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CDC40/YDR364C Single Page Format

This page provides an alternative format to the SGD Locus Summary Page. Note that additional information may be available on or linked from the standard format SGD Locus Summary page.

Contents

Names and Identifiers GO Annotations Pathways Summary Paragraph Mutant Phenotypes Interactions Homologs Protein Info (physical properties, transcript info) PDB Homologs (protein structure info) Motifs Genome-wide Expression (and other large-scale analyses) Locus History (misc. notes) Sequence Retrieval and Analysis Map and Displays Localization Community Annotation Literature Guide

Sequence Coordinates   ChrIV: 1204203 to 1202836 CDS: 1204203 - 1202836 Genetic position: 211 cM Genetic Map Data Click on map for expanded view SGD ORF map GBrowse

SGD Locus Page

Names and Identifiers [TOP] [NEXT]
Standard Name	Systematic Name	Alias	Feature Type	SGDID
CDC40	YDR364C	PRP17, SLT15, SLU4	ORF, Verified	S000002772
Description
Pre-mRNA splicing factor, important for catalytic step II of pre-mRNA splicing and plays a role in cell cycle progression; required for DNA synthesis during mitosis and meiosis; has WD repeats

GO Annotations [TOP] [NEXT]
Molecular Function Annotation(s) Reference(s) Evidence Assigned By contributes_to second spliceosomal transesterification activity Lindsey-Boltz LA, et al. (2000) The carboxy terminal WD domain of the pre-mRNA splicing factor Prp17p is critical for function. RNA 6(9):1289-305      IMP : Inferred from Mutant Phenotype IGI : Inferred from Genetic Interaction Assigned on 2009-10-30 SGD
Biological Process Annotation(s) Reference(s) Evidence Assigned By G1/S transition of mitotic cell cycle Kaplan Y and Kupiec M (2007) A role for the yeast cell cycle/splicing factor Cdc40 in the G(1)/S transition. Curr Genet 51(2):123-40        IMP : Inferred from Mutant Phenotype Assigned on 2007-04-18 SGD RNA splicing GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0508 Assigned on 2007-05-23 UniProtKB cell cycle GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0131 Assigned on 2007-05-23 UniProtKB cell division GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0132 Assigned on 2007-05-23 UniProtKB generation of catalytic spliceosome for second transesterification step Lindsey-Boltz LA, et al. (2000) The carboxy terminal WD domain of the pre-mRNA splicing factor Prp17p is critical for function. RNA 6(9):1289-305      IMP : Inferred from Mutant Phenotype IGI : Inferred from Genetic Interaction Assigned on 2009-10-30 SGD mRNA processing GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0507 Assigned on 2007-05-23 UniProtKB nuclear mRNA 3'-splice site recognition Ben-Yehuda S, et al. (2000) Extensive genetic interactions between PRP8 and PRP17/CDC40, two yeast genes involved in pre-mRNA splicing and cell cycle progression. Genetics 154(1):61-71        IGI : Inferred from Genetic Interaction with SGD:PRP8 Assigned on 2006-09-29 SGD Dahan O and Kupiec M (2004) The Saccharomyces cerevisiae gene CDC40/PRP17 controls cell cycle progression through splicing of the ANC1 gene. Nucleic Acids Res 32(8):2529-40        IGI : Inferred from Genetic Interaction with SGD:TAF14 Assigned on 2006-09-29 SGD nuclear mRNA branch site recognition Dahan O and Kupiec M (2004) The Saccharomyces cerevisiae gene CDC40/PRP17 controls cell cycle progression through splicing of the ANC1 gene. Nucleic Acids Res 32(8):2529-40        IGI : Inferred from Genetic Interaction with SGD:TAF14 Assigned on 2006-09-29 SGD
Cellular Component Annotation(s) Reference(s) Evidence Assigned By nucleus GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0539 Assigned on 2007-05-23 UniProtKB GOA curators and UniProt curators (2007) Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping.      IEA : Inferred from Electronic Annotation with EBI:SL-0191 Assigned on 2008-02-13 UniProtKB spliceosomal complex Ben Yehuda S, et al. (1998) Identification and functional analysis of hPRP17, the human homologue of the PRP17/CDC40 yeast gene involved in splicing and cell cycle control. RNA 4(10):1304-12      IDA : Inferred from Direct Assay Assigned on 2006-09-29 SGD GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0747 Assigned on 2007-05-23 UniProtKB

Pathways [TOP] [NEXT]
No pathways available

Summary Paragraph [TOP] [NEXT]
No summary paragraph available

Basic References [TOP]

BASIC INFORMATION REFERENCES forCDC40/YDR364C for CDC40 1) Lindsey-Boltz LA, et al. (2000) The carboxy terminal WD domain of the pre-mRNA splicing factor Prp17p is critical for function. RNA 6(9):1289-305      2) Kassir Y and Simchen G (1978) Meiotic recombination and DNA synthesis in a new cell cycle mutant of Saccharomyces cerevisiae. Genetics 90(1):49-68      3) Kassir, Y., et al. (1985) Personal Communication, Mortimer Map Edition 9

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for CDC40/YDR364C

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for CDC40/YDR364C

Homologs [TOP] [NEXT]
Comparison Resources PSI-BLAST Results Ashbya Homologs (AGD) BLASTN vs. fungi BLASTP at NCBI BLASTP vs. fungi Candida Homologs (CGD) Candida Homologs (CandidaDB) Fungal Alignment Fungal Orthogroups Repository Ortholog Search (P-POD) PhylomeDB Synteny Viewer Yeast Gene Order Browser (YGOB) eukarYotic OrtholoGY (YOGY)

Physical Properties and Transcript Information: predicted from sequence [TOP] [NEXT]

Protein Sequence Calculations from Predicted Full length Translation N-term MGLVDGY C-term GKIYVCD Length(aa) 455 MW(Da) 52,047 pI 7.2 Amino Acid Composition (full length) GCG tools: PepPlot, Helical Wheel, PepStruct Transcript Translation Calculations Codon Bias -0.014   Codon Adaptation Index 0.136   Frequency of Optimal Codons 0.408   Hydropathicity of Protein -0.844   Aromaticity Score 0.103

