RTA1/YGR213C 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: 919470 to 918517
CDS: 919470 - 918517

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

RTA1 YGR213C ORF, Verified S000003445

Description
Protein involved in 7-aminocholesterol resistance; has seven potential membrane-spanning regions; expression is induced under both low-heme and low-oxygen conditions; member of the fungal lipid-translocating exporter (LTE) family of protein

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 2002-08-01 SGD
Biological Process
Annotation(s) Reference(s) Evidence Assigned By
biological_process
unknown SGD (2002) Use of the ND evidence code for Gene Ontology (GO) terms in SGD
   ND : No Biological Data Available
Assigned on 2009-08-26 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
response to stress DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.
     IEA : Inferred from Electronic Annotation with EBI:IPR007568
Assigned on 2008-02-13 UniProtKB
Cellular Component
Annotation(s) Reference(s) Evidence Assigned By
integral to membrane Soustre I, et al. (1996) Characterization of the Saccharomyces cerevisiae RTA1 gene involved in 7-aminocholesterol resistance. Curr Genet 30(2):121-5
       ISM : Inferred from Sequence Model
Assigned on 2009-08-26 SGD
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
DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.
     IEA : Inferred from Electronic Annotation with EBI:IPR007568
Assigned on 2007-05-23 UniProtKB
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 forRTA1/YGR213C for RTA1
1) Soustre I, et al. (1996) Characterization of the Saccharomyces cerevisiae RTA1 gene involved in 7-aminocholesterol resistance. Curr Genet 30(2):121-5

2) Protchenko O, et al. (2008) Role of PUG1 in inducible porphyrin and heme transport in Saccharomyces cerevisiae. Eukaryot Cell 7(5):859-71

3) Manente M and Ghislain M (2009) The lipid-translocating exporter family and membrane phospholipid homeostasis in yeast. FEMS Yeast Res 9(5):673-87

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for RTA1/YGR213C

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for RTA1/YGR213C

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 MAKDGFE

C-term DLASKSE

Length(aa) 317

MW(Da) 35,485

pI 7.94

Amino Acid Composition (full length)

GCG tools: PepPlot, Helical Wheel, PepStruct

Transcript Translation Calculations

Codon Bias 0.075

Codon Adaptation Index 0.118

Frequency of Optimal Codons 0.449

Hydropathicity of Protein 0.647

Aromaticity Score 0.145

10 20 30 40 50 | | | | | MAKDGFELYRYTPELGASILFTVLFAVSGVAFVILLFHYSVKSKRRVGSL MKSQPVLRYYGTVNLAGAYIPFIFGCFVECVGFAFRCKSSKDTTLLNPYI IQTVFLLVSPTLYAASIYMIFGRMATLLFAENLMIMPARFNTTIFVIGDV GSLLLQAIGGAMMSKVTSASSGSHLVTAGLFIQIAFFGLFIINEVLFIFK MSKKPTNVSVRYGSWKYLNIALLVNSFLILIRSIVRAVEFIQGYDGEIAS HEWYLYIFDGLPMFLLVLIFIVAFPLINIFRIHEESIQAQQSARFDGTDY PDVEVTSIEEDLASKSE*

Protein Structures from PDB: proteins of known structure with sequence similarity to RTA1/YGR213C, 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 Reference
RTA1 SGD (2007) Information without a citation in SGD

Standard Name	Reference
RTA1	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
Sequence from other databases

