SKN1/YGR143W 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: 775198 to 777513
CDS: 775198 - 777513
Genetic position: 88.14 cM
Genetic Map Data

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

SKN1 YGR143W ORF, Verified S000003375

Description
Protein involved in sphingolipid biosynthesis; type II membrane protein with similarity to Kre6p

GO Annotations [TOP] [NEXT]
Molecular Function
Annotation(s) Reference(s) Evidence Assigned By
glucosidase activity Montijn RC, et al. (1999) Localization of synthesis of beta1,6-glucan in Saccharomyces cerevisiae. J Bacteriol 181(24):7414-20
       ISS : Inferred from Sequence or structural Similarity
IMP : Inferred from Mutant Phenotype
Assigned on 2002-11-11 SGD
Biological Process
Annotation(s) Reference(s) Evidence Assigned By
1,6-beta-glucan biosynthetic process Roemer T, et al. (1994) Characterization of the yeast (1-->6)-beta-glucan biosynthetic components, Kre6p and Skn1p, and genetic interactions between the PKC1 pathway and extracellular matrix assembly. J Cell Biol 127(2):567-79
     ISS : Inferred from Sequence or structural Similarity
IMP : Inferred from Mutant Phenotype
Assigned on 2002-07-18 SGD
cellular cell wall organization GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.
     IEA : Inferred from Electronic Annotation with EBI:KW-0961
Assigned on 2008-02-14 UniProtKB
fungal-type cell wall organization Roemer T, et al. (1994) Characterization of the yeast (1-->6)-beta-glucan biosynthetic components, Kre6p and Skn1p, and genetic interactions between the PKC1 pathway and extracellular matrix assembly. J Cell Biol 127(2):567-79
     IMP : Inferred from Mutant Phenotype
Assigned on 2002-07-18 SGD
sphingolipid biosynthetic process Thevissen K, et al. (2005) SKN1, a novel plant defensin-sensitivity gene in Saccharomyces cerevisiae, is implicated in sphingolipid biosynthesis. FEBS Lett 579(9):1973-7
         IMP : Inferred from Mutant Phenotype
IGI : Inferred from Genetic Interaction with SGD:IPT1
Assigned on 2005-04-22 SGD
Cellular Component
Annotation(s) Reference(s) Evidence Assigned By
integral to membrane Roemer T, et al. (1994) Characterization of the yeast (1-->6)-beta-glucan biosynthetic components, Kre6p and Skn1p, and genetic interactions between the PKC1 pathway and extracellular matrix assembly. J Cell Biol 127(2):567-79
     IDA : Inferred from Direct Assay
Assigned on 2002-07-18 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-9906
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 forSKN1/YGR143W for SKN1
1) Montijn RC, et al. (1999) Localization of synthesis of beta1,6-glucan in Saccharomyces cerevisiae. J Bacteriol 181(24):7414-20

2) Roemer T, et al. (1993) SKN1 and KRE6 define a pair of functional homologs encoding putative membrane proteins involved in beta-glucan synthesis. Mol Cell Biol 13(7):4039-48

3) Thevissen K, et al. (2005) SKN1, a novel plant defensin-sensitivity gene in Saccharomyces cerevisiae, is implicated in sphingolipid biosynthesis. FEBS Lett 579(9):1973-7

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for SKN1/YGR143W

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for SKN1/YGR143W

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 MSVRNLT

C-term SSKFSLS

Length(aa) 771

MW(Da) 86,240

pI 4.52

Amino Acid Composition (full length)

GCG tools: PepPlot, Helical Wheel, PepStruct

Transcript Translation Calculations

Codon Bias 0.076

Codon Adaptation Index 0.137

Frequency of Optimal Codons 0.447

Hydropathicity of Protein -0.636

Aromaticity Score 0.123

10 20 30 40 50 | | | | | MSVRNLTNNRHSNSENSVSGSENSFYSSNEQSRQSSSLEPADGQNVRVSG NPFLGSEEFDEDYNSPSGDDERRGANEYSSSSSINYNNDPNSDTSLLANE KNSPERNGQRMSDYKGYYAKTNLTSANNLNNHNNNNYKNIISSSNDNSFA SHLQPPDRNLPSHPSSNNMSSFSNNSLIKSPPPFDRYPLVGTRHISAAQS QSQNLINEKKRANMTGSSSSAHDSSLSSTNLYMGEQDFSPFGGYPASFFP LTLDEKEDDDYIHNPNVEEEAKLDRRRFVDDFKHMDRRSFLGLLGILFLF MAGIFIFIVLPAITFSGVVYHHEHVHAANSAGSSSSNTTSKSLTEYQYPQ LAAIRTTLVDPDTPDSAKTRVAKDGSKWQLVFSDEFNAEGRTFYDGDDQF WTAPDIHYDATKDLEWYSPDAVTTTNGTLTLRMDAFRNHDLYYRSGMVQS WNKLCFTEGALEVSANLPNYGRVTGLWPGMWTMGNLGRPGYLASTQGVWP YSYEACDAGITPNQSSPDGISYLPGQKLSVCTCDNEDHPNQGVGRGAPEI DILEGEADTILGVGVASQSLQIAPFDIWYMPDYDFIEVYNFTTTTMNTYA GGPFQQAVSAISTLNVTWYEFGEEAGYFQKYAIEYLNDDDNGYIRWFVGE NPTFTLYATSLHPSGNIDWRRISKEPMSAILNLGISNNWAYIDWQYIFFP VTMSIDYVRLYQPKGSTSITCDPEDYPTYDYIQSHLNAYYNANLTDWEQA GYTFPKNILTGGCSSSKFSLS*