10 20 30 40 50 | | | | | MGLVDGYDTSSDSDLNFDEGKSVHEKKNGNLHEDTSYEPSSNNIHKRKSH FTKSELKRRRKTRKGDGPWGSWSSSDDETSQASETQKEDQDIFVHALAED NLDSEQIEVEEVSHFYGKSEKDYQGRGYLYPPNDVDVDLREERISFRCYL PKKVIRNYPGHPEGTTALKFLPKTGHLILSGGNDHTIKIWDFYHDYECLR DFQGHNKPIKALRFTEDCQSFLSSSFDRSVKIWDTETGKVKTRLHLNSTP ADVESRPTNPHEFIVGLSNSKILHYDDRVSENQGLVQTYDHHLSSILALK YFPDGSKFISSSEDKTVRIWENQINVPIKQISDTAQHSMPFLNVHPSQNY FCAQSMDNRIYSFSLKPKYKRHPKKIFKGHSSAGYGISLAFSGDGRYICS GDSKSRLFTWDWNTSRLLNNIKIPGNKPITQVDWHPQETSKVICSGAAGK IYVCD*

Protein Structures from PDB: proteins of known structure with sequence similarity to CDC40/YDR364C, based on Smith-Waterman analysis. [TOP] [NEXT]

PDB protein structure(s) homologous to CDC40 Homolog Source (per PDB) Protein Alignment: CDC40 vs. Homolog External Links P-Value %Identical %Similar Alignment 2g99 ( Chain: B, A) Structural basis for the specific recognition of methylated histone h3 lysine 4 by the wd-40 protein wdr5 PDB_Info PDB_Structure Homo sapiens Chain B = 3.1e-15 28 33 View alignment SCOP MMDB CATH Chain A = 3.1e-15 28 33 View alignment 2h68 ( Chain: B, A) Histone h3 recognition and presentation by the wdr5 module of the mll1 complex PDB_Info PDB_Structure Homo sapiens Chain B = 3.2e-15 28 33 View alignment SCOP MMDB CATH Chain A = 3.2e-15 28 33 View alignment 2h6q ( Chain: A, B) Histone h3 recognition and presentation by the wdr5 module of the mll1 complex PDB_Info PDB_Structure Homo sapiens Chain A = 3.2e-15 28 33 View alignment SCOP MMDB CATH Chain B = 3.2e-15 28 33 View alignment 2h6n ( Chain: B, A) Histone h3 recognition and presentation by the wdr5 module of the mll1 complex PDB_Info PDB_Structure Homo sapiens Chain B = 3.2e-15 28 33 View alignment SCOP MMDB CATH Chain A = 3.2e-15 28 33 View alignment 3eg6 ( Chain: A) Structure of wdr5 bound to mll1 peptide PDB_Info PDB_Structure Homo sapiens 3.2e-15 28 33 View alignment SCOP MMDB CATH 2h6k ( Chain: B, A) Histone h3 recognition and presentation by the wdr5 module of the mll1 complex PDB_Info PDB_Structure Homo sapiens Chain B = 3.2e-15 28 33 View alignment SCOP MMDB CATH Chain A = 3.2e-15 28 33 View alignment 2h9m ( Chain: C, A) Wdr5 in complex with unmodified h3k4 peptide PDB_Info PDB_Structure Homo sapiens Chain C = 3.2e-15 28 33 View alignment SCOP MMDB CATH Chain A = 3.2e-15 28 33 View alignment 2g9a ( Chain: A) Structural basis for the specific recognition of methylated histone h3 lysine 4 by the wd-40 protein wdr5 PDB_Info PDB_Structure Homo sapiens 3.2e-15 28 33 View alignment SCOP MMDB CATH 2h9n ( Chain: C, A) Wdr5 in complex with monomethylated h3k4 peptide PDB_Info PDB_Structure Homo sapiens Chain C = 3.2e-15 28 33 View alignment SCOP MMDB CATH Chain A = 3.2e-15 28 33 View alignment 2co0 ( Chain: C, A) Wdr5 and unmodified histone h3 complex at 2.25 angstrom PDB_Info PDB_Structure Homo sapiens Chain C = 3.2e-15 28 32 View alignment SCOP MMDB CATH Chain A = 4.4e-15 28 32 View alignment 2cnx ( Chain: A) Wdr5 and histone h3 lysine 4 dimethyl complex at 2.1 angstrom PDB_Info PDB_Structure Homo sapiens 3.2e-15 28 32 View alignment SCOP MMDB CATH 2o9k ( Chain: A, C) Wdr5 in complex with dimethylated h3k4 peptide PDB_Info PDB_Structure Homo sapiens Chain A = 3.2e-15 28 33 View alignment SCOP MMDB CATH Chain C = 3.2e-15 28 33 View alignment 2h13 ( Chain: A) Crystal structure of wdr5/histone h3 complex PDB_Info PDB_Structure Homo sapiens 3.4e-15 28 33 View alignment SCOP MMDB CATH 2h14 ( Chain: A) Crystal of wdr5 (apo-form) PDB_Info PDB_Structure Homo sapiens 3.4e-15 28 33 View alignment SCOP MMDB CATH 3emh ( Chain: A) Structural basis of wdr5-mll interaction PDB_Info PDB_Structure Homo sapiens 3.4e-15 28 33 View alignment SCOP MMDB CATH 2h9l ( Chain: A) Wdr5delta23 PDB_Info PDB_Structure Homo sapiens 3.5e-15 28 33 View alignment SCOP MMDB CATH 2h9p ( Chain: A) Wdr5 in complex with trimethylated h3k4 peptide PDB_Info PDB_Structure Homo sapiens 3.5e-15 28 33 View alignment SCOP MMDB CATH 2gnq ( Chain: A) Structure of wdr5 PDB_Info PDB_Structure Homo sapiens 3.5e-15 28 33 View alignment SCOP MMDB CATH 2ovq ( Chain: B) Structure of the skp1-fbw7-cyclinedegc complex PDB_Info PDB_Structure Homo sapiens 8.9e-11 25 31 View alignment SCOP