---

• Site Map |
• Search Options |
• Help |
• Home |
•   |
•  

•  
• Community Info
• Submit Data
• BLAST
• Primers
• PatMatch
• Gene/Seq Resources
• Advanced Search
• Community Wiki

---

BRE4/YDL231C 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: 42245 to 38868 CDS: 42245 - 38868 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
BRE4	YDL231C		ORF, Verified	S000002390
This name is reserved with SGD according to the Gene Naming Guidelines agreed upon by the yeast community. Gene name reserved on: 2000-06-21. Gene name expires on 2001-06-21.
Description
Zinc finger protein containing five transmembrane domains; null mutant exhibits strongly fragmented vacuoles and sensitivity to brefeldin A, a drug which is known to affect intracellular transport

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 2003-01-28 SGD
Biological Process Annotation(s) Reference(s) Evidence Assigned By endocytosis Wiederkehr A, et al. (2001) Identification and characterization of Saccharomyces cerevisiae mutants defective in fluid-phase endocytosis. Yeast 18(8):759-73      IMP : Inferred from Mutant Phenotype Assigned on 2002-10-04 SGD protein transport GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0653 Assigned on 2007-05-23 UniProtKB 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 transport GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0813 Assigned on 2007-05-23 UniProtKB
Cellular Component Annotation(s) Reference(s) Evidence Assigned By integral to membrane Muren E, et al. (2001) Identification of yeast deletion strains that are hypersensitive to brefeldin A or monensin, two drugs that affect intracellular transport. Yeast 18(2):163-72        ISS : Inferred from Sequence or structural Similarity Assigned on 2001-10-18 SGD GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0812 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-9909 Assigned on 2009-10-01 UniProtKB membrane GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0472 Assigned on 2009-06-29 UniProtKB

Pathways [TOP] [NEXT]
No pathways available

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

Basic References [TOP]

BASIC INFORMATION REFERENCES forBRE4/YDL231C for BRE4 1) Bohm S, et al. (1997) Variations of the C2H2 zinc finger motif in the yeast genome and classification of yeast zinc finger proteins. Nucleic Acids Res 25(12):2464-9        2) Wiederkehr A, et al. (2001) Identification and characterization of Saccharomyces cerevisiae mutants defective in fluid-phase endocytosis. Yeast 18(8):759-73      3) Muren E, et al. (2001) Identification of yeast deletion strains that are hypersensitive to brefeldin A or monensin, two drugs that affect intracellular transport. Yeast 18(2):163-72

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for BRE4/YDL231C

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for BRE4/YDL231C

Homologs [TOP] [NEXT]
Comparison Resources PSI-BLAST Results Ashbya Homologs (AGD) BLASTN vs. fungi BLASTP at NCBI BLASTP vs. fungi 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 MKRYERD C-term ILGEENF Length(aa) 1,125 MW(Da) 129,724 pI 9.59 Amino Acid Composition (full length) GCG tools: PepPlot, Helical Wheel, PepStruct Transcript Translation Calculations Codon Bias 0.086   Codon Adaptation Index 0.141   Frequency of Optimal Codons 0.455   Hydropathicity of Protein -0.165   Aromaticity Score 0.124

