BUD31/YCR063W 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

ChrIII: 228314 to 228787
CDS: 228314 - 228787

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

BUD31 YCR063W CWC14 ORF, Verified S000000659

This name is reserved with SGD according to the Gene Naming Guidelines agreed upon by the yeast community.
Gene name reserved on: 2001-02-13. Gene name expires on 2002-02-13.
Description
Component of the SF3b subcomplex of the U2 snRNP; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern

GO Annotations [TOP] [NEXT]
Molecular Function
Annotation(s) Reference(s) Evidence Assigned By
metal ion binding GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.
     IEA : Inferred from Electronic Annotation with EBI:KW-0479
Assigned on 2007-05-23 UniProtKB
molecular_function
unknown SGD (2002) Use of the ND evidence code for Gene Ontology (GO) terms in SGD
   ND : No Biological Data Available
Assigned on 2009-11-10 SGD
zinc ion binding GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.
     IEA : Inferred from Electronic Annotation with EBI:KW-0862
Assigned on 2007-05-23 UniProtKB
Biological Process
Annotation(s) Reference(s) Evidence Assigned By
RNA splicing Masciadri B, et al. (2004) Characterization of the BUD31 gene of Saccharomyces cerevisiae. Biochem Biophys Res Commun 320(4):1342-50
     IPI : Inferred from Physical Interaction
Assigned on 2004-10-31 SGD
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
cellular bud site selection Ni L and Snyder M (2001) A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol Biol Cell 12(7):2147-70
       IMP : Inferred from Mutant Phenotype
Assigned on 2002-10-10 SGD
nuclear mRNA splicing, via spliceosome Wang Q, et al. (2005) Interactions of the yeast SF3b splicing factor. Mol Cell Biol 25(24):10745-54
       IPI : Inferred from Physical Interaction
Assigned on 2008-10-27 SGD
translational elongation Huttenhower C and Troyanskaya OG (2009) Prediction of Gene Ontology annotations by integrating high-throughput datasets
   RCA : Reviewed Computational Analysis
Assigned on 2009-08-06 bioPIXIE_MEFIT
Cellular Component
Annotation(s) Reference(s) Evidence Assigned By
U2 snRNP Wang Q, et al. (2005) Interactions of the yeast SF3b splicing factor. Mol Cell Biol 25(24):10745-54
       IDA : Inferred from Direct Assay
Assigned on 2008-10-27 SGD
nucleus Huh WK, et al. (2003) Global analysis of protein localization in budding yeast. Nature 425(6959):686-91
         IDA : Inferred from Direct Assay
Assigned on 2003-10-28 SGD
DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.
     IEA : Inferred from Electronic Annotation with EBI:IPR001748 , EBI:IPR018230
Assigned on 2007-05-23 UniProtKB
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 Tian W, et al. (2008) Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome Biol 9 Suppl 1:S7
             RCA : Reviewed Computational Analysis
Assigned on 2009-09-03 YeastFunc

Pathways [TOP] [NEXT]
No pathways available

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

Basic References [TOP]
BASIC INFORMATION REFERENCES forBUD31/YCR063W for BUD31
1) 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

2) Ni L and Snyder M (2001) A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol Biol Cell 12(7):2147-70

3) Troyanskaya OG, et al. (2003) A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci U S A 100(14):8348-53

4) Wang Q, et al. (2005) Interactions of the yeast SF3b splicing factor. Mol Cell Biol 25(24):10745-54

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for BUD31/YCR063W

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for BUD31/YCR063W

Homologs [TOP] [NEXT]

Comparison Resources

Physical Properties and Transcript Information: predicted from sequence [TOP] [NEXT]
Protein Sequence Calculations
from Predicted Full length Translation

N-term MPRIKTR

C-term RGCASTD

Length(aa) 157

MW(Da) 18,447

pI 10.19

Amino Acid Composition (full length)

GCG tools: PepPlot, Helical Wheel, PepStruct

Transcript Translation Calculations

Codon Bias 0.109

Codon Adaptation Index 0.130

Frequency of Optimal Codons 0.474

Hydropathicity of Protein -0.852

Aromaticity Score 0.083

10 20 30 40 50 | | | | | MPRIKTRRSKPAPDGFEKIKPTLTDFEIQLRDAQKDKSSKLAAKSNEQLW EIMQLHHQRSRYIYTLYYKRKAISKDLYDWLIKEKYADKLLIAKWRKTGY EKLCCLRCIQKNETNNGSTCICRVPRAQLEEEARKKGTQVSFHQCVHCGC RGCASTD*

Protein Structures from PDB: proteins of known structure with sequence similarity to BUD31/YCR063W, based on Smith-Waterman analysis. [TOP] [NEXT]
No protein structure information available.

