---

• Site Map |
• Search Options |
• Help |
• Home |
•   |
•  

•  
• Community Info
• Submit Data
• BLAST
• Primers
• PatMatch
• Gene/Seq Resources
• Advanced Search
• Community Wiki

---

BUD23/YCR047C 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   ChrIII: 211541 to 210714 CDS: 211541 - 210714 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
BUD23	YCR047C		ORF, Verified	S000000643
This name is reserved with SGD according to the Gene Naming Guidelines agreed upon by the yeast community. Gene name reserved on: 2001-02-13. Gene name expires on 2002-02-13.
Description
Methyltransferase, methylates residue G1575 of 18S rRNA; required for rRNA processing and nuclear export of 40S ribosomal subunits independently of methylation activity; diploid mutant displays random budding pattern

GO Annotations [TOP] [NEXT]
Molecular Function Annotation(s) Reference(s) Evidence Assigned By S-adenosylmethionine-dependent methyltransferase activity Niewmierzycka A and Clarke S (1999) S-Adenosylmethionine-dependent methylation in Saccharomyces cerevisiae. Identification of a novel protein arginine methyltransferase. J Biol Chem 274(2):814-24        ISS : Inferred from Sequence or structural Similarity Assigned on 2003-05-07 SGD methyltransferase activity DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.      IEA : Inferred from Electronic Annotation with EBI:IPR013216 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-0489 Assigned on 2007-05-23 UniProtKB rRNA (guanine) methyltransferase activity White J, et al. (2008) Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of Pre-40S subunits. Mol Cell Biol 28(10):3151-61        IMP : Inferred from Mutant Phenotype Assigned on 2008-03-24 SGD transferase activity GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0808 Assigned on 2007-05-23 UniProtKB
Biological Process Annotation(s) Reference(s) Evidence Assigned By RNA modification 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 bud site selection Ni L and Snyder M (2001) A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol Biol Cell 12(7):2147-70        IMP : Inferred from Mutant Phenotype Assigned on 2002-10-10 SGD endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) White J, et al. (2008) Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of Pre-40S subunits. Mol Cell Biol 28(10):3151-61        IMP : Inferred from Mutant Phenotype Assigned on 2008-03-24 SGD metabolic process DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.      IEA : Inferred from Electronic Annotation with EBI:IPR013216 Assigned on 2007-05-23 UniProtKB rRNA modification White J, et al. (2008) Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of Pre-40S subunits. Mol Cell Biol 28(10):3151-61        IMP : Inferred from Mutant Phenotype Assigned on 2008-03-24 SGD ribosomal small subunit export from nucleus White J, et al. (2008) Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of Pre-40S subunits. Mol Cell Biol 28(10):3151-61        IMP : Inferred from Mutant Phenotype Assigned on 2008-03-24 SGD
Cellular Component Annotation(s) Reference(s) Evidence Assigned By cytoplasm Huh WK, et al. (2003) Global analysis of protein localization in budding yeast. Nature 425(6959):686-91          IDA : Inferred from Direct Assay Assigned on 2003-10-28 SGD GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0963 Assigned on 2008-02-14 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-0086 Assigned on 2008-02-13 UniProtKB nucleolus White J, et al. (2008) Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of Pre-40S subunits. Mol Cell Biol 28(10):3151-61        IDA : Inferred from Direct Assay Assigned on 2009-10-09 SGD nucleus Huh WK, et al. (2003) Global analysis of protein localization in budding yeast. Nature 425(6959):686-91          IDA : Inferred from Direct Assay Assigned on 2003-10-28 SGD GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0539 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-0191 Assigned on 2008-02-13 UniProtKB

Pathways [TOP] [NEXT]
No pathways available

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

Basic References [TOP]
BASIC INFORMATION REFERENCES forBUD23/YCR047C for BUD23 1) Ni L and Snyder M (2001) A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol Biol Cell 12(7):2147-70        2) White J, et al. (2008) Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of Pre-40S subunits. Mol Cell Biol 28(10):3151-61

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for BUD23/YCR047C

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for BUD23/YCR047C

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 MSRPEEL C-term RKRRHRF Length(aa) 275 MW(Da) 30,742 pI 9.69 Amino Acid Composition (full length) GCG tools: PepPlot, Helical Wheel, PepStruct Transcript Translation Calculations Codon Bias 0.022   Codon Adaptation Index 0.075   Frequency of Optimal Codons 0.400   Hydropathicity of Protein -0.543   Aromaticity Score 0.076	10 20 30 40 50 | | | | | MSRPEELAPPEIFYNDSEAHKYTGSTRVQHIQAKMTLRALELLNLQPCSF ILDIGCGSGLSGEILTQEGDHVWCGLDISPSMLATGLSRELEGDLMLQDM GTGIPFRAGSFDAAISISAIQWLCNADTSYNDPKQRLMRFFNTLYAALKK GGKFVAQFYPKNDDQVDDILQSAKVAGFSGGLVVDDPESKKNKKYYLVLS SGAPPQGEEQVNLDGVTMDEENVNLKKQLRQRLKGGKDKESAKSFILRKK ELMKRRGRKVAKDSKFTGRKRRHRF*

