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DSL1/YNL258C 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   ChrXIV: 160374 to 158110 CDS: 160374 - 158110 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
DSL1	YNL258C	RNS1	ORF, Verified	S000005202
This name is reserved with SGD according to the Gene Naming Guidelines agreed upon by the yeast community. Gene name reserved on: 1999-02-09. Gene name expires on 2000-02-09.
Description
Peripheral membrane protein needed for Golgi-to-ER retrograde traffic; forms a complex with Sec39p and Tip20p that interacts with ER SNAREs Sec20p and Use1p; component of the ER target site that interacts with coatomer; interacts with Cin5p

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 2002-12-09 SGD
Biological Process Annotation(s) Reference(s) Evidence Assigned By ER-dependent peroxisome organization Perry RJ, et al. (2009) Endoplasmic Reticulum-Associated Secretory Proteins Sec20p, Sec39p, and Dsl1p Are Involved in Peroxisome Biogenesis. Eukaryot Cell 8(6):830-843        IMP : Inferred from Mutant Phenotype Assigned on 2009-05-15 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 Reilly BA, et al. (2001) Golgi-to-endoplasmic reticulum (ER) retrograde traffic in yeast requires Dsl1p, a component of the ER target site that interacts with a COPI coat subunit. Mol Biol Cell 12(12):3783-96        IMP : Inferred from Mutant Phenotype Assigned on 2002-12-09 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 Dsl1p complex 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        IDA : Inferred from Direct Assay Assigned on 2009-09-25 SGD endoplasmic reticulum Reilly BA, et al. (2001) Golgi-to-endoplasmic reticulum (ER) retrograde traffic in yeast requires Dsl1p, a component of the ER target site that interacts with a COPI coat subunit. Mol Biol Cell 12(12):3783-96        IDA : Inferred from Direct Assay Assigned on 2002-08-14 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 extrinsic to membrane 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-9903 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 nucleus Ishikawa T, et al. (2005) Isolation of Saccharomyces cerevisiae RNase T1 hypersensitive (rns) mutants and genetic analysis of the RNS1/DSL1 gene. J Gen Appl Microbiol 51(1):73-82      IDA : Inferred from Direct Assay Assigned on 2007-12-04 SGD colocalizes_with peroxisome Perry RJ, et al. (2009) Endoplasmic Reticulum-Associated Secretory Proteins Sec20p, Sec39p, and Dsl1p Are Involved in Peroxisome Biogenesis. Eukaryot Cell 8(6):830-843        IDA : Inferred from Direct Assay Assigned on 2009-05-15 SGD

Pathways [TOP] [NEXT]
No pathways available

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

Basic References [TOP]

BASIC INFORMATION REFERENCES forDSL1/YNL258C for DSL1 1) Ishikawa T, et al. (2005) Isolation of Saccharomyces cerevisiae RNase T1 hypersensitive (rns) mutants and genetic analysis of the RNS1/DSL1 gene. J Gen Appl Microbiol 51(1):73-82      2) Andag U, et al. (2001) The coatomer-interacting protein Dsl1p is required for Golgi-to-endoplasmic reticulum retrieval in yeast. J Biol Chem 276(42):39150-60        3) Reilly BA, et al. (2001) Golgi-to-endoplasmic reticulum (ER) retrograde traffic in yeast requires Dsl1p, a component of the ER target site that interacts with a COPI coat subunit. Mol Biol Cell 12(12):3783-96        4) 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        5) Vanrheenen SM, et al. (2001) Dsl1p, an essential protein required for membrane traffic at the endoplasmic reticulum/Golgi interface in yeast. Traffic 2(3):212-31

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for DSL1/YNL258C

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for DSL1/YNL258C

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 MESLFPN C-term RGTALDD Length(aa) 754 MW(Da) 88,071 pI 4.69 Amino Acid Composition (full length) GCG tools: PepPlot, Helical Wheel, PepStruct Transcript Translation Calculations Codon Bias -0.034   Codon Adaptation Index 0.139   Frequency of Optimal Codons 0.400   Hydropathicity of Protein -0.474   Aromaticity Score 0.098