Sequence ID Source

YGR213C SGD Systematic Sequence

853127 NCBI: Gene ID

NP_011729.1 NCBI: RefSeq protein version ID

NP_011729.1 NCBI: RefSeq protein version ID

6321652 NCBI: NCBI protein GI

Sequence from other databases
Sequence ID	Source
YGR213C	SGD Systematic Sequence
853127	NCBI: Gene ID
NP_011729.1	NCBI: RefSeq protein version ID
NP_011729.1	NCBI: RefSeq protein version ID
6321652	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
19 curated references; 0 references not yet curated
Evolution
Fungal Related Genes/Proteins
Non-Fungal Related Genes/Proteins
Protein Sequence Features
Reviews
Manente M and Ghislain M (2009) The lipid-translocating exporter family and membrane phospholipid homeostasis in yeast. FEMS Yeast Res 9(5):673-87
       |PUG1 |RSB1 |RTM1 |YLR046C
Mutants/Phenotypes
Transcription
Sundstrom L, et al. (2009) Identification of Saccharomyces cerevisiae Genes Involved in the Resistance to Phenolic Fermentation Inhibitors. Appl Biochem Biotechnol
     |AAD4 |AAD6 |ARR2 |ATR1 |FLR1 |GLR1 |GPX2 |GTT2 |JLP1 |OYE2 |OYE3 |PAU17 |SNQ2 |SSA1 |MORE
Genomic expression study
RNA Levels and Processing
Del Vescovo V, et al. (2008) Role of Hog1 and Yaf9 in the transcriptional response of Saccharomyces cerevisiae to cesium chloride. Physiol Genomics 33(1):110-20
       |AGA1 |ALD3 |ARO10 |ATG1 |BRL1 |CAR2 |CMK2 |COX5B |CPR1 |CPR7 |CWP1 |CYC7 |DAN4 |DDR48 |MORE
Fungal Related Genes/Proteins
RNA Levels and Processing
Regulation of
Protchenko O, et al. (2008) Role of PUG1 in inducible porphyrin and heme transport in Saccharomyces cerevisiae. Eukaryot Cell 7(5):859-71
       |FET3 |FRE1 |HEM1 |PUG1 |RSB1 |RTM1
RNA Levels and Processing
Regulation of
Dardalhon M, et al. (2007) Specific transcriptional responses induced by 8-methoxypsoralen and UVA in yeast. FEMS Yeast Res 7(6):866-878
       |AAD6 |ARG3 |ARG5,6 |ARG80 |BCH2 |CDC27 |CDC45 |COT1 |CTF19 |DDI2 |DIN7 |DUN1 |ECL1 |ECM13 |MORE
Function/Process
RNA Levels and Processing
Iwahashi H, et al. (2007) Evaluation of toxicity of the mycotoxin citrinin using yeast ORF DNA microarray and Oligo DNA microarray. BMC Genomics 8:95
         |AAD10 |AAD14 |AAD15 |AAD16 |AAD3 |AAD4 |AAD6 |ECM4 |FLR1 |FRM2 |GRE2 |GTT2 |MET17 |OYE3 |MORE
Evolution
Fungal Related Genes/Proteins
De Hertogh B, et al. (2006) Emergence of species-specific transporters during evolution of the hemiascomycete phylum. Genetics 172(2):771-81
       |AAC1 |AAC3 |ACS2 |ADP1 |ADY2 |AGC1 |AGP1 |AGP2 |AGP3 |ALP1 |ALR1 |ALR2 |ANT1 |AQR1 |MORE
Genetic Interactions
Mutants/Phenotypes
Strains/Constructs
Hallberg M, et al. (2006) Functional and physical interactions within the middle domain of the yeast mediator. Mol Genet Genomics 276(2):197-210
       |AIM31 |ASH1 |ERP6 |MED4 |MED6 |MED7 |NUT2 |POP2 |RSM27 |SRB7 |STE24 |TUP1
Fungal Related Genes/Proteins
Vermitsky JP, et al. (2006) Pdr1 regulates multidrug resistance in Candida glabrata: gene disruption and genome-wide expression studies. Mol Microbiol 61(3):704-22
     |ARE1 |ATF2 |CTA1 |HSP12 |MEC3 |MKC7 |MNT3 |PDH1 |PDR1 |PDR12 |PDR3 |QDR2 |RPN4 |RSB1 |MORE
Fungal Related Genes/Proteins
Hsiang T and Baillie DL (2005) Comparison of the yeast proteome to other fungal genomes to find core fungal genes. J Mol Evol 60(4):475-83
         |ARN2 |KTR1 |KTR7 |MDM31 |MSS51 |PCL2 |RSM27 |SGA1 |SPT10 |SYH1 |TRL1 |VPS17 |VTS1 |YAL004W |MORE
RNA Levels and Processing
Iwahashi H, et al. (2005) Adaptation of Saccharomyces cerevisiae to high hydrostatic pressure causing growth inhibition. FEBS Lett 579(13):2847-52
           |AFR1 |CRG1 |GPG1 |HSP12 |INO1 |MET13 |MET6 |MOH1 |OPI3 |PIR3 |POX1 |PRM5 |PST1 |PTP2 |MORE
Genomic expression study
RNA Levels and Processing
Regulation of
Parveen M, et al. (2004) Response of Saccharomyces cerevisiae to a monoterpene: evaluation of antifungal potential by DNA microarray analysis. J Antimicrob Chemother 54(1):46-55
               |AAD6 |ADH5 |ADH7 |ADY2 |AGA2 |AMS1 |ARG1 |ARN2 |ATF2 |ATX1 |BCK1 |BFR1 |BSC1 |BUD7 |MORE
RNA Levels and Processing
Regulation of
Sirisattha S, et al. (2004) Toxicity of anionic detergents determined by Saccharomyces cerevisiae microarray analysis. Water Res 38(1):61-70
           |ATX1 |CMK2 |CRS5 |DIA1 |GPX1 |GRE2 |GRX1 |GRX2 |GRX6 |GTT2 |GYP8 |HSP12 |HSP26 |HYR1 |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 |ECM7 |ERP2 |ERV15 |FCY2 |FLD1 |HHY1 |IZH4 |MEP1 |MUP1 |MORE
Regulation of
Transcription
Rubin-Bejerano I, et al. (2003) Phagocytosis by neutrophils induces an amino acid deprivation response in Saccharomyces cerevisiae and Candida albicans. Proc Natl Acad Sci U S A 100(19):11007-12
             |ADE1 |ADE12 |ADE13 |ADE16 |ADE17 |ADE2 |ADE3 |ADE4 |ADE5,7 |ADE6 |ADE8 |AKR2 |ALD5 |ARG1 |MORE
Regulation of
Transcription
Santiago TC and Mamoun CB (2003) Genome expression analysis in yeast reveals novel transcriptional regulation by inositol and choline and new regulatory functions for Opi1p, Ino2p, and Ino4p. J Biol Chem 278(40):38723-30
       |AAD10 |ACH1 |AMS1 |ANB1 |BIO2 |BIO3 |BIO4 |BIO5 |CIT3 |CRC1 |CWP1 |DAN1 |DUR3 |ECM13 |MORE
Fungal Related Genes/Proteins
Kihara A and Igarashi Y (2002) Identification and characterization of a Saccharomyces cerevisiae gene, RSB1, involved in sphingoid long-chain base release. J Biol Chem 277(33):30048-54
       |PUG1 |RSB1 |RTM1 |YLR046C
Regulation of
Transcription
Holstege FC, et al. (1998) Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95(5):717-28
             |AGA1 |AGA2 |ALD3 |ARD1 |BAR1 |BCK1 |BIM1 |CAC2 |CDC13 |CDC5 |CLB2 |CTR9 |CTT1 |CYC7 |MORE
DNA/RNA Sequence Features
Mapping
Mutants/Phenotypes
Protein Sequence Features
Strains/Constructs
Soustre I, et al. (1996) Characterization of the Saccharomyces cerevisiae RTA1 gene involved in 7-aminocholesterol resistance. Curr Genet 30(2):121-5
       |RPS0A

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