Protein Structures from PDB: proteins of known structure with sequence similarity to BUD23/YCR047C, based on Smith-Waterman analysis. [TOP] [NEXT]

PDB protein structure(s) homologous to BUD23 Homolog Source (per PDB) Protein Alignment: BUD23 vs. Homolog External Links P-Value %Identical %Similar Alignment 3ccf ( Chain: A, B) Crystal structure of putative methyltransferase (yp_321342.1) from anabaena variabilis atcc 29413 at 1.90 a resolution PDB_Info PDB_Structure Anabaena variabilis ATCC 29413 Chain A = 1.8e-05 33 29 View alignment SCOP MMDB CATH Chain B = 1.8e-05 33 29 View alignment 2azt ( Chain: B, A) Crystal structure of h176n mutant of human glycine n- methyltransferase PDB_Info PDB_Structure Homo sapiens Chain B = 0.001100 27 26 View alignment SCOP MMDB CATH Chain A = 0.001100 27 26 View alignment 1nbi ( Chain: C, D, B, A) Structure of r175k mutated glycine n-methyltransferase complexed with s-adenosylmethionine, r175k:sam. PDB_Info PDB_Structure Rattus norvegicus Chain C = 0.001200 27 26 View alignment SCOP MMDB CATH Chain D = 0.001200 27 26 View alignment Chain B = 0.001200 27 26 View alignment Chain A = 0.001200 27 26 View alignment 1d2h ( Chain: B, C, D, A) Crystal structure of r175k mutant glycine n- methyltransferase complexed with s-adenosylhomocysteine PDB_Info PDB_Structure Rattus norvegicus Chain B = 0.001200 27 26 View alignment SCOP MMDB CATH Chain C = 0.001200 27 26 View alignment Chain D = 0.001200 27 26 View alignment Chain A = 0.001200 27 26 View alignment 1d2g ( Chain: B, A) Crystal structure of r175k mutant glycine n- methyltransferase from rat liver PDB_Info PDB_Structure Rattus norvegicus Chain B = 0.001200 27 26 View alignment SCOP MMDB CATH Chain A = 0.001200 27 26 View alignment 2idk ( Chain: D, A, B, C) Crystal structure of rat glycine n-methyltransferase complexed with folate PDB_Info PDB_Structure Rattus norvegicus Chain D = 0.001999 27 26 View alignment SCOP MMDB CATH Chain A = 0.001999 27 26 View alignment Chain B = 0.001999 27 26 View alignment Chain C = 0.001999 27 26 View alignment 2idj ( Chain: D, C, B, A) Crystal structure of rat glycine n-methyltransferase apoprotein, monoclinic form PDB_Info PDB_Structure Rattus norvegicus Chain D = 0.001999 27 26 View alignment SCOP MMDB CATH Chain C = 0.001999 27 26 View alignment Chain B = 0.001999 27 26 View alignment Chain A = 0.001999 27 26 View alignment 1nbh ( Chain: D, B, A, C) Structure of glycine n-methyltransferase complexed with s- adenosylmethionine and acetate, gnmt:sam:ace PDB_Info PDB_Structure Rattus norvegicus Chain D = 0.001999 27 26 View alignment SCOP MMDB CATH Chain B = 0.001999 27 26 View alignment Chain A = 0.001999 27 26 View alignment Chain C = 0.001999 27 26 View alignment 1kia ( Chain: C, A, B, D) Crystal structure of glycine n-methyltransferase complexed with s-adenosylmethionine and acetate PDB_Info PDB_Structure Rattus norvegicus Chain C = 0.001999 27 26 View alignment SCOP MMDB CATH Chain A = 0.001999 27 26 View alignment Chain B = 0.001999 27 26 View alignment Chain D = 0.001999 27 26 View alignment 1d2c ( Chain: B, A) Methyltransferase PDB_Info PDB_Structure Rattus norvegicus Chain B = 0.001999 27 26 View alignment SCOP MMDB CATH Chain A = 0.001999 27 26 View alignment 1xva ( Chain: A, B) Methyltransferase PDB_Info PDB_Structure Escherichia coli Chain A = 0.001999 27 26 View alignment SCOP MMDB CATH Chain B = 0.001999 27 26 View alignment 1bhj ( Chain: B, A) Crystal structure of apo-glycine n-methyltransferase (gnmt) PDB_Info PDB_Structure Rattus norvegicus Chain B = 0.001999 27 26 View alignment SCOP MMDB CATH Chain A = 0.001999 27 26 View alignment 1r8y ( Chain: C, A, E, F, G, B, D, H) Crystal structure of mouse glycine n-methyltransferase (monoclinic form) PDB_Info PDB_Structure Mus musculus Chain C = 0.002400 27 25 View alignment SCOP MMDB CATH Chain A = 0.002400 27 25 View alignment Chain E = 0.002400 27 25 View alignment Chain F = 0.002400 27 25 View alignment Chain G = 0.002400 27 25 View alignment Chain B = 0.002400 27 25 View alignment Chain D = 0.002400 27 25 View alignment Chain H = 0.002400 27 25 View alignment 1r8x ( Chain: B, A) Crystal structure of mouse glycine n-methyltransferase (tetragonal form) PDB_Info PDB_Structure Mus musculus Chain B = 0.002400 27 25 View alignment SCOP MMDB CATH Chain A = 0.002400 27 25 View alignment 1r74 ( Chain: A, B) Crystal structure of human glycine n-methyltransferase PDB_Info PDB_Structure Homo sapiens Chain A = 0.002800 27 26 View alignment SCOP MMDB CATH Chain B = 0.002800 27 26 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
BUD23	2001-08-13	Ni L and Snyder M (2001) A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol Biol Cell 12(7):2147-70