Protein Structures from PDB: proteins of known structure with sequence similarity to SKN1/YGR143W, based on Smith-Waterman analysis. [TOP] [NEXT]
PDB protein structure(s) homologous to SKN1 Homolog Source (per PDB) Protein Alignment: SKN1 vs. Homolog External Links
P-Value %Identical %Similar Alignment
2vy0 ( Chain: A, B)
The x-ray structure of endo-beta-1,3-glucanase from pyrococcus furiosus
PDB_Info
PDB_Structure
Pyrococcus furiosus Chain A = 0.007498 29 31 View alignment SCOP
MMDB
CATH
Chain B = 0.007498 29 31 View alignment

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 Reference
SKN1 Roemer T, et al. (1993) SKN1 and KRE6 define a pair of functional homologs encoding putative membrane proteins involved in beta-glucan synthesis. Mol Cell Biol 13(7):4039-48

Standard Name	Reference
SKN1	*Roemer T, et al.* (1993)** SKN1 and KRE6 define a pair of functional homologs encoding putative membrane proteins involved in beta-glucan synthesis. Mol Cell Biol 13(7):4039-48

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

YGR143W SGD Systematic Sequence

853045 NCBI: Gene ID

NP_011659.1 NCBI: RefSeq protein version ID

NP_011659.1 NCBI: RefSeq protein version ID

6321582 NCBI: NCBI protein GI

Sequence from other databases
Sequence ID	Source
YGR143W	SGD Systematic Sequence
853045	NCBI: Gene ID
NP_011659.1	NCBI: RefSeq protein version ID
NP_011659.1	NCBI: RefSeq protein version ID
6321582	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
20 curated references; 0 references not yet curated
Function/Process
Genetic Interactions
Mutants/Phenotypes
Strains/Constructs
Thevissen K, et al. (2010) Skn1 and Ipt1 negatively regulate autophagy in Saccharomyces cerevisiae. FEMS Microbiol Lett 303(2):163-8
       |IPT1
Mutants/Phenotypes
Strains/Constructs
Francois IE, et al. (2009) Membrane rafts are involved in intracellular miconazole accumulation in yeast cells. J Biol Chem 284(47):32680-5
       |ADH1 |DOS2 |ERG3 |IPT1 |LCL1 |MRPL23 |PTH1 |SIP3 |SUR1 |YDR114C |YOR292C
Genetic Interactions
Mutants/Phenotypes
Kitamura A, et al. (2009) Discovery of a Small-Molecule Inhibitor of {beta}-1,6-Glucan Synthesis. Antimicrob Agents Chemother 53(2):670-677
       |KRE6
Evolution
Fungal Related Genes/Proteins
Coronado JE, et al. (2007) Conserved processes and lineage-specific proteins in fungal cell wall evolution. Eukaryot Cell 6(12):2269-77
       |ACF2 |AGA1 |AGA2 |ANS1 |BAR1 |BGL2 |BSC1 |CCW12 |CCW14 |CDA1 |CDA2 |CHS1 |CHS2 |CHS3 |MORE
Genetic Interactions
Wright CM, et al. (2007) The Hsp40 molecular chaperone Ydj1p, along with the protein kinase C pathway, affects cell-wall integrity in the yeast Saccharomyces cerevisiae. Genetics 175(4):1649-64
       |BCK1 |CIS1 |CYC8 |HSP82 |MID2 |MKK1 |PKC1 |SLG1 |SSA1 |SYP1 |YDJ1
Genetic Interactions
Mutants/Phenotypes
Aerts AM, et al. (2006) Level of M(IP)2C sphingolipid affects plant defensin sensitivity, oxidative stress resistance and chronological life-span in yeast. FEBS Lett 580(7):1903-7
       |IPT1
Reviews
Dickson RC, et al. (2006) Functions and metabolism of sphingolipids in Saccharomyces cerevisiae. Prog Lipid Res 45(6):447-65
       |ARV1 |AUR1 |CSH1 |DPL1 |FEN1 |IPT1 |LCB1 |LCB2 |LCB3 |LCB4 |LCB5 |NCR1 |PKH1 |PKH2 |MORE
Reviews