10 20 30 40 50 | | | | | MESLFPNKGEIIRELLKDPLILKNDSKRSNGSELELDSSDLLQREAILAN ELNILDNLKTFLNLIKEVKTNLNILELENCYYSLQSLRKKMRNNAAYLKQ SFNFQQSISTYVDTLHLELVSTLYKILTNGFWKITENSIQFTPTVEWGKD KVHIEYDTFMDFVAQQYFPKGSLDNQAWFILDMTSADSQEQVRAKLNTIM KEYMNLSRIVSMIKNSIFISGKEISYENEKNILVFSKSSSHGQHCVSTVL TSFEAVCDFMLDGLAFRDRKTLSYELGPLFNTEFTKFVKNNASIILESLD SPLKNLVSVINNKLTRLVAKSEVTNWTHSGKEIQDLLMNKQLYYNLLLDK VLESHISEIRSIFEDPKKSWQNLEVVELTTSNTNTMSEKIGKNDSDVQNE KELHNAVSKDDDWNWEVEDDDADAWGDEIDVNIDDEEEKTNQEKEKEPEE EENAWDEAWAIDENIDDASLENGKEHLKAHDVGSLDKDHIEVTQLPKLFL AISQNFKSSFADSHVDEQYFAYKYNLLQTSYMAMCTANFSHNWCQLYVDM RYLIERDEKLYRIKELTRNLLETKLNMKYRIVCQLIRHQLTEFRENERNP SWDATIEKLLPYILKEIVRPLQKIRGEEGSRYLLSFLNFLYNDCVTKEIL KWQIISEVNSENLGELVSLLVNNTDIQLLAKEPSYKKMREKFATMGKFLP LHLKEIMEMFYNGDFYLFATDELIQWIELLFADTPLRRNAIDDIYEIRGT ALDD*

Protein Structures from PDB: proteins of known structure with sequence similarity to DSL1/YNL258C, based on Smith-Waterman analysis. [TOP] [NEXT]

PDB protein structure(s) homologous to DSL1 Homolog Source (per PDB) Protein Alignment: DSL1 vs. Homolog External Links P-Value %Identical %Similar Alignment 3etu ( Chain: A) Crystal structure of yeast dsl1p PDB_Info PDB_Structure Saccharomyces cerevisiae 2.2e-140 100 0 View alignment SCOP MMDB CATH 3etv ( Chain: A) Crystal structure of a tip20p-dsl1p fusion protein PDB_Info PDB_Structure Saccharomyces cerevisiae,undefined, saccharomyces cerevisiae 1.6e-117 93 3 View alignment SCOP MMDB CATH

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
DSL1	2001-10-08	Vanrheenen SM, et al. (2001) Dsl1p, an essential protein required for membrane traffic at the endoplasmic reticulum/Golgi interface in yeast. Traffic 2(3):212-31

Alias Name(s)	Reference
RNS1	Ishikawa T, et al. (2005) Isolation of Saccharomyces cerevisiae RNase T1 hypersensitive (rns) mutants and genetic analysis of the RNS1/DSL1 gene. J Gen Appl Microbiol 51(1):73-82

