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PRM7/YDL039C 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   ChrIV: 384079 to 381983 CDS: 384079 - 381983 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
PRM7	YDL039C	YDL038C	ORF, Verified	S000002197
This name is reserved with SGD according to the Gene Naming Guidelines agreed upon by the yeast community. Gene name reserved on: 2000-09-05. Gene name expires on 2001-09-05.
Description
Pheromone-regulated protein, predicted to have one transmembrane segment; promoter contains Gcn4p binding elements

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 2001-01-19 SGD
Biological Process Annotation(s) Reference(s) Evidence Assigned By conjugation with cellular fusion Heiman MG and Walter P (2000) Prm1p, a pheromone-regulated multispanning membrane protein, facilitates plasma membrane fusion during yeast mating. J Cell Biol 151(3):719-30        IEP : Inferred from Expression Pattern Assigned on 2001-01-18 SGD response to drug Dilda PJ, et al. (2005) Mechanism of selectivity of an angiogenesis inhibitor from screening a genome-wide set of Saccharomyces cerevisiae deletion strains. J Natl Cancer Inst 97(20):1539-47                IMP : Inferred from Mutant Phenotype Assigned on 2007-01-08 SGD translational elongation 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 Heiman MG and Walter P (2000) Prm1p, a pheromone-regulated multispanning membrane protein, facilitates plasma membrane fusion during yeast mating. J Cell Biol 151(3):719-30        ISS : Inferred from Sequence or structural Similarity Assigned on 2001-01-18 SGD

Pathways [TOP] [NEXT]
No pathways available

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

Basic References [TOP]

BASIC INFORMATION REFERENCES forPRM7/YDL039C for PRM7 1) Prelich G (2008)    2) Schuldiner O, et al. (1998) Computer analysis of the entire budding yeast genome for putative targets of the GCN4 transcription factor. Curr Genet 33(1):16-20        3) Heiman MG and Walter P (2000) Prm1p, a pheromone-regulated multispanning membrane protein, facilitates plasma membrane fusion during yeast mating. J Cell Biol 151(3):719-30

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for PRM7/YDL039C

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for PRM7/YDL039C

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 MYRTRSS C-term ALPLAFI Length(aa) 698 MW(Da) 70,122 pI 4.03 Amino Acid Composition (full length) GCG tools: PepPlot, Helical Wheel, PepStruct Transcript Translation Calculations Codon Bias 0.224   Codon Adaptation Index 0.188   Frequency of Optimal Codons 0.541   Hydropathicity of Protein -0.067   Aromaticity Score 0.029

10 20 30 40 50 | | | | | MYRTRSSDEVTTSTDLTSSSDVATSVDPTTSVISSTSADPTTSADSTTST VQTTSAGPSNNIGNSTLANSTTFAVSSTSIDPTSSSDVITSTVQTTSIEP TTSLVSSNDITTSTSLNISVVISTSTDSTSLIESTTTVGPHASSSVAGMY RTRSSDEVTTSTDPTSSSDVATSADPTSSSAVTTLVDPTTSVVISTSVDQ TSSSDVATSVDPTTSVISSTSADPTTSADSTTSTVQTTSVDPTSSVVSSA PVDPASSVVSLTSSYPTSSSTVTISANSNGSATLAAQTTSIDPVSSIVSS SGATTIISSASIDPASSVVSSTSSEPTSFIVSSTSVYSTRPSGPTTSTDL ATFSDTIILRVSTTSTSQDTQTVSSSLTDMVSSTGSADLSVSSIQRSQVD PSTFAVSNSPVYPTASTGSTSTGIPIASESLSLSRQQGISATSSSSIVTL TPVDSASSSRSSATSIIKPNMPVSSNDSKTQSSVSVVDAFQSTKSSYPSI TSADPTTLASENGLVGSSSSAHPITLDRTYASAHASVTDIVSRVTDSTRH TTLVTSNINIQSEVGNPNYSGPKDTTITKQSAFMTSPASTSTISNVQSTA SVMNHSIEDNISAAASLESVSGTSTKDYSSQSSAIHYTNSFTTTTTNAFI TSKHSIAAVSTGAITSSASISLIMEGSANIEAVGKLVWLAAALPLAFI*