MMDB CATH 2ovr ( Chain: B) Structure of the skp1-fbw7-cyclinedegn complex PDB_Info PDB_Structure Homo sapiens 8.9e-11 25 31 View alignment SCOP MMDB CATH 2ovp ( Chain: B) Structure of the skp1-fbw7 complex PDB_Info PDB_Structure Homo sapiens 8.9e-11 25 31 View alignment SCOP MMDB CATH 3frx ( Chain: C, A, D, B) Crystal structure of the yeast orthologue of rack1, asc1. PDB_Info PDB_Structure Saccharomyces cerevisiae Chain C = 9.4e-10 25 32 View alignment SCOP MMDB CATH Chain A = 9.4e-10 25 32 View alignment Chain D = 9.4e-10 25 32 View alignment Chain B = 9.4e-10 25 32 View alignment 1trj ( Chain: A) Homology model of yeast rack1 protein fitted into 11.7a cryo-em map of yeast 80s ribosome PDB_Info PDB_Structure Saccharomyces cerevisiae 1.0e-09 25 31 View alignment SCOP MMDB CATH 1vyh ( Chain: H, K, C, P, G, L, D, T, S, O) Paf-ah holoenzyme: lis1/alfa2 PDB_Info PDB_Structure Mus musculus | Homo sapiens Chain H = 1.2e-09 25 34 View alignment SCOP MMDB CATH Chain K = 1.2e-09 25 34 View alignment Chain C = 1.2e-09 25 34 View alignment Chain P = 1.2e-09 25 34 View alignment Chain G = 1.2e-09 25 34 View alignment Chain L = 1.2e-09 25 34 View alignment Chain D = 1.2e-09 25 34 View alignment Chain T = 1.2e-09 25 34 View alignment Chain S = 1.2e-09 25 34 View alignment Chain O = 1.2e-09 25 34 View alignment 1erj ( Chain: B, C, A) Crystal structure of the c-terminal wd40 domain of tup1 PDB_Info PDB_Structure Saccharomyces cerevisiae Chain B = 5.8e-09 25 32 View alignment SCOP MMDB CATH Chain C = 5.8e-09 25 32 View alignment Chain A = 5.8e-09 25 32 View alignment 2pbi ( Chain: D, B) The multifunctional nature of gbeta5/rgs9 revealed from its crystal structure PDB_Info PDB_Structure Mus musculus Chain D = 3.7e-08 23 29 View alignment SCOP MMDB CATH Chain B = 3.7e-08 23 29 View alignment 2zkq ( Chain: a) Structure of a mammalian ribosomal 40s subunit within an 80s complex obtained by docking homology models of the rna and proteins into an 8.7 a cryo-em map PDB_Info PDB_Structure Canis familiaris 8.4e-08 23 34 View alignment SCOP MMDB CATH 3fm0 ( Chain: A) Crystal structure of wd40 protein ciao1 PDB_Info PDB_Structure Homo sapiens 1.4e-07 24 27 View alignment SCOP MMDB CATH 2bcj ( Chain: B) Crystal structure of g protein-coupled receptor kinase 2 in complex with galpha-q and gbetagamma subunits PDB_Info PDB_Structure Bos taurus 1.9e-07 24 30 View alignment SCOP MMDB CATH 1gg2 ( Chain: B) G protein heterotrimer mutant gi_alpha_1(g203a) beta_1 gamma_2 with gdp bound PDB_Info PDB_Structure Rattus norvegicus | Bos taurus 1.9e-07 24 30 View alignment SCOP MMDB CATH 3cik ( Chain: B) Human grk2 in complex with gbetagamma subunits PDB_Info PDB_Structure Homo sapiens | Bos taurus 1.9e-07 24 30 View alignment SCOP MMDB CATH 1tbg ( Chain: D, B, A, C) Beta-gamma dimer of the heterotrimeric g-protein transducin PDB_Info PDB_Structure Bos taurus Chain D = 1.9e-07 24 30 View alignment SCOP MMDB CATH Chain B = 1.9e-07 24 30 View alignment Chain A = 1.9e-07 24 30 View alignment Chain C = 1.9e-07 24 30 View alignment 1b9x ( Chain: A) Structural analysis of phosducin and its phosphorylation- regulated interaction with transducin PDB_Info PDB_Structure Bos taurus | Rattus norvegicus 1.9e-07 24 30 View alignment SCOP MMDB CATH 1omw ( Chain: B) Crystal structure of the complex between g protein-coupled receptor kinase 2 and heterotrimeric g protein beta 1 and gamma 2 subunits PDB_Info PDB_Structure Bos taurus 1.9e-07 24 30 View alignment SCOP MMDB CATH 2trc ( Chain: B) Phosducin/transducin beta-gamma complex PDB_Info PDB_Structure Bos taurus | Rattus norvegicus 1.9e-07 24 30 View alignment SCOP MMDB CATH 1gp2 ( Chain: B) G protein heterotrimer gi_alpha_1 beta_1 gamma_2 with gdp bound PDB_Info PDB_Structure Rattus norvegicus | Bos taurus 1.9e-07 24 30 View alignment SCOP MMDB CATH 1b9y ( Chain: A) Structural analysis of phosducin and its phosphorylation- regulated interaction with transducin beta-gamma PDB_Info PDB_Structure Bos taurus | Rattus norvegicus 1.9e-07 24 30 View alignment SCOP MMDB CATH 2qns ( Chain: A) Crystal structure of the g-protein betagamma subunit bound to a c-terminal region of the pth1 parathyroid hormone