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
YCR047C	SGD Systematic Sequence
850414	NCBI: Gene ID
NP_009976.1	NCBI: RefSeq protein version ID
NP_009976.1	NCBI: RefSeq protein version ID
6319895	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) Organelle DB (UMich) YGAC Triples YeastGFP DB (UCSF) at SGD

Community Annotation [TOP] [NEXT]

DNA & RNA Details Topic Research Highlight Reference Contributor Other DNA & RNA Details Description: Specifically higher expression in phosphorus limited chemostat cultures versus phosphorus excess. otherTopic: expression Boer VM, et al. (2003) The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur. J Biol Chem 278(5):3265-74            Viktor Boer 2003-07-25

Literature Guide: papers categorized by topic. [TOP]
Topics	Reference	Other Genes Addressed
17 curated references; 0 references not yet curated
Function/Process Mutants/Phenotypes Strains/Constructs	Li Z, et al. (2009) Rational extension of the ribosome biogenesis pathway using network-guided genetics. PLoS Biol 7(10):e1000213	|AFG2 |ASC1 |BCP1 |BFR2 |BUD22 |DED1 |EAP1 |ENO1 |ENP2 |FCF1 |FCF2 |FUN12 |HAS1 |JIP5 |MORE
Reviews	Petrossian T and Clarke S (2009) Bioinformatic identification of novel methyltransferases Epigenomics 1(1):163-175	|ABD1 |ABP140 |AML1 |BIO2 |CHO2 |COQ3 |COQ5 |CRG1 |CTM1 |DIM1 |DOT1 |DPH5 |ELP3 |EMG1 |MORE
Mutants/Phenotypes Strains/Constructs	Bockhorn J, et al. (2008) Genome-wide screen of Saccharomyces cerevisiae null allele strains identifies genes involved in selenomethionine resistance. Proc Natl Acad Sci U S A 105(46):17682-17687	|AAH1 |APQ13 |ARC18 |ARE1 |ARO7 |ASI3 |BSD2 |CGR1 |CSG2 |CYS3 |DAL3 |GRE2 |HHT2 |HMG1 |MORE
Cellular Location Function/Process Fungal Related Genes/Proteins Mutants/Phenotypes Non-Fungal Related Genes/Proteins Protein Sequence Features Strains/Constructs	White J, et al. (2008) Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of Pre-40S subunits. Mol Cell Biol 28(10):3151-61	|ITS1-1 |ITS1-2 |RDN18-1 |RDN18-2 |RPS2 |RPS3
Genomic expression study RNA Levels and Processing	Yiu G, et al. (2008) Pathways change in expression during replicative aging in Saccharomyces cerevisiae. J Gerontol A Biol Sci Med Sci 63(1):21-34	|AML1 |BNI4 |BUD14 |DIM1 |GAC1 |GCD10 |GLC7 |GLC8 |GSY2 |HXT15 |HXT17 |HXT2 |HXT3 |HXT5 |MORE
DNA/RNA Sequence Features	Buhler C, et al. (2007) Mapping meiotic single-strand dna reveals a new landscape of DNA double-strand breaks in Saccharomyces cerevisiae. PLoS Biol 5(12):e324	|CDC13 |DMC1 |ECM30 |GBP2 |PET18 |PYK2 |RAD50 |RAD51 |SAE2 |SPO11 |YCR022C |YDR187C |YGR176W |YIR020C
Mutants/Phenotypes Strains/Constructs	Lockshon D, et al. (2007) The sensitivity of yeast mutants to oleic Acid implicates the peroxisome and other processes in membrane function. Genetics 175(1):77-91	|ADO1 |ADR1 |AIM38 |AKR1 |ARP6 |ATG17 |AVL9 |BUD14 |BUD22 |BUD31 |CAR2 |CBS1 |CLA4 |CTF8 |MORE