10 20 30 40 50 | | | | | MKRYERDRSPTPDPDIVKGSYSQTSLRSLHELNYKNPAGISGLSFAGSPQ QSVASLSQMRLENLVKDKHWEEVEDFGLEELRDGFFDAAFTKPDSKARSP NSDIDDDNGAARKKLQSGFTKLSEYVWTAIYRPIIHFPRDIRKNGVSIFK FFIAYFIAIVICVIRPSGRWIGHEFRYFLPIAVLIHHPVRNIGVQLEMTI SSIIGASFGLGWSALAWYISTATKPTANYQGGILFQSLTMALLFAIWLRS VYRRFFYFTTSFSISIIFTHTVRLASSKFDLKWQIFWDFGISYLFGLLLS LLVCVCVSPHSGNAELMEHYNKCLQTTKTFLMALVDTELIKSKEQIYLAQ VKMVKTLNIDLSQGFRDFVNQLTISRFDLQSLKSLRNSLTAMETSLRVLP IAPKIFNDDELKKMYEELEKYRSDSATLSKEASASPQSSGIPTRENTPSA FKPIGPGLLKNEIYINALKASFSKSIFNLILEMIFVLENLSRVLKKYESP NQKNNLDECVKILSHSHSKLKRKIYKLDVCYRDFVNSSFFSQELLNDEES VDIFLFLRYLRNSARQLVTVIHDCQVLGENIHWRIALPSYPLSRALTRLP KQCVLDEGAGNVLHYFEAKRDVDEIFERVYNTYTSRHKYNKGEEEALRLD SQGGDEKSQNRKNHTISIRAIDHNDFNFHTTQNPWRFKLWKLSRILSGDE CKWTLKITFCMIFLCLPTWLPESYHWYQEFHCWWAPLTFYLLAHRRYSGN WALVMRRLICGIVGIFWGWAANQSRHFGSPYVVCTFAGLIVVPFSINFLV YRNTKSSFTALMCFTIIALEPYSKPNRHYNLTTAGIWKSTWVTGLALIIG ILVSIPINWIVWPFRARTELRDSMSSLLAHLGQSYQTVADRYLYRDADDA PTDLTFAFSHIREVRLTQSLEAIRELLKKARHEPIIISNFNPEKYASLIN SCQFLLSKIIEARISGAFFEIWDQDFDIETTRALLSLRRDSVSSVIFVFY ILSNCFRSKNKIPRYLPNPIMSRKKLYHFIKKFSEMKDQSHSNLNSGGNS MEKNLFKKIYQQKASSSGQQQLPLPSVANSSEIDSEKMHWTEVHGIAFAR AFTDISEALFQVESCAKDILGEENF*

Protein Structures from PDB: proteins of known structure with sequence similarity to BRE4/YDL231C, based on Smith-Waterman analysis. [TOP] [NEXT]
No protein structure information available.

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	Date Standardized	Reference
BRE4	2001-10-18	SGD (2007) Information without a citation in SGD

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
YDL231C	SGD Systematic Sequence
851367	NCBI: Gene ID
NP_010050.1	NCBI: RefSeq protein version ID
NP_010050.1	NCBI: RefSeq protein version ID
6319970	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 Organelle DB (UMich) 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
5 curated references; 0 references not yet curated
Function/Process Mutants/Phenotypes Strains/Constructs	Briza P, et al. (2002) Systematic analysis of sporulation phenotypes in 624 non-lethal homozygous deletion strains of Saccharomyces cerevisiae. Yeast 19(5):403-22	|ADE16 |AMA1 |ATG1 |ATG14 |ATG2 |ATG3 |ATG4 |BRE5 |BUD32 |CAF40 |CCZ1 |CNM67 |DTR1 |ECM8 |MORE
Function/Process Mutants/Phenotypes Strains/Constructs	Muren E, et al. (2001) Identification of yeast deletion strains that are hypersensitive to brefeldin A or monensin, two drugs that affect intracellular transport. Yeast 18(2):163-72	|ALG12 |ALG9 |BRE1 |BRE2 |BRE5 |ENT4 |ERG4 |HOS2 |IRC20 |LEM3 |LSM1 |MON1 |MON2 |NOP6 |MORE
Function/Process Mutants/Phenotypes Strains/Constructs	Wiederkehr A, et al. (2001) Identification and characterization of Saccharomyces cerevisiae mutants defective in fluid-phase endocytosis. Yeast 18(8):759-73	|COS10 |EDE1 |EHD3 |FTH1 |JJJ1 |MON2 |MRPL22 |RCY1 |SDS24 |SLM6 |SYS1 |TLG2 |VMA2 |VPS53
Function/Process Mutants/Phenotypes Strains/Constructs	de Groot PW, et al. (2001) A genomic approach for the identification and classification of genes involved in cell wall formation and its regulation in Saccharomyces cerevisiae. Comp Funct Genomics 2(3):124-42	|AAD4 |AIM22 |ALG12 |ALK2 |ARE2 |ARG2 |ARP5 |ASI2 |ATG4 |ATG9 |AVL9 |AVT1 |AVT4 |BFA1 |MORE
Protein Sequence Features	Bohm S, et al. (1997) Variations of the C2H2 zinc finger motif in the yeast genome and classification of yeast zinc finger proteins. Nucleic Acids Res 25(12):2464-9	|ACE2 |ADR1 |AZF1 |BUD20 |CMR3 |COM2 |CRZ1 |FZF1 |GIS1 |IRC2 |JJJ1 |MET31 |MET32 |MIG1 |MORE

Return to SGD

Send a Message to the SGD Curators