receptor PDB_Info PDB_Structure Homo sapiens 1.9e-07 24 30 View alignment SCOP MMDB CATH 1got ( Chain: B) Heterotrimeric complex of a gt-alpha/gi-alpha chimera and the gt-beta-gamma subunits PDB_Info PDB_Structure Bos taurus 1.9e-07 24 30 View alignment SCOP MMDB CATH 1xhm ( Chain: A) The crystal structure of a biologically active peptide (sigk) bound to a g protein beta:gamma heterodimer PDB_Info PDB_Structure Bos taurus 1.9e-07 24 30 View alignment SCOP MMDB CATH 1a0r ( Chain: B) Heterotrimeric complex of phosducin/transducin beta-gamma PDB_Info PDB_Structure Bos taurus 1.9e-07 24 30 View alignment SCOP MMDB CATH 1p22 ( Chain: A) Structure of a beta-trcp1-skp1-beta-catenin complex: destruction motif binding and lysine specificity on the scfbeta-trcp1 ubiquitin ligase PDB_Info PDB_Structure Homo sapiens 9.4e-07 22 33 View alignment SCOP MMDB CATH 3dm0 ( Chain: A) Maltose binding protein fusion with rack1 from a. thaliana PDB_Info PDB_Structure Escherichia coli, arabidopsis thaliana 1.1e-06 24 28 View alignment SCOP MMDB CATH 2ce8 ( Chain: B, D, A, C) An eh1 peptide bound to the groucho-tle wd40 domain. PDB_Info PDB_Structure Homo sapiens Chain B = 2.0e-05 24 35 View alignment SCOP MMDB CATH Chain D = 2.0e-05 24 35 View alignment Chain A = 2.0e-05 24 35 View alignment Chain C = 2.0e-05 24 35 View alignment 2ce9 ( Chain: B, D, C, A) A wrpw peptide bound to the groucho-tle wd40 domain. PDB_Info PDB_Structure Homo sapiens Chain B = 2.0e-05 24 35 View alignment SCOP MMDB CATH Chain D = 2.0e-05 24 35 View alignment Chain C = 2.0e-05 24 35 View alignment Chain A = 2.0e-05 24 35 View alignment 1gxr ( Chain: B, A) Wd40 region of human groucho/tle1 PDB_Info PDB_Structure Homo sapiens Chain B = 2.0e-05 24 35 View alignment SCOP MMDB CATH Chain A = 2.0e-05 24 35 View alignment 3iiy ( Chain: A) Polycomb protein EED PDB_Info PDB_Structure Unknown 5.8e-05 21 33 View alignment SCOP MMDB CATH 3ij0 ( Chain: A) Polycomb protein EED PDB_Info PDB_Structure Unknown 5.8e-05 21 33 View alignment SCOP MMDB CATH 3ij1 ( Chain: A) Polycomb protein EED PDB_Info PDB_Structure Unknown 5.8e-05 21 33 View alignment SCOP MMDB CATH 3ijc ( Chain: A) Polycomb protein EED PDB_Info PDB_Structure Unknown 5.8e-05 21 33 View alignment SCOP MMDB CATH 2qxv ( Chain: A) Structural basis of ezh2 recognition by eed PDB_Info PDB_Structure Mus musculus 7.7e-05 21 33 View alignment SCOP MMDB CATH 3iiw ( Chain: A) Polycomb protein EED PDB_Info PDB_Structure Unknown 7.9e-05 21 33 View alignment SCOP MMDB CATH 1nex ( Chain: D, B) Crystal structure of scskp1-sccdc4-cpd peptide complex PDB_Info PDB_Structure Saccharomyces cerevisiae Chain D = 9.0e-05 21 33 View alignment SCOP MMDB CATH Chain B = 9.0e-05 21 33 View alignment 3c99 ( Chain: A) Structural basis of histone h4 recognition by p55 PDB_Info PDB_Structure Drosophila melanogaster 0.000210 25 36 View alignment SCOP MMDB CATH 3c9c ( Chain: A) Structural basis of histone h4 recognition by p55 PDB_Info PDB_Structure Drosophila melanogaster 0.000210 25 36 View alignment SCOP MMDB CATH 3gfc ( Chain: A) Crystal structure of histone-binding protein rbbp4 PDB_Info PDB_Structure Homo sapiens 0.000380 25 35 View alignment SCOP MMDB CATH 1pev ( Chain: A) Crystal structure of the actin interacting protein from caenorhabditis elegans PDB_Info PDB_Structure Caenorhabditis elegans 0.000380 22 32 View alignment SCOP MMDB CATH 1nr0 ( Chain: A) Two seven-bladed beta-propeller domains revealed by the structure of a c. elegans homologue of yeast actin interacting protein 1 (aip1). PDB_Info PDB_Structure Caenorhabditis elegans 0.000380 22 32 View alignment SCOP MMDB CATH 2hes ( Chain: X) Cytosolic iron-sulphur assembly protein- 1 PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000519 24 31 View alignment SCOP MMDB CATH 3cfs ( Chain: B) Structural basis of the interaction of rbap46/rbap48 with histone h4 PDB_Info PDB_Structure Homo sapiens 0.000810 26 35 View alignment SCOP MMDB CATH 3cfv ( Chain: B, A) Structural basis of the interaction of rbap46/rbap48 with histone h4 PDB_Info PDB_Structure Homo sapiens Chain B = 0.000810 26 35 View alignment SCOP MMDB CATH Chain A = 0.000810 26 35 View alignment

