USE1/YGL098W 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

ChrVII: 317345 to 318082
CDS: 317345 - 318082

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

USE1 YGL098W SLT1 ORF, Verified S000003066

This name is reserved with SGD according to the Gene Naming Guidelines agreed upon by the yeast community.
Gene name reserved on: 2002-09-05. Gene name expires on 2003-09-05.
Description
Essential SNARE protein localized to the ER, involved in retrograde traffic from the Golgi to the ER; forms a complex with the SNAREs Sec22p, Sec20p and Ufe1p

GO Annotations [TOP] [NEXT]
Molecular Function
Annotation(s) Reference(s) Evidence Assigned By
SNAP receptor activity Dilcher M, et al. (2003) Use1p is a yeast SNARE protein required for retrograde traffic to the ER. EMBO J 22(14):3664-74
     IGI : Inferred from Genetic Interaction
ISS : Inferred from Sequence or structural Similarity
IPI : Inferred from Physical Interaction
Assigned on 2003-07-17 SGD
Biological Process
Annotation(s) Reference(s) Evidence Assigned By
ER to Golgi vesicle-mediated transport Belgareh-Touze N, et al. (2003) Yeast functional analysis: identification of two essential genes involved in ER to Golgi trafficking. Traffic 4(9):607-17
       IMP : Inferred from Mutant Phenotype
Assigned on 2005-07-12 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
retrograde vesicle-mediated transport, Golgi to ER Dilcher M, et al. (2003) Use1p is a yeast SNARE protein required for retrograde traffic to the ER. EMBO J 22(14):3664-74
     IMP : Inferred from Mutant Phenotype
IGI : Inferred from Genetic Interaction
Assigned on 2003-07-17 SGD
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
vesicle-mediated transport GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.
     IEA : Inferred from Electronic Annotation with EBI:KW-0931
Assigned on 2008-02-14 UniProtKB
Cellular Component
Annotation(s) Reference(s) Evidence Assigned By
endoplasmic reticulum Dilcher M, et al. (2003) Use1p is a yeast SNARE protein required for retrograde traffic to the ER. EMBO J 22(14):3664-74
     IDA : Inferred from Direct Assay
Assigned on 2003-07-17 SGD
GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.
     IEA : Inferred from Electronic Annotation with EBI:KW-0256
Assigned on 2007-05-23 UniProtKB
integral to membrane 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-9908
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 2007-05-23 UniProtKB

Pathways [TOP] [NEXT]
No pathways available

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

Basic References [TOP]
BASIC INFORMATION REFERENCES forUSE1/YGL098W for USE1
1) Burri L, et al. (2003) A SNARE required for retrograde transport to the endoplasmic reticulum. Proc Natl Acad Sci U S A 100(17):9873-7

2) Dilcher M, et al. (2003) Use1p is a yeast SNARE protein required for retrograde traffic to the ER. EMBO J 22(14):3664-74

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for USE1/YGL098W

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for USE1/YGL098W

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 MAETSND

C-term IQLFPAL

Length(aa) 245

MW(Da) 28,106

pI 5.01

Amino Acid Composition (full length)

GCG tools: PepPlot, Helical Wheel, PepStruct

Transcript Translation Calculations

Codon Bias 0.058

Codon Adaptation Index 0.138

Frequency of Optimal Codons 0.444

Hydropathicity of Protein -0.524

Aromaticity Score 0.094

10 20 30 40 50 | | | | | MAETSNDPFLSYVLSSKQLTNLNRLRRKAVTKQLGSSDDNKVSEEFLRYQ HTYQREAFEYLQTKHDAHKIMESQYEQYQSSSKTRRYSIDLDSVDAVDTE SQTEYPNEEFIDRNEDSEAVMELRKRLLGKGQNKGLGYETTKSVDRQIED QDTLQQDLIQDMSKLVGSLKQGAVAFQSALDEDKQVLGAAEIGIQVASQG LMDVSGKLRKYDKSKLSYLFYITVFIFMILGLVFTFIIIQLFPAL*

Protein Structures from PDB: proteins of known structure with sequence similarity to USE1/YGL098W, 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
USE1 2003-06-04 Dilcher M, et al. (2003) Use1p is a yeast SNARE protein required for retrograde traffic to the ER. EMBO J 22(14):3664-74

Alias Name(s) Reference
SLT1 Burri L, et al. (2003) A SNARE required for retrograde transport to the endoplasmic reticulum. Proc Natl Acad Sci U S A 100(17):9873-7

Standard Name	Date Standardized	Reference
USE1	2003-06-04	*Dilcher M, et al.* (2003)** Use1p is a yeast SNARE protein required for retrograde traffic to the ER. EMBO J 22(14):3664-74