Genome-wide Expression and Other Large-Scale Analyses [TOP] [NEXT]

Functional Analysis
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 Date Standardized Reference
BUD31 2001-08-13 Ni L and Snyder M (2001) A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol Biol Cell 12(7):2147-70

Alias Name(s) Reference
CWC14 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

Sequence Annotation Notes
Date Note
2000-09-13 The systematic sequence was updated in the region between ORFs YCR063W and YCR065W. Note that coordinates listed are chromosomal coordinates.
Old: 227780 AATCAAAAAATTACTTCTTCTCCTCC-TTACGGTGCCCTTTGATCCTTCTCAAACTTTAA 227838 |||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| New: 229048 AATCAAAAAATTACTTCTTCTCCTCCCTTACGGTGCCCTTTGATCCTTCTCAAACTTTAA 229107

Standard Name	Date Standardized	Reference
BUD31	2001-08-13	Ni L and Snyder M (2001) A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol Biol Cell 12(7):2147-70

Alias Name(s)	Reference
CWC14	*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

Date	Note
2000-09-13	The systematic sequence was updated in the region between ORFs YCR063W and YCR065W. Note that coordinates listed are chromosomal coordinates. Old: 227780 AATCAAAAAATTACTTCTTCTCCTCC-TTACGGTGCCCTTTGATCCTTCTCAAACTTTAA 227838 \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\| New: 229048 AATCAAAAAATTACTTCTTCTCCTCCCTTACGGTGCCCTTTGATCCTTCTCAAACTTTAA 229107

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
Sequence from other databases

Sequence ID Source

YCR063W SGD Systematic Sequence

850427 NCBI: Gene ID

NP_009990.1 NCBI: RefSeq protein version ID

NP_009990.1 NCBI: RefSeq protein version ID

6319908 NCBI: NCBI protein GI

Sequence from other databases
Sequence ID	Source
YCR063W	SGD Systematic Sequence
850427	NCBI: Gene ID
NP_009990.1	NCBI: RefSeq protein version ID
NP_009990.1	NCBI: RefSeq protein version ID
6319908	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

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

Literature Guide: papers categorized by topic. [TOP]
Topics Reference Other Genes Addressed
17 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 |CBC2 |CDC40 |CEF1 |CLF1 |CUS1 |CWC15 |CWC2 |CWC21 |CWC22 |CWC23 |CWC24 |MORE
Reviews
Wahl MC, et al. (2009) The spliceosome: design principles of a dynamic RNP machine. Cell 136(4):701-18
       |AAR2 |BRR2 |BUD13 |CDC40 |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 |CBF2 |CDC40 |CEF1 |CIC1 |CKB2 |CLF1 |CSN12 |CTK1 |CTK2 |MORE
Mutants/Phenotypes
Strains/Constructs
Liao C, et al. (2007) Genomic Screening in Vivo Reveals the Role Played by Vacuolar H+ ATPase and Cytosolic Acidification in Sensitivity to DNA-Damaging Agents Such as Cisplatin. Mol Pharmacol 71(2):416-25
       |ASF1 |ATP2 |BUR2 |CLB2 |CTF18 |CTF4 |CTF8 |DBF2 |DCC1 |DOC1 |EAP1 |ERG24 |GCN5 |GUP1 |MORE
Mutants/Phenotypes
Strains/Constructs
Lockshon D, et al. (2007) The sensitivity of yeast mutants to oleic Acid implicates the peroxisome and other processes in membrane function. Genetics 175(1):77-91
       |ADO1 |ADR1 |AIM38 |AKR1 |ARP6 |ATG17 |AVL9 |BUD14 |BUD22 |BUD23 |CAR2 |CBS1 |CLA4 |CTF8 |MORE
Protein-protein Interactions
Lebaron S, et al. (2005) The splicing ATPase prp43p is a component of multiple preribosomal particles. Mol Cell Biol 25(21):9269-82
       |ALB1 |ARB1 |ARP9 |ARX1 |BMS1 |BRR2 |BRX1 |CBF5 |CIC1 |CLF1 |CWC2 |CWC23 |DBP10 |DBP2 |MORE
Function/Process
Genetic Interactions
Mutants/Phenotypes
Protein-protein Interactions
Strains/Constructs
Wang Q, et al. (2005) Interactions of the yeast SF3b splicing factor. Mol Cell Biol 25(24):10745-54
       |BUD13 |CLF1 |CUS1 |HSH155 |HSH49 |IST3 |MUD2 |PML1 |PRP5 |RDS3 |RSE1 |YRA1 |YSF3
Function/Process
Mutants/Phenotypes
Non-Fungal Related Genes/Proteins
Protein-protein Interactions
Strains/Constructs
Masciadri B, et al. (2004) Characterization of the BUD31 gene of Saccharomyces cerevisiae. Biochem Biophys Res Commun 320(4):1342-50