Genome-wide Expression and Other Large-Scale Analyses [TOP] [NEXT]
Functional Analysis Expression Connection Summary Cell cycle and metabolic oscillation Cell cycle transcript profile Cyclebase Genevestigator GermOnline SPELL Microarray Search YGAC Triples Yeast Microarray Global Viewer YeastFunc	You can also search multiple datasets simultaneously using Expression Connection for expression studies or Function Junction for other large scale analyses.

Locus History (misc. notes) [TOP] [NEXT]

Nomenclature History

Standard Name	Reference
CDC40	Kassir Y and Simchen G (1978) Meiotic recombination and DNA synthesis in a new cell cycle mutant of Saccharomyces cerevisiae. Genetics 90(1):49-68      Kassir, Y., et al. (1985) Personal Communication, Mortimer Map Edition 9

Alias Name(s)	Reference
PRP17	Vijayraghavan U, et al. (1989) Isolation and characterization of pre-mRNA splicing mutants of Saccharomyces cerevisiae. Genes Dev 3(8):1206-16
SLT15	Xu D, et al. (1998) Synthetic lethality of yeast slt mutations with U2 small nuclear RNA mutations suggests functional interactions between U2 and U5 snRNPs that are important for both steps of pre-mRNA splicing. Mol Cell Biol 18(4):2055-66
SLU4	Frank D, et al. (1992) Synthetic lethal mutations suggest interactions between U5 small nuclear RNA and four proteins required for the second step of splicing. Mol Cell Biol 12(11):5197-205

Mapping Notes

Date	Note
1989-10-01	Edition 10: cdc40 data in 1985 mapping review; new reference Mortimer RK, et al. (1989) Genetic map of Saccharomyces cerevisiae, edition 10. Yeast 5(5):321-403

Sequence Retrieval [TOP] [NEXT]
Sequence Type	Output Format
Genomic DNA	GCG | FASTA | NoHeader
Genomic DNA with 1 kb up and downstream	GCG | FASTA | NoHeader
DNA coding sequence (without introns, without flanking regions)	GCG | FASTA | NoHeader
Protein Translation of ORF	GCG | FASTA | NoHeader
6-Frame Translation(with Restriction Map)	GCG
Restriction Fragment Sizes	GCG
Sequence Analysis Tools BLASTP BLASTN Design Primers FASTA aa FASTA nt Restriction Fragment Map Restriction Fragment Sizes Six-Frame Translation

Sequence from other databases
Sequence ID	Source
YDR364C	SGD Systematic Sequence
851968	NCBI: Gene ID
NP_010652.1	NCBI: RefSeq protein version ID
NP_010652.1	NCBI: RefSeq protein version ID
6320572	NCBI: NCBI protein GI

Map and Displays [TOP] [NEXT]
Physical, Genetic Maps:	Chromosomal Feature Map	GBrowse	Combined Physical and Genetic Map	Genetic Distance vs. Physical Distance Ratios
Similarity Viewers:	Synteny Viewer	Genomic Stripe View	SAGE Results Map

Localization [TOP] [NEXT]
Localization Resources YeastRC Localization (Seattle) YGAC Triples YeastGFP DB (UCSF) at SGD

Community Annotation [TOP] [NEXT]
No community annotation available.

