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ECM7/YLR443W 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: 1022622 to 1023968 CDS: 1022622 - 1023968 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
ECM7	YLR443W	ZRG15	ORF, Verified	S000004435
Description
Non-essential putative integral membrane protein; mutant has cell wall defects; transcription is induced under conditions of zinc deficiency

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 2008-02-22 SGD zinc ion binding GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0862 Assigned on 2007-05-23 UniProtKB
Biological Process Annotation(s) Reference(s) Evidence Assigned By 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 Lussier M, et al. (1997) Large scale identification of genes involved in cell surface biosynthesis and architecture in Saccharomyces cerevisiae. Genetics 147(2):435-50      IMP : Inferred from Mutant Phenotype Assigned on 2002-09-27 SGD protein sumoylation 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
Cellular Component Annotation(s) Reference(s) Evidence Assigned By integral to membrane Kim H, et al. (2003) Topology models for 37 Saccharomyces cerevisiae membrane proteins based on C-terminal reporter fusions and predictions. J Biol Chem 278(12):10208-13          ISM : Inferred from Sequence Model Assigned on 2009-08-26 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 forECM7/YLR443W for ECM7 1) Yuan DS (2000) Zinc-regulated genes in Saccharomyces cerevisiae revealed by transposon tagging. Genetics 156(1):45-58        2) Lussier M, et al. (1997) Large scale identification of genes involved in cell surface biosynthesis and architecture in Saccharomyces cerevisiae. Genetics 147(2):435-50      3) Kim H, et al. (2003) Topology models for 37 Saccharomyces cerevisiae membrane proteins based on C-terminal reporter fusions and predictions. J Biol Chem 278(12):10208-13

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for ECM7/YLR443W

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for ECM7/YLR443W

Homologs [TOP] [NEXT]
Comparison Resources PSI-BLAST Results Ashbya Homologs (AGD) BLASTN vs. fungi BLASTP at NCBI BLASTP vs. fungi Candida Homologs (CGD) Candida Homologs (CandidaDB) 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 MVMSRIR C-term PSSALQF Length(aa) 448 MW(Da) 50,327 pI 4.88 Amino Acid Composition (full length) GCG tools: PepPlot, Helical Wheel, PepStruct Transcript Translation Calculations Codon Bias -0.007   Codon Adaptation Index 0.102   Frequency of Optimal Codons 0.397   Hydropathicity of Protein -0.114   Aromaticity Score 0.112

10 20 30 40 50 | | | | | MVMSRIRDTIARPFQNLTALEKVVQWLRLGTTLLIISFGLALTVGPLSSP RTLYMSRLDTYSADITTGLFTVLRESMEQSTSTEENNGVGLTTSELYILT AYTESQIKNVPQYITVSLYGRCDSTYTMVEVFDSEGNMHSVKNSTTKSTC SSIGTDYLFDYREVLESLGLDIILDYAYNKIGSQQAESSAYTTYMRSLKH KKANVLHLLYAVISFQVCMLFFMIWYYYIKGRFMNALKERALVHINSLLS LVVFIGGLISSISLAWVNYTIQSRINTELEAFGFSYHLGVTWFALLWCFA GLISVSCLAWSGLEWCISDNGTSYGGGIDDKFLGYQAGVFTDADLDDETS YSQRYPQRQSTSGEAELMRNSDTMATIRKTSDVDLNSENDANTSLDHGNP TANISNGGKHEPFATREEFELQDIRFRSSNDSEESMQRVIKPSSALQF*

Protein Structures from PDB: proteins of known structure with sequence similarity to ECM7/YLR443W, 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	Reference
ECM7	Lussier M, et al. (1997) Large scale identification of genes involved in cell surface biosynthesis and architecture in Saccharomyces cerevisiae. Genetics 147(2):435-50

Alias Name(s)	Reference
ZRG15	Yuan DS (2000) Zinc-regulated genes in Saccharomyces cerevisiae revealed by transposon tagging. Genetics 156(1):45-58

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
YLR443W	SGD Systematic Sequence
851164	NCBI: Gene ID
NP_013548.1	NCBI: RefSeq protein version ID
NP_013548.1	NCBI: RefSeq protein version ID
6323476	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 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
7 curated references; 0 references not yet curated
DNA/RNA Sequence Features Reviews	Hood HM, et al. (2009) Evolutionary roles of upstream open reading frames in mediating gene regulation in fungi. Annu Rev Microbiol 63:385-409	|APC2 |ARV1 |AVT2 |CAD1 |CBS1 |CLN3 |CPA1 |DCD1 |FOL1 |GCN4 |HAP4 |HEM3 |HOL1 |IMD4 |MORE
Other Features	Selpi S, et al. (2009) Predicting functional upstream open reading frames in Saccharomyces cerevisiae. BMC Bioinformatics 10(1):451	|ACC1 |APP1 |ATH1 |BCK2 |CAD1 |CBS1 |CIN8 |CKA2 |CLN3 |CPA1 |DCD1 |FAS1 |FOL1 |GCN4 |MORE
DNA/RNA Sequence Features RNA Levels and Processing Regulation of Strains/Constructs	Zhang Z and Dietrich FS (2005) Identification and characterization of upstream open reading frames (uORF) in the 5' untranslated regions (UTR) of genes in Saccharomyces cerevisiae. Curr Genet 48(2):77-87	|APC2 |ARV1 |AVT2 |CPA1 |FOL1 |GCN4 |HAP4 |HEM3 |IMD4 |MBR1 |MKK1 |RPC11 |SLM2 |SPE4 |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
Cellular Location Protein Physical Properties	Kim H, et al. (2003) Topology models for 37 Saccharomyces cerevisiae membrane proteins based on C-terminal reporter fusions and predictions. J Biol Chem 278(12):10208-13	|AQY1 |ASG7 |ATO2 |AVT6 |CDC1 |ERP2 |ERV15 |FCY2 |FLD1 |HHY1 |IZH4 |MEP1 |MUP1 |OSW5 |MORE
Mutants/Phenotypes RNA Levels and Processing Strains/Constructs Techniques and Reagents Transcription	Yuan DS (2000) Zinc-regulated genes in Saccharomyces cerevisiae revealed by transposon tagging. Genetics 156(1):45-58	|ADH4 |DFG16 |DPP1 |HEF3 |MCD4 |MET30 |OYE3 |THO2 |TSA1 |ZAP1 |ZRG17 |ZRG8
Mutants/Phenotypes	Lussier M, et al. (1997) Large scale identification of genes involved in cell surface biosynthesis and architecture in Saccharomyces cerevisiae. Genetics 147(2):435-50	|ACS1 |ALG12 |ALG9 |ARG7 |ATG32 |BUD8 |COX11 |CWP2 |DCG1 |DFG16 |DIT2 |ECM10 |ECM11 |ECM12 |MORE

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