BUD28/YLR062C 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

ChrXII: 263955 to 263578
CDS: 263955 - 263578

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

BUD28 YLR062C ORF, Dubious S000004052

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
Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species; 98% of ORF overlaps the verified gene RPL22A; diploid mutant displays a weak budding pattern phenotype in a systematic assay

GO Annotations [TOP] [NEXT]
Molecular Function
Annotation(s) Reference(s) Evidence Assigned By
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 2002-10-10 SGD
Biological Process
Annotation(s) Reference(s) Evidence Assigned By
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
Cellular Component
Annotation(s) Reference(s) Evidence Assigned By
cellular_component
unknown SGD (2002) Use of the ND evidence code for Gene Ontology (GO) terms in SGD
   ND : No Biological Data Available
Assigned on 2001-03-02 SGD

Pathways [TOP] [NEXT]
No pathways available

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

Basic References [TOP]
BASIC INFORMATION REFERENCES forBUD28/YLR062C for BUD28
1) 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

2) Fisk DG, et al. (2006) Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 23(12):857-65

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for BUD28/YLR062C

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for BUD28/YLR062C

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 MNLFFVF

C-term GSLYQKN

Length(aa) 125

MW(Da) 13,880

pI 3.95

Amino Acid Composition (full length)

GCG tools: PepPlot, Helical Wheel, PepStruct

Transcript Translation Calculations

Codon Bias 0.315

Codon Adaptation Index 0.175

Frequency of Optimal Codons 0.587

Hydropathicity of Protein 0.218

Aromaticity Score 0.120

10 20 30 40 50 | | | | | MNLFFVFFFVFFWSDLVEGQSVFVGLGRDKSDPVSQLVLLQVLLCQVLQV LTRELGSGNNSNNGTIFSDSDSVTQVTDSTFDLDVVDQVLSVGSWVEDTV FSWRRDIDGKGLGNLLLSGSLYQKN*

Protein Structures from PDB: proteins of known structure with sequence similarity to BUD28/YLR062C, 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
BUD28 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

Standard Name	Date Standardized	Reference
BUD28	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

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

YLR062C SGD Systematic Sequence

Sequence from other databases
Sequence ID	Source
YLR062C	SGD Systematic Sequence

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
6 curated references; 0 references not yet curated
Mutants/Phenotypes
Huang B, et al. (2008) A genome-wide screen identifies genes required for formation of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces cerevisiae. RNA 14(10):2183-94
       |ADO1 |ARX1 |ATS1 |BUD19 |BUD21 |CFD1 |CHS3 |CHS7 |CIA1 |CKA2 |CST6 |CUP5 |DBP3 |DBP7 |MORE
Mutants/Phenotypes
Shima J, et al. (2008) Possible roles of vacuolar H(+)-ATPase and mitochondrial function in tolerance to air-drying stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains. Yeast 25(3):179-90
       |ADA2 |ADK1 |ADO1 |AEP2 |AFG3 |ANP1 |APQ13 |ARF1 |ARG82 |ARV1 |ATG17 |ATP17 |BDF1 |BEM1 |MORE
Regulation of
Swaminathan S, et al. (2006) Rck2 is required for reprogramming of ribosomes during oxidative stress. Mol Biol Cell 17(3):1472-82
       |AHP1 |AIM17 |ALD3 |ARX1 |ATC1 |BNA3 |BRX1 |BUD19 |CLG1 |CLN3 |CYS3 |DBP3 |DDR48 |DFM1 |MORE
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
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
           |BUD31 |CBF5 |CEF1 |LSG1 |NOP56 |PRP8 |PRS1 |RAD23 |RGT1 |RPA49 |RPC40 |RPN14 |RRB1 |SNF3 |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 |BUD30 |MORE

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