Literature Guide: papers categorized by topic. [TOP]
Topics	Reference	Other Genes Addressed
55 curated references; 0 references not yet curated
Non-Fungal Related Genes/Proteins Protein Physical Properties Protein-protein Interactions Protein/Nucleic Acid Structure Techniques and Reagents	Fabrizio P, et al. (2009) The Evolutionarily Conserved Core Design of the Catalytic Activation Step of the Yeast Spliceosome. Mol Cell 36(4):593-608	|ACT1 |BRR2 |BUD13 |BUD31 |CBC2 |CEF1 |CLF1 |CUS1 |CWC15 |CWC2 |CWC21 |CWC22 |CWC23 |CWC24 |MORE
Alias Genetic Interactions Mutants/Phenotypes Strains/Constructs	Gahura O, et al. (2009) Prp45 affects Prp22 partition in spliceosomal complexes and splicing efficiency of non-consensus substrates. J Cell Biochem 106(1):139-51	|CEF1 |CLF1 |NTC20 |PRP18 |PRP22 |PRP45 |SLU7 |SYF1
Genetic Interactions Mutants/Phenotypes Strains/Constructs	Kawashima T, et al. (2009) Nonsense-mediated mRNA decay mutes the splicing defects of spliceosome component mutations. RNA 15(12):2236-47	|ACT1 |BOS1 |CIN2 |LSB3 |MTR2 |MUD1 |NAM7 |NAM8 |PRP18 |PRP2 |PRP22 |REC107 |RPL16A |RPS11B |MORE
Reviews	Wahl MC, et al. (2009) The spliceosome: design principles of a dynamic RNP machine. Cell 136(4):701-18	|AAR2 |BRR2 |BUD13 |BUD31 |CEF1 |CLF1 |CUS1 |CUS2 |CWC15 |CWC2 |CWC21 |CWC22 |CWC23 |CWC24 |MORE
Function/Process Protein Physical Properties	Warkocki Z, et al. (2009) Reconstitution of both steps of Saccharomyces cerevisiae splicing with purified spliceosomal components. Nat Struct Mol Biol 16(12):1237-43	|BFR1 |BRE5 |BRR1 |BRR2 |BUD13 |BUD31 |CBF2 |CEF1 |CIC1 |CKB2 |CLF1 |CSN12 |CTK1 |CTK2 |MORE
Function/Process Strains/Constructs	Nyswaner KM, et al. (2008) Chromatin-associated genes protect the yeast genome from ty1 insertional mutagenesis. Genetics 178(1):197-214	|AGP2 |AGP3 |ALR2 |ARC1 |ARG4 |ARG82 |ASC1 |ASF1 |BEM4 |BRE1 |BUD27 |CAN1 |CDC73 |CKB2 |MORE
Cellular Location Function/Process Mutants/Phenotypes Protein-Nucleic Acid Interactions Strains/Constructs	Sapra AK, et al. (2008) The splicing factor Prp17 interacts with the U2, U5 and U6 snRNPs and associates with the spliceosome pre- and post-catalysis. Biochem J 416(3):365-74	|LSR1 |PRP8 |SNR6 |SNR7-L |SNR7-S |SNU114
Mutants/Phenotypes	Cheng V, et al. (2007) Genome-Wide Screen for Oxalate-Sensitive Mutants of Saccharomyces cerevisiae. Appl Environ Microbiol 73(18):5919-27	|ADA2 |AFT1 |CCR4 |CNM67 |CTK3 |DRS2 |ERG2 |ERG24 |GLY1 |GON7 |HOM6 |KEM1 |MCH5 |MTQ2 |MORE
Reviews	Ishtar Snoek IS and Yde Steensma H (2007) Factors involved in anaerobic growth of Saccharomyces cerevisiae. Yeast 24(1):1-10	|ADH3 |ARG82 |ARV1 |BTS1 |CAX4 |CNM67 |DBP7 |DRS2 |FZO1 |GPD2 |GUP1 |HFI1 |HPR1 |IES2 |MORE
Cell Cycle Phase Involved Function/Process Genetic Interactions Large-scale phenotype analysis Mutants/Phenotypes Regulation of Strains/Constructs	Kaplan Y and Kupiec M (2007) A role for the yeast cell cycle/splicing factor Cdc40 in the G(1)/S transition. Curr Genet 51(2):123-40	|CLN2 |CLN3 |DCR2 |GID8 |PRP8 |RCK2 |RNR1 |RNR2 |SSB1 |TDH3 |TIF2 |YGR035C
Function/Process Mutants/Phenotypes	Pleiss JA, et al. (2007) Transcript specificity in yeast pre-mRNA splicing revealed by mutations in core spliceosomal components. PLoS Biol 5(4):e90	|ACT1 |BRR1 |BRR2 |COX4 |GLC7 |HNT1 |MEX67 |NMD2 |NYV1 |OM14 |PFY1 |PRP16 |PRP18 |PRP19 |MORE
Mutants/Phenotypes	Morillo-Huesca M, et al. (2006) A simple in vivo assay for measuring the efficiency of gene length-dependent processes in yeast mRNA biogenesis. FEBS J 273(4):756-69	|CUS2 |CWC15 |DST1 |LEO1 |MFT1 |PHO5 |REF2 |RPB9 |RTF1 |SPT4 |SPT6 |SYC1 |THP2
Fungal Related Genes/Proteins Mutants/Phenotypes	Snoek IS and Steensma HY (2006) Why does Kluyveromyces lactis not grow under anaerobic conditions? Comparison of essential anaerobic genes of Saccharomyces cerevisiae with the Kluyveromyces lactis genome. FEMS Yeast Res 6(3):393-403	|ACP1 |ARB1 |ARG82 |ARH1 |ARV1 |ATM1 |BTS1 |BUR6 |CAB2 |CAX4 |CNM67 |CTF4 |DBP7 |DRS2 |MORE
Mutants/Phenotypes Strains/Constructs	Woolstencroft RN, et al. (2006) Ccr4 contributes to tolerance of replication stress through control of CRT1 mRNA poly(A) tail length. J Cell Sci 119(Pt 24):5178-92	|AKR1 |CCR4 |CHK1 |CIK1 |CTF4 |DCC1 |DIA2 |DUN1 |ELG1 |GRR1 |HFI1 |KAR3 |MEC1 |MET18 |MORE
Genetic Interactions Mutants/Phenotypes Strains/Constructs	Davierwala AP, et al. (2005) The synthetic genetic interaction spectrum of essential genes. Nat Genet 37(10):1147-52	|ABD1 |ACT1 |ALG13 |ALG14 |ALG7 |APC11 |ARL3 |ARP2 |ARP7 |ASK1 |AVO1 |BET3 |BET5 |BIM1 |MORE
Mutants/Phenotypes	Luna R, et al. (2005) Interdependence between transcription and mRNP processing and export, and its impact on genetic stability. Mol Cell 18(6):711-22	|BRR6 |CAF20 |CCR4 |CFT1 |CRM1 |DBP1 |DBP5 |DBP7 |DCP1 |FIP1 |GBP2 |GLE1 |HRB1 |HRP1 |MORE
Function/Process Genetic Interactions Mutants/Phenotypes Strains/Constructs	Dahan O and Kupiec M (2004) The Saccharomyces cerevisiae gene CDC40/PRP17 controls cell cycle progression through splicing of the ANC1 gene. Nucleic Acids Res 32(8):2529-40	|TAF14