Lesage G and Bussey H (2006) Cell wall assembly in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 70(2):317-43
       |ANP1 |BGL2 |BIG1 |CDA1 |CDA2 |CHS1 |CHS2 |CHS3 |CHS6 |CHS7 |CNE1 |CRH1 |CRR1 |CTS1 |MORE
Function/Process
Genetic Interactions
Mutants/Phenotypes
Strains/Constructs
Substrates/Ligands/Cofactors
Thevissen K, et al. (2005) SKN1, a novel plant defensin-sensitivity gene in Saccharomyces cerevisiae, is implicated in sphingolipid biosynthesis. FEBS Lett 579(9):1973-7
         |IPT1
Regulation of
Transcription
Daran-Lapujade P, et al. (2004) Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture study. J Biol Chem 279(10):9125-38
           |AAD16 |ACH1 |ACO1 |ACO2 |ACS1 |ACS2 |ADH1 |ADH2 |ADH3 |ADH4 |ADH5 |AGP2 |AHP1 |ALD2 |MORE
Genetic Interactions
Strains/Constructs
Tong AH, et al. (2004) Global mapping of the yeast genetic interaction network. Science 303(5659):808-13
           |AAD4 |AAH1 |ABF2 |ACE2 |ADH6 |AEP2 |AFG1 |AGP1 |AHC1 |AHC2 |AIM21 |AIM22 |AIM26 |AIM29 |MORE
Evolution
Friedman R and Hughes AL (2001) Gene duplication and the structure of eukaryotic genomes. Genome Res 11(3):373-81
       |AAD10 |AAD16 |AAD4 |ARF1 |ARF2 |ASK10 |ASN1 |ASN2 |CLA4 |CLB1 |CLB2 |CLB5 |CLB6 |COS1 |MORE
Cell Cycle Phase Involved
RNA Levels and Processing
Regulation of
Simon I, et al. (2001) Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106(6):697-708
               |ACE2 |AGA1 |AGA2 |ALK1 |APC1 |ARP7 |ASH1 |BUD4 |BUD8 |BUD9 |CDC20 |CDC21 |CDC45 |CDC6 |MORE
Regulation of
Lee J, et al. (1999) Yap1 and Skn7 control two specialized oxidative stress response regulons in yeast. J Biol Chem 274(23):16040-6
       |ADH6 |AHP1 |CCP1 |CDC48 |CTT1 |CYS3 |DAK1 |DNM1 |GLR1 |GOR1 |GRE2 |GSH1 |HSP78 |HSP82 |MORE
Function/Process
Fungal Related Genes/Proteins
Montijn RC, et al. (1999) Localization of synthesis of beta1,6-glucan in Saccharomyces cerevisiae. J Bacteriol 181(24):7414-20
       |KRE5 |KRE6 |SEC1
Fungal Related Genes/Proteins
Mio T, et al. (1997) Isolation of the Candida albicans homologs of Saccharomyces cerevisiae KRE6 and SKN1: expression and physiological function. J Bacteriol 179(7):2363-72
       |KRE6
Reviews
Klis FM (1994) Review: cell wall assembly in yeast. Yeast 10(7):851-69
     |BGL2 |KRE11 |KTR6 |MNN1 |MNN10 |MNN9 |SAG1 |SED1 |SKT5
DNA/RNA Sequence Features
Function/Process
Other Features
Protein Processing/Modification/Regulation
Roemer T, et al. (1994) Characterization of the yeast (1-->6)-beta-glucan biosynthetic components, Kre6p and Skn1p, and genetic interactions between the PKC1 pathway and extracellular matrix assembly. J Cell Biol 127(2):567-79
     |KRE6 |KRE9 |PKC1
Genetic Interactions
Brown JL and Bussey H (1993) The yeast KRE9 gene encodes an O glycoprotein involved in cell surface beta-glucan assembly. Mol Cell Biol 13(10):6346-56
     |KRE1 |KRE11 |KRE5 |KRE6 |KRE9
DNA/RNA Sequence Features
Function/Process
Fungal Related Genes/Proteins
Genetic Interactions
Mapping
Mutants/Phenotypes
Protein Sequence Features
Strains/Constructs
Roemer T, et al. (1993) SKN1 and KRE6 define a pair of functional homologs encoding putative membrane proteins involved in beta-glucan synthesis. Mol Cell Biol 13(7):4039-48
     |ADE3 |KRE6

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