Mutants/Phenotypes Techniques and Reagents	Freimoser FM, et al. (2006) Systematic screening of polyphosphate (poly P) levels in yeast mutant cells reveals strong interdependence with primary metabolism. Genome Biol 7(11):R109	|ADE1 |ADE3 |AKR1 |ALT2 |APL5 |APL6 |APM3 |APS3 |ARO1 |ARP5 |ATG12 |ATG20 |ATP15 |AVT6 |MORE
Mutants/Phenotypes	Rand JD and Grant CM (2006) The thioredoxin system protects ribosomes against stress-induced aggregation. Mol Biol Cell 17(1):387-401	|AAT2 |ADH1 |ADK1 |AFR1 |AKR1 |ANP1 |APQ13 |ARO2 |ARP8 |ARV1 |ARX1 |ATP12 |ATP2 |BEM1 |MORE
Cellular Location Strains/Constructs	Huh WK, et al. (2003) Global analysis of protein localization in budding yeast. Nature 425(6959):686-91	|AAH1 |AAP1 |ABZ1 |ABZ2 |ACB1 |ACO2 |ADD37 |ADD66 |ADE1 |ADE12 |ADE2 |ADE3 |ADE4 |ADE6 |MORE
Function/Process Fungal Related Genes/Proteins Non-Fungal Related Genes/Proteins Protein Sequence Features	Katz JE, et al. (2003) Automated identification of putative methyltransferases from genomic open reading frames. Mol Cell Proteomics 2(8):525-40	|ABP140 |CRG1 |IRC15 |MNI1 |MTF1 |MTQ2 |NOP2 |OMS1 |SEE1 |TAE1 |TRM11 |TRM12 |YBR271W |YJR129C |MORE
Function/Process Mutants/Phenotypes	Dimmer KS, et al. (2002) Genetic basis of mitochondrial function and morphology in Saccharomyces cerevisiae. Mol Biol Cell 13(3):847-53	|ABF2 |ACO1 |ADA2 |ADK1 |AEP1 |AEP2 |AEP3 |AFG3 |AFT1 |AIM10 |AIM22 |ALY1 |APQ13 |ARG82 |MORE
Function/Process Fungal Related Genes/Proteins Mutants/Phenotypes Strains/Constructs	Ni L and Snyder M (2001) A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol Biol Cell 12(7):2147-70	|ALG8 |BUD13 |BUD14 |BUD16 |BUD17 |BUD19 |BUD20 |BUD21 |BUD22 |BUD25 |BUD26 |BUD27 |BUD28 |BUD30 |MORE
Non-Fungal Related Genes/Proteins	Stanchi F, et al. (2001) Characterization of 16 novel human genes showing high similarity to yeast sequences. Yeast 18(1):69-80	|ALG8 |ARB1 |DIM1 |GRX4 |HSL1 |LIP5 |NEO1 |NFS1 |NPA3 |NSA2 |PMR1 |ROK1 |RPE1 |RSA4 |MORE
Mutants/Phenotypes Non-Fungal Related Genes/Proteins Protein Sequence Features Strains/Constructs	Niewmierzycka A and Clarke S (1999) S-Adenosylmethionine-dependent methylation in Saccharomyces cerevisiae. Identification of a novel protein arginine methyltransferase. J Biol Chem 274(2):814-24	|ABD1 |ABP140 |BDH2 |COQ3 |COQ5 |COX1 |CRG1 |DIM1 |ERG6 |GCD14 |HMT1 |MET1 |MNI1 |MTQ2 |MORE
Non-Fungal Related Genes/Proteins	Claudio JO, et al. (1998) Identification of sequence-tagged transcripts differentially expressed within the human hematopoietic hierarchy. Genomics 50(1):44-52	|RIO1 |RPC11 |RRP3 |TIF6 |TUP1 |YBL036C
Mutants/Phenotypes Strains/Constructs	Rieger KJ, et al. (1997) Large-scale phenotypic analysis--the pilot project on yeast chromosome III. Yeast 13(16):1547-62	|BPH1 |CSM1 |CTR86 |CWH43 |FEN1 |IMG1 |IMG2 |KRR1 |MRPL32 |NFS1 |PBN1 |RRP7 |RSA4 |SAT4 |MORE

Return to SGD

Send a Message to the SGD Curators