Function/Process Mutants/Phenotypes Strains/Constructs	Sapra AK, et al. (2004) Genome-wide analysis of pre-mRNA splicing: intron features govern the requirement for the second-step factor, Prp17 in Saccharomyces cerevisiae and Schizosaccharomyces pombe. J Biol Chem 279(50):52437-46	|PRP2 |PRP22
Alias Cell Cycle Phase Involved Function/Process Genetic Interactions Mutants/Phenotypes Strains/Constructs	Chawla G, et al. (2003) Dependence of pre-mRNA introns on PRP17, a non-essential splicing factor: implications for efficient progression through cell cycle transitions. Nucleic Acids Res 31(9):2333-43	|CLB5 |CLN1 |CLN2 |PRP16 |PRP18 |PRP22 |PRP8 |RNR1 |SLU7 |TUB1 |TUB3
Function/Process Mutants/Phenotypes	Enyenihi AH and Saunders WS (2003) Large-scale functional genomic analysis of sporulation and meiosis in Saccharomyces cerevisiae. Genetics 163(1):47-54	|ADA2 |ADY2 |AKR1 |APS3 |APT1 |ARC1 |ARG82 |ARO2 |ATF1 |ATG11 |ATG15 |ATG16 |ATG5 |BPH1 |MORE
Regulation of Transcription	He F, et al. (2003) Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5' to 3' mRNA decay pathways in yeast. Mol Cell 12(6):1439-52	|AMD2 |APN2 |ARG81 |BRR1 |CAT2 |CPA1 |CUS1 |DAL2 |DAL3 |DAL7 |DBR1 |DCI1 |DCP1 |DNL4 |MORE
Genetic Interactions Mutants/Phenotypes Strains/Constructs	Vincent K, et al. (2003) Genetic interactions with CLF1 identify additional pre-mRNA splicing factors and a link between activators of yeast vesicular transport and splicing. Genetics 164(3):895-907	|BET4 |BTS1 |BUD13 |CET1 |CLF1 |CWC2 |MUD2 |NTC20 |PRP16 |PRP19 |PRP22 |RDS3 |SSD1 |SYF2
Function/Process Genetic Interactions Mutants/Phenotypes Regulatory Role Strains/Constructs Substrates/Ligands/Cofactors	Burns CG, et al. (2002) Removal of a single alpha-tubulin gene intron suppresses cell cycle arrest phenotypes of splicing factor mutations in Saccharomyces cerevisiae. Mol Cell Biol 22(3):801-15	|CEF1 |PRP22 |TUB1
Mutants/Phenotypes Strains/Constructs	Chang M, et al. (2002) A genome-wide screen for methyl methanesulfonate-sensitive mutants reveals genes required for S phase progression in the presence of DNA damage. Proc Natl Acad Sci U S A 99(26):16934-9	|AAT2 |APN1 |ARO1 |ARO7 |ASF1 |BDF1 |BUD25 |BUR2 |CAC2 |CCS1 |CDC50 |CHL1 |CIK1 |COA4 |MORE
Alias Function/Process Protein-Nucleic Acid Interactions	Clark TA, et al. (2002) Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296(5569):907-10	|PRP18
Function/Process Genetic Interactions Mutants/Phenotypes Strains/Constructs	Dahan O and Kupiec M (2002) Mutations in genes of Saccharomyces cerevisiae encoding pre-mRNA splicing factors cause cell cycle arrest through activation of the spindle checkpoint. Nucleic Acids Res 30(20):4361-70	|ISY1 |NTC20 |SYF2 |TUB1 |TUB3
Non-Fungal Related Genes/Proteins	Jurica MS, et al. (2002) Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis. RNA 8(4):426-39	|BRR2 |CEF1 |CLF1 |CUS1 |DBP2 |ECM2 |ISY1 |LEA1 |LSM2 |LSM3 |MSL1 |MUD1 |MUD2 |PRP11 |MORE
Protein-protein Interactions	Ohi MD, et al. (2002) Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs. Mol Cell Biol 22(7):2011-24	|BRR2 |BUD13 |BUD31 |CEF1 |CLF1 |CUS1 |CWC15 |CWC2 |CWC21 |CWC22 |CWC23 |CWC24 |CWC25 |CWC27 |MORE
Alias Function/Process Genetic Interactions Mutants/Phenotypes Protein-Nucleic Acid Interactions	Dagher SF and Fu XD (2001) Evidence for a role of Sky1p-mediated phosphorylation in 3' splice site recognition involving both Prp8 and Prp17/Slu4. RNA 7(9):1284-97	|ACT1 |PRP8 |SKY1
Cell Cycle Phase Involved Function/Process Genetic Interactions Mutants/Phenotypes Protein-protein Interactions Strains/Constructs	Ben-Yehuda S, et al. (2000) Extensive genetic interactions between PRP8 and PRP17/CDC40, two yeast genes involved in pre-mRNA splicing and cell cycle progression. Genetics 154(1):61-71	|ACT1 |CUP1-1 |CUP1-2 |PRP8
Cell Cycle Phase Involved Function/Process Genetic Interactions Mutants/Phenotypes Strains/Constructs	Ben-Yehuda S, et al. (2000) Genetic and physical interactions between factors involved in both cell cycle progression and pre-mRNA splicing in Saccharomyces cerevisiae. Genetics 156(4):1503-17	|CEF1 |CLF1 |ECM2 |ISY1 |LSR1 |NTC20 |PRP16 |PRP22 |PRP8 |SLU7 |SYF1 |SYF2
Alias Function/Process Mutants/Phenotypes Protein Sequence Features Protein/Nucleic Acid Structure Strains/Constructs	Lindsey-Boltz LA, et al. (2000) The carboxy terminal WD domain of the pre-mRNA splicing factor Prp17p is critical for function. RNA 6(9):1289-305
Cell Cycle Phase Involved Cellular Location Function/Process Genetic Interactions Mutants/Phenotypes Protein-protein Interactions Strains/Constructs	Russell CS, et al. (2000) Functional analyses of interacting factors involved in both pre-mRNA splicing and cell cycle progression in Saccharomyces cerevisiae. RNA 6(11):1565-72	|CLF1 |ISY1 |SYF1 |SYF2
Non-Fungal Related Genes/Proteins Protein Sequence Features	Yu L, et al. (2000) Thirty-plus functional families from a single motif. Protein Sci 9(12):2470-6	|CDC20 |CDC4 |DIP2 |DOA1 |GLE2 |MET30 |POP2 |PRP19 |PRP4 |SEC13 |SOF1 |TUP1
Reviews	Burge CB et al. (1999) "Splicing of precursors to mRNAs by the spliceosomes." Pp. 525-560 in The RNA World, Second Edition, edited by Gesteland RF, Cech TR, Atkins JF. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press	|AAR2 |BRR1 |BRR2 |CBC2 |CUS1 |CUS2 |DBR1 |DED1 |DHR2 |HSH49 |LSM1 |LSM2 |LSM3 |LSM4 |MORE