Protein Structures from PDB: proteins of known structure with sequence similarity to PRM7/YDL039C, based on Smith-Waterman analysis. [TOP] [NEXT]
PDB protein structure(s) homologous to PRM7 Homolog Source (per PDB) Protein Alignment: PRM7 vs. Homolog External Links P-Value %Identical %Similar Alignment 3h0g ( Chain: A, M) DNA-directed RNA polym PDB_Info PDB_Structure Unknown Chain A = 0.007797 32 20 View alignment SCOP MMDB CATH Chain M = 0.007797 32 20 View alignment

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
PRM7	2000-10-30	Heiman MG and Walter P (2000) Prm1p, a pheromone-regulated multispanning membrane protein, facilitates plasma membrane fusion during yeast mating. J Cell Biol 151(3):719-30

Alias Name(s)	Reference
YDL038C	Prelich G (2008)

Sequence Annotation Notes

Date

Note

2008-06-05

Greg Prelich's lab discovered an error in the systematic reference sequence for Chromosome 4. This error was verified in the S288C strain background. Therefore, the following correction was made: insert a G after the G at 382381. New: 1737 TTTGGTGATGGTAGTGTCTTTGGGACCCGAGTAATTTGGGTTCCCAACCTCAGACTGAAT 1678 ||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| Old: 382343 TTTGGTGATGGTAGTGTCTTTGGGACCCGAGTAATTTGG-TTCCCAACCTCAGACTGAAT 382401 As a result of this change, ORF YDL038C was merged into ORF PRM7/YDL039C. The new longer ORF is 2097 nt long. The name YDL038C is being retained as an alias for PRM7/YDL039C. Prelich G (2008)

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
YDL039C	SGD Systematic Sequence
851522	NCBI: Gene ID
NP_010245.1	NCBI: RefSeq protein version ID
NP_010245.1	NCBI: RefSeq protein version ID
6320165	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
8 curated references; 0 references not yet curated
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
DNA/RNA Sequence Features Transcription	Bekaert M, et al. (2005) Identification of programmed translational -1 frameshifting sites in the genome of Saccharomyces cerevisiae. Genome Res 15(10):1411-20	|AAD16 |AAD6 |ADE17 |MRPL24 |RAD17 |SCO2 |SRL3 |STE4 |YKL033W-A |YMR084W |YMR085W
Mutants/Phenotypes	Dilda PJ, et al. (2005) Mechanism of selectivity of an angiogenesis inhibitor from screening a genome-wide set of Saccharomyces cerevisiae deletion strains. J Natl Cancer Inst 97(20):1539-47	|ACO1 |ADE1 |ARG82 |BRE1 |CBF1 |CCR4 |CSG2 |CSM1 |CYS3 |CYS4 |EAP1 |ECM25 |ELM1 |EMI2 |MORE
Regulation of Transcription	Lamb TM and Mitchell AP (2003) The transcription factor Rim101p governs ion tolerance and cell differentiation by direct repression of the regulatory genes NRG1 and SMP1 in Saccharomyces cerevisiae. Mol Cell Biol 23(2):677-86	|CTS1 |ENA1 |NRG1 |PRB1 |RIM101 |RIM8 |SMP1 |YJR061W |ZPS1
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
Function/Process Protein Sequence Features Regulation of	Heiman MG and Walter P (2000) Prm1p, a pheromone-regulated multispanning membrane protein, facilitates plasma membrane fusion during yeast mating. J Cell Biol 151(3):719-30	|AGA1 |PRM1 |PRM10 |PRM2 |PRM3 |PRM4 |PRM5 |PRM6 |PRM8 |PRM9
DNA/RNA Sequence Features Regulation of	Schuldiner O, et al. (1998) Computer analysis of the entire budding yeast genome for putative targets of the GCN4 transcription factor. Curr Genet 33(1):16-20	|ECM21 |GCN4 |HER1 |HMI1 |NST1 |OPI7 |RTC2 |YAH1 |YBL104C |YBP2 |YGL109W |YLL007C |YMR099C |YMR254C
Protein Physical Properties Protein Sequence Features	Saren AM, et al. (1997) The sequence of a 36.7 kb segment on the left arm of chromosome IV from Saccharomyces cerevisiae reveals 20 non-overlapping open reading frames (ORFs) including SIT4, FAD1, NAM1, RNA11, SIR2, NAT1, PRP9, ACT2 and MPS1 and 11 new ORFs. Yeast 13(1):65-71	|ARP2 |FAD1 |MPS1 |MTF2 |NAT1 |PRP11 |PRP9 |PUS9 |SIR2 |SIT4 |YDL027C |YDL032W |YDL034W

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