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
YNL258C	SGD Systematic Sequence
855463	NCBI: Gene ID
NP_014141.1	NCBI: RefSeq protein version ID
NP_014141.1	NCBI: RefSeq protein version ID
6324071	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
21 curated references; 0 references not yet curated
Reviews	Nagotu S, et al. (2010) Divide et impera: the dictum of peroxisomes. Traffic 11(2):175-84	|ARF1 |ARF3 |CAF4 |DNM1 |EMP24 |FIS1 |MDV1 |PEX11 |PEX2 |PEX3 |PEX30 |PEX31 |SEC20 |SEC39 |MORE
Cellular Location Function/Process Mutants/Phenotypes Protein Processing/Modification/Regulation Strains/Constructs	Perry RJ, et al. (2009) Endoplasmic Reticulum-Associated Secretory Proteins Sec20p, Sec39p, and Dsl1p Are Involved in Peroxisome Biogenesis. Eukaryot Cell 8(6):830-843	|BOS1 |COP1 |PEX3 |POT1 |SEC1 |SEC11 |SEC12 |SEC13 |SEC14 |SEC17 |SEC18 |SEC20 |SEC21 |SEC26 |MORE
Fungal Related Genes/Proteins Mutants/Phenotypes Protein Sequence Features Protein-protein Interactions Protein/Nucleic Acid Structure Regulatory Role 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	|EXO70 |SEC17 |SEC20 |SEC22 |SEC39 |TIP20 |UFE1 |USE1
Reviews	Schmitt HD and Jahn R (2009) A tethering complex recruits SNAREs and grabs vesicles. Cell 139(6):1053-5	|BET3 |BET5 |GSG1 |SEC1 |SEC20 |SEC23 |SEC39 |TIP20 |TRS20 |TRS23 |TRS31 |TRS33 |USE1
Cellular Location Mutants/Phenotypes Protein Sequence Features Protein-protein Interactions Protein/Nucleic Acid Structure 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	|EXO70 |EXO84 |SEC15 |SEC20 |SEC39 |SEC6 |TIP20 |USE1
Genetic Interactions Mutants/Phenotypes Protein Sequence Features Protein-protein Interactions Strains/Constructs	Zink S, et al. (2009) A link between ER tethering and COP-I vesicle uncoating. Dev Cell 17(3):403-16	|ARF1 |ARF2 |COP1 |EMP47 |GCS1 |GLO3 |RER1 |RET2 |RET3 |SEC12 |SEC13 |SEC27 |SEC28 |SEC39 |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
Cellular Location Computational analysis	Qi Y, et al. (2008) Finding friends and enemies in an enemies-only network: A graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions. Genome Res 18(12):1991-2004	|AAH1 |ADA2 |AGE1 |AGE2 |AIM29 |ALG3 |ALG5 |ALG6 |ALG8 |ALG9 |ANP1 |ARL3 |ARP3 |ARP4 |MORE
Evolution Fungal Related Genes/Proteins Non-Fungal Related Genes/Proteins	Koumandou VL, et al. (2007) Control systems for membrane fusion in the ancestral eukaryote; evolution of tethering complexes and SM proteins. BMC Evol Biol 7():29	|BET3 |BET5 |COG1 |COG2 |COG3 |COG4 |COG5 |COG6 |COG7 |COG8 |EXO70 |EXO84 |GSG1 |KRE11 |MORE
Mutants/Phenotypes Strains/Constructs	Michelsen K, et al. (2007) Novel cargo-binding site in the beta and delta subunits of coatomer. J Cell Biol 179(2):209-17	|COP1 |ERG26 |PAC10 |PMP2 |RET2 |RET3 |RSC6 |SEC15 |SEC21 |SEC26 |SEC27 |SEC39 |SEC65 |SER33 |MORE
Function/Process Other Features Protein/Nucleic Acid Structure	Ferre S and King RD (2006) Finding motifs in protein secondary structure for use in function prediction. J Comput Biol 13(3):719-31	|AFG2 |ANT1 |CFD1 |COS8 |CSM2 |CSN12 |CUE3 |DBP9 |ESL1 |GIP4 |HAL9 |MON1 |PNC1 |PRM2 |MORE
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 |ERG1 |ERG10 |ERG12 |ERG13 |ERG25 |MORE
Cellular Location Function/Process Genomic expression study Mutants/Phenotypes Protein-protein Interactions Strains/Constructs	Ishikawa T, et al. (2005) Isolation of Saccharomyces cerevisiae RNase T1 hypersensitive (rns) mutants and genetic analysis of the RNS1/DSL1 gene. J Gen Appl Microbiol 51(1):73-82	|CIN5 |SEC17 |SEC39 |UMP1
Cellular Location Function/Process 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	|SEC20 |SEC39 |TIP20 |UFE1 |USE1
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 |SEC20 |SEC22 |SLY1 |TIP20 |UFE1 |USE1
Cellular Location Function/Process Mutants/Phenotypes Protein Sequence Features Protein-protein Interactions Strains/Constructs Substrates/Ligands/Cofactors	Andag U and Schmitt HD (2003) Dsl1p, an essential component of the Golgi-endoplasmic reticulum retrieval system in yeast, uses the same sequence motif to interact with different subunits of the COPI vesicle coat. J Biol Chem 278(51):51722-34	|TIP20
Cellular Location Function/Process Genetic Interactions Mutants/Phenotypes Protein-protein Interactions Strains/Constructs Substrates/Ligands/Cofactors	Andag U, et al. (2001) The coatomer-interacting protein Dsl1p is required for Golgi-to-endoplasmic reticulum retrieval in yeast. J Biol Chem 276(42):39150-60	|COP1 |ERD2 |KAR2 |SEC20 |SEC22 |TIP20
Cellular Location Function/Process Genetic Interactions Mutants/Phenotypes Protein-protein Interactions Strains/Constructs	Reilly BA, et al. (2001) Golgi-to-endoplasmic reticulum (ER) retrograde traffic in yeast requires Dsl1p, a component of the ER target site that interacts with a COPI coat subunit. Mol Biol Cell 12(12):3783-96	|KAR2 |RET2 |SEC20 |SLY1 |TIP20 |UFE1
Function/Process Genetic Interactions Mutants/Phenotypes Strains/Constructs	Vanrheenen SM, et al. (2001) Dsl1p, an essential protein required for membrane traffic at the endoplasmic reticulum/Golgi interface in yeast. Traffic 2(3):212-31	|ERV14 |SEC21 |SLY1
Mutants/Phenotypes Strains/Constructs	Entian KD, et al. (1999) Functional analysis of 150 deletion mutants in Saccharomyces cerevisiae by a systematic approach. Mol Gen Genet 262(4-5):683-702	|ABM1 |AIM3 |ALT1 |AMN1 |APD1 |APL2 |AVT3 |BIO3 |BIO4 |BIO5 |BNA3 |BUD4 |CFD1 |CHA4 |MORE
Protein Sequence Features	Sen-Gupta M, et al. (1997) Sequence analysis of the 33 kb long region between ORC5 and SUI1 from the left arm of chromosome XIV from Saccharomyces cerevisiae. Yeast 13(9):849-60	|ATX1 |CDC25 |CWC25 |FOL1 |GIS2 |MPA43 |MRPL17 |NRD1 |ORC5 |RAD50 |RPA49 |RTC4 |SIP3 |SUI1 |MORE

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