Alias Name(s)	Reference
SLT1	*Burri L, et al.* (2003)** A SNARE required for retrograde transport to the endoplasmic reticulum. Proc Natl Acad Sci U S A 100(17):9873-7

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

YGL098W SGD Systematic Sequence

852780 NCBI: Gene ID

NP_011417.1 NCBI: RefSeq protein version ID

NP_011417.1 NCBI: RefSeq protein version ID

6321340 NCBI: NCBI protein GI

Sequence from other databases
Sequence ID	Source
YGL098W	SGD Systematic Sequence
852780	NCBI: Gene ID
NP_011417.1	NCBI: RefSeq protein version ID
NP_011417.1	NCBI: RefSeq protein version ID
6321340	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
22 curated references; 0 references not yet curated
Computational analysis
Evolution
Fungal Related Genes/Proteins
Kienle N, et al. (2009) Phylogeny of the SNARE vesicle fusion machinery yields insights into the conservation of the secretory pathway in fungi. BMC Evol Biol 9:19
       |BET1 |BOS1 |NYV1 |PEP12 |SEC22 |SEC9 |SED5 |SFT1 |SNC1 |SNC2 |SPO20 |SRO7 |SRO77 |SSO1 |MORE
Mutants/Phenotypes
Protein Physical Properties
Protein Sequence Features
Protein-protein Interactions
Strains/Constructs
Ren Y, et al. (2009) A structure-based mechanism for vesicle capture by the multisubunit tethering complex Dsl1. Cell 139(6):1119-29
       |DSL1 |EXO70 |SEC17 |SEC20 |SEC22 |SEC39 |TIP20 |UFE1
Techniques and Reagents
Transcription
Rossouw D and Bauer FF (2009) Comparing the transcriptomes of wine yeast strains: toward understanding the interaction between environment and transcriptome during fermentation. Appl Microbiol Biotechnol 84(5):937-54
       |AGP3 |ARG80 |ARG81 |ARG82 |ARN1 |ARN2 |ARO2 |AUA1 |AUS1 |CBF1 |CHA1 |DAL1 |DAL2 |DAL3 |MORE
Reviews
Saito C and Ueda T (2009) Chapter 4 Functions of RAB and SNARE Proteins in Plant Life. Int Rev Cell Mol Biol 274:183-233
       |MSO1 |PEP12 |PEP3 |PEP5 |PEP7 |SAR1 |SEC1 |SEC2 |SEC20 |SEC4 |SEC9 |SFT1 |SNC1 |SSO1 |MORE
Reviews
Schmitt HD and Jahn R (2009) A tethering complex recruits SNAREs and grabs vesicles. Cell 139(6):1053-5
       |BET3 |BET5 |DSL1 |GSG1 |SEC1 |SEC20 |SEC23 |SEC39 |TIP20 |TRS20 |TRS23 |TRS31 |TRS33
Mutants/Phenotypes
Strains/Constructs
Singh J and Tyers M (2009) A Rab escort protein integrates the secretion system with TOR signaling and ribosome biogenesis. Genes Dev 23(16):1944-58
       |AKR1 |AVL9 |DPM1 |ERG5 |ERV29 |GAB1 |GPI16 |MRS6 |MSB4 |MSN5 |PKC1 |ROT1 |SEC17 |SEC20 |MORE
Genetic Interactions
Mutants/Phenotypes
Protein-protein Interactions
Strains/Constructs
Tripathi A, et al. (2009) Structural characterization of Tip20p and Dsl1p, subunits of the Dsl1p vesicle tethering complex. Nat Struct Mol Biol 16(2):114-23
       |DSL1 |EXO70 |EXO84 |SEC15 |SEC20 |SEC39 |SEC6 |TIP20
Mutants/Phenotypes
Wagner A, et al. (2009) Mobilization of steryl esters from lipid particles of the yeast Saccharomyces cerevisiae. Biochim Biophys Acta 1791(2):118-24
       |ATG15 |BSC2 |COY1 |CST26 |EHT1 |HFD1 |LDB16 |NUS1 |OSW5 |PET10 |SNA2 |SNX41 |SSO1 |TGL1 |MORE
Mutants/Phenotypes
Strains/Constructs
Breslow DK, et al. (2008) A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Nat Methods 5(8):711-8
       |AAR2 |ABD1 |ABF1 |ACC1 |ACP1 |ADE13 |AFG2 |ALA1 |ALG1 |ALG13 |ALG14 |ALG2 |ALG7 |ALR1 |MORE
Fungal Related Genes/Proteins
Kuratsu M, et al. (2007) Systematic analysis of SNARE localization in the filamentous fungus Aspergillus oryzae. Fungal Genet Biol 44(12):1310-23
       |BET1 |BOS1 |GOS1 |NYV1 |PEP12 |SEC20 |SEC22 |SEC9 |SED5 |SFT1 |SNC1 |SNC2 |SPO20 |SSO1 |MORE
Protein Physical Properties
White MA, et al. (2007) Characteristics affecting expression and solubilization of yeast membrane proteins. J Mol Biol 365(3):621-36
         |ALG1 |ALG7 |APQ12 |AQY1 |ARE2 |ATG9 |ATP4 |BET1 |BIG1 |BOS1 |BRR6 |CAX4 |CHO1 |COS7 |MORE
Non-Fungal Related Genes/Proteins
Okumura AJ, et al. (2006) Involvement of a novel Q-SNARE, D12, in quality control of the endomembrane system. J Biol Chem 281(7):4495-506