Cellular Location
Strains/Constructs
Huh WK, et al. (2003) Global analysis of protein localization in budding yeast. Nature 425(6959):686-91
         |AAH1 |AAP1 |ABZ1 |ABZ2 |ACB1 |ACO2 |ADD37 |ADD66 |ADE1 |ADE12 |ADE2 |ADE3 |ADE4 |ADE6 |MORE
Mutants/Phenotypes
Strains/Constructs
Kushner DB, et al. (2003) Systematic, genome-wide identification of host genes affecting replication of a positive-strand RNA virus. Proc Natl Acad Sci U S A 100(26):15764-9
           |ACB1 |ALF1 |AML1 |BRO1 |BUB1 |BUD26 |CBC2 |CDC50 |DBR1 |DED1 |DHH1 |DOA1 |DOA4 |DRS2 |MORE
Function/Process
Troyanskaya OG, et al. (2003) A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci U S A 100(14):8348-53
           |BUD28 |CBF5 |CEF1 |LSG1 |NOP56 |PRP8 |PRS1 |RAD23 |RGT1 |RPA49 |RPC40 |RPN14 |RRB1 |SNF3 |MORE
RNA Levels and Processing
Nautiyal S, et al. (2002) The genome-wide expression response to telomerase deletion in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 99(14):9316-21
           |ALG14 |CAK1 |CRP1 |DIN7 |DMA1 |DUN1 |EBS1 |EMG1 |FMP52 |MSC1 |PLM2 |RAD50 |RAD51 |RAD52 |MORE
Protein-protein Interactions
Strains/Constructs
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 |CDC40 |CEF1 |CLF1 |CUS1 |CWC15 |CWC2 |CWC21 |CWC22 |CWC23 |CWC24 |CWC25 |CWC27 |MORE
Protein-protein Interactions
Stevens SW, et al. (2002) Composition and functional characterization of the yeast spliceosomal penta-snRNP. Mol Cell 9(1):31-44
       |ASC1 |BNA7 |BRR2 |CEF1 |CLF1 |CUS1 |CUS2 |DED1 |DHH1 |DIB1 |ECM2 |GPM1 |HSH155 |HSH49 |MORE
Function/Process
Fungal Related Genes/Proteins
Mutants/Phenotypes
Strains/Constructs
Ni L and Snyder M (2001) A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol Biol Cell 12(7):2147-70
       |ALG8 |BUD13 |BUD14 |BUD16 |BUD17 |BUD19 |BUD20 |BUD21 |BUD22 |BUD23 |BUD25 |BUD26 |BUD27 |BUD28 |MORE
Non-Fungal Related Genes/Proteins
Hla T, et al. (1995) Characterization of edg-2, a human homologue of the Xenopus maternal transcript G10 from endothelial cells. Biochim Biophys Acta 1260(2):227-9

DNA/RNA Sequence Features
Mapping
Mutants/Phenotypes
Strains/Constructs
Benit P, et al. (1992) Sequence of the sup61-RAD18 region on chromosome III of Saccharomyces cerevisiae. Yeast 8(2):147-53
     |HCM1 |RAD18 |SED4 |SUP61

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