol 322(1):27-39
6)	Hartwell LH, et al. (1970) Genetic control of the cell-division cycle in yeast. I. Detection of mutants. Proc Natl Acad Sci U S A 66(2):352-9