Function/Process
Mutants/Phenotypes
Strains/Constructs
Altmann K and Westermann B (2005) Role of essential genes in mitochondrial morphogenesis in Saccharomyces cerevisiae. Mol Biol Cell 16(11):5410-7
           |ARC35 |ARC40 |ARP2 |BFR2 |CCT4 |CCT6 |CDC34 |CDC53 |COF1 |DSL1 |ERG1 |ERG10 |ERG12 |ERG13 |MORE
Reviews
Hong W (2005) SNAREs and traffic. Biochim Biophys Acta 1744(2):120-44
       |BET1 |BOS1 |GOS1 |NYV1 |PEP12 |SEC20 |SEC22 |SEC9 |SED5 |SFT1 |SNC1 |SNC2 |SPO20 |SSO1 |MORE
Cellular Location
Protein-protein Interactions
Kraynack BA, et al. (2005) Dsl1p, Tip20p, and the novel Dsl3(Sec39) protein are required for the stability of the Q/t-SNARE complex at the endoplasmic reticulum in yeast. Mol Biol Cell 16(9):3963-77
       |DSL1 |SEC20 |SEC39 |TIP20 |UFE1
Genetic Interactions
Mutants/Phenotypes
Strains/Constructs
Li Y, et al. (2005) Structure-based functional analysis reveals a role for the SM protein Sly1p in retrograde transport to the endoplasmic reticulum. Mol Biol Cell 16(9):3951-62
       |BOS1 |DSL1 |SEC20 |SEC22 |SLY1 |TIP20 |UFE1
Function/Process
Mutants/Phenotypes
Strains/Constructs
Davydenko SG, et al. (2004) Screening for novel essential genes of Saccharomyces cerevisiae involved in protein secretion. Yeast 21(6):463-71
       |HSP150 |NOG2 |NOP15 |RER2 |RPN5 |RRP40 |SDA1
Cellular Location
Protein Sequence Features
Beilharz T, et al. (2003) Bipartite signals mediate subcellular targeting of tail-anchored membrane proteins in Saccharomyces cerevisiae. J Biol Chem 278(10):8219-23
       |CSM4 |CYB5 |FAR10 |FAR3 |FIS1 |FMP32 |FRT1 |HLJ1 |PGC1 |PRM3 |VPS64 |YBL100C |YBR016W |YDL012C
Function/Process
Mutants/Phenotypes
Strains/Constructs
Belgareh-Touze N, et al. (2003) Yeast functional analysis: identification of two essential genes involved in ER to Golgi trafficking. Traffic 4(9):607-17
       |RER2
Alias
Cellular Location
Function/Process
Mutants/Phenotypes
Protein Sequence Features
Protein-protein Interactions
Strains/Constructs
Burri L, et al. (2003) A SNARE required for retrograde transport to the endoplasmic reticulum. Proc Natl Acad Sci U S A 100(17):9873-7
     |SEC20 |SEC22 |UFE1 |YKT6
Cellular Location
Function/Process
Fungal Related Genes/Proteins
Genetic Interactions
Mutants/Phenotypes
Non-Fungal Related Genes/Proteins
Protein Sequence Features
Protein-protein Interactions
Strains/Constructs
Techniques and Reagents
Dilcher M, et al. (2003) Use1p is a yeast SNARE protein required for retrograde traffic to the ER. EMBO J 22(14):3664-74
     |BET1 |BOS1 |SEC20 |SEC22 |SED5 |UFE1
Mutants/Phenotypes
Strains/Constructs
Lillo JA, et al. (2000) Disruption and phenotypic analysis of six open reading frames from the left arm of Saccharomyces cerevisiae chromosome VII. Yeast 16(4):365-75
       |LSG1 |PAB1 |PAN2 |SEH1 |TOS8 |YGL101W

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