Mutants/Phenotypes Strains/Constructs	Lygerou Z, et al. (1999) A novel genetic screen for snRNP assembly factors in yeast identifies a conserved protein, Sad1p, also required for pre-mRNA splicing. Mol Cell Biol 19(3):2008-20	|PRP19 |PRP24 |PRP3 |PRP4 |SAD1
Alias Cell Cycle Phase Involved Cellular Location Cross-species Expression Function/Process Fungal Related Genes/Proteins Non-Fungal Related Genes/Proteins Protein Sequence Features Strains/Constructs	Ben Yehuda S, et al. (1998) Identification and functional analysis of hPRP17, the human homologue of the PRP17/CDC40 yeast gene involved in splicing and cell cycle control. RNA 4(10):1304-12
Alias Cell Cycle Phase Involved Cellular Location DNA/RNA Sequence Features Mutants/Phenotypes	Boger-Nadjar E, et al. (1998) Efficient initiation of S-phase in yeast requires Cdc40p, a protein involved in pre-mRNA splicing. Mol Gen Genet 260(2-3):232-41	|MEC1 |MEC3 |RAD17
Function/Process Non-Fungal Related Genes/Proteins	Lindsey LA and Garcia-Blanco MA (1998) Functional conservation of the human homolog of the yeast pre-mRNA splicing factor Prp17p. J Biol Chem 273(49):32771-5	|PRP16 |PRP18 |SLU7
Function/Process Genetic Interactions Mutants/Phenotypes Strains/Constructs	Xu D, et al. (1998) Synthetic lethality of yeast slt mutations with U2 small nuclear RNA mutations suggests functional interactions between U2 and U5 snRNPs that are important for both steps of pre-mRNA splicing. Mol Cell Biol 18(4):2055-66	|BRR2 |ECM2 |LSR1 |PRP16 |PRP8 |SLU7 |SMD3
Alias Non-Fungal Related Genes/Proteins	Zhou Z and Reed R (1998) Human homologs of yeast prp16 and prp17 reveal conservation of the mechanism for catalytic step II of pre-mRNA splicing. EMBO J 17(7):2095-106	|PRP16 |PRP18 |SLU7
Alias DNA/RNA Sequence Features Genetic Interactions Mutants/Phenotypes	Seshadri V, et al. (1996) Genetic studies of the PRP17 gene of Saccharomyces cerevisiae: a domain essential for function maps to a nonconserved region of the protein. Genetics 143(1):45-55	|PRP16 |PRP18 |SNR7-L |SNR7-S
Alias Function/Process Genetic Interactions Mutants/Phenotypes Regulation of	Jones MH, et al. (1995) Characterization and functional ordering of Slu7p and Prp17p during the second step of pre-mRNA splicing in yeast. Proc Natl Acad Sci U S A 92(21):9687-91	|PRP16 |PRP18 |SLU7
Alias Fungal Related Genes/Proteins Other Features	Umen JG and Guthrie C (1995) Prp16p, Slu7p, and Prp8p interact with the 3' splice site in two distinct stages during the second catalytic step of pre-mRNA splicing. RNA 1(6):584-97	|PRP16 |PRP18 |PRP8 |SLU7
Cell Cycle Phase Involved DNA/RNA Sequence Features Function/Process Mutants/Phenotypes	Vaisman N, et al. (1995) The role of Saccharomyces cerevisiae Cdc40p in DNA replication and mitotic spindle formation and/or maintenance. Mol Gen Genet 247(2):123-36
Genetic Interactions	Chepurnaia OV, et al. (1993) [The xrs2 gene controls recombination repair in yeast] Genetika 29(4):571-80	|RAD50 |RAD51 |RAD52 |SRS2 |XRS2
Alias Mutants/Phenotypes	Frank D and Guthrie C (1992) An essential splicing factor, SLU7, mediates 3' splice site choice in yeast. Genes Dev 6(11):2112-24	|SLU7
Alias Function/Process Genetic Interactions Mutants/Phenotypes	Frank D, et al. (1992) Synthetic lethal mutations suggest interactions between U5 small nuclear RNA and four proteins required for the second step of splicing. Mol Cell Biol 12(11):5197-205	|PRP16 |PRP18 |PRP4 |PRP8 |SLU1 |SLU2 |SLU7
Reviews	Guthrie C (1991) Messenger RNA splicing in yeast: clues to why the spliceosome is a ribonucleoprotein. Science 253(5016):157-63	|DED1 |LSR1 |PRP11 |PRP16 |PRP18 |PRP2 |PRP22 |PRP24 |PRP28 |PRP4 |PRP5 |PRP6 |PRP8 |PRP9 |MORE
Reviews	Ruby SW and Abelson J (1991) Pre-mRNA splicing in yeast. Trends Genet 7(3):79-85	|DBR1 |PRP11 |PRP16 |PRP18 |PRP19 |PRP2 |PRP21 |PRP22 |PRP24 |PRP28 |PRP3 |PRP4 |PRP5 |PRP6 |MORE
Alias Genetic Interactions Mutants/Phenotypes Strains/Constructs	Vijayraghavan U, et al. (1989) Isolation and characterization of pre-mRNA splicing mutants of Saccharomyces cerevisiae. Genes Dev 3(8):1206-16	|DBR1 |PRP11 |PRP16 |PRP18 |PRP19 |PRP2 |PRP21 |PRP22 |PRP24 |PRP3 |PRP4 |PRP5 |PRP6 |PRP8 |MORE
Genetic Interactions Mutants/Phenotypes Strains/Constructs	Kupiec M and Simchen G (1986) DNA-repair characterization of cdc40-1, a cell-cycle mutant of Saccharomyces cerevisiae. Mutat Res 162(1):33-40	|RAD50 |RAD6
Mutants/Phenotypes	Kupiec M and Simchen G (1986) Regulation of the RAD6 gene of Saccharomyces cerevisiae in the mitotic cell cycle and in meiosis. Mol Gen Genet 203(3):538-43	|RAD6
DNA/RNA Sequence Features Function/Process Mapping Mutants/Phenotypes Protein Sequence Features Strains/Constructs	Kassir Y, et al. (1985) Cloning and mapping of CDC40, a Saccharomyces cerevisiae gene with a role in DNA repair. Curr Genet 9(4):253-7	|ADE8 |TRP4
Cell Cycle Phase Involved Function/Process Mutants/Phenotypes Strains/Constructs	Kassir Y and Simchen G (1978) Meiotic recombination and DNA synthesis in a new cell cycle mutant of Saccharomyces cerevisiae. Genetics 90(1):49-68

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