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YRB2/YIL063C 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   ChrIX: 243741 to 242758 CDS: 243741 - 242758 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
YRB2	YIL063C		ORF, Verified	S000001325
Description
Protein of unknown function involved in nuclear processes of the Ran-GTPase cycle; involved in nuclear protein export; contains Ran Binding Domain and FxFG repeats; interacts with Srm1p, GTP-Gsp1p, Rna1p and Crm1p; is not essential

GO Annotations [TOP] [NEXT]
Molecular Function Annotation(s) Reference(s) Evidence Assigned By GTPase activator activity GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0343 Assigned on 2007-05-23 UniProtKB 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 2005-09-28 SGD
Biological Process Annotation(s) Reference(s) Evidence Assigned By intracellular transport DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.      IEA : Inferred from Electronic Annotation with EBI:IPR000156 Assigned on 2007-05-23 UniProtKB protein export from nucleus Taura T, et al. (1998) A member of the Ran-binding protein family, Yrb2p, is involved in nuclear protein export. Proc Natl Acad Sci U S A 95(13):7427-32        IMP : Inferred from Mutant Phenotype Assigned on 2001-01-18 SGD protein transport GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0653 Assigned on 2007-05-23 UniProtKB regulation of chromatin silencing at telomere Hayashi N, et al. (2007) Mutations in Ran system affected telomere silencing in Saccharomyces cerevisiae. Biochem Biophys Res Commun 363(3):788-94          IMP : Inferred from Mutant Phenotype Assigned on 2007-10-08 SGD ribosomal small subunit export from nucleus Moy TI and Silver PA (2002) Requirements for the nuclear export of the small ribosomal subunit. J Cell Sci 115(Pt 14):2985-95        IMP : Inferred from Mutant Phenotype Assigned on 2006-12-15 SGD ribosomal subunit export from nucleus 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 transport GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0813 Assigned on 2007-05-23 UniProtKB
Cellular Component Annotation(s) Reference(s) Evidence Assigned By nuclear pore Rout MP, et al. (2000) The yeast nuclear pore complex: composition, architecture, and transport mechanism. J Cell Biol 148(4):635-51        IDA : Inferred from Direct Assay Assigned on 2005-09-28 SGD nucleus Taura T, et al. (1997) Yrb2p is a nuclear protein that interacts with Prp20p, a yeast Rcc1 homologue. J Biol Chem 272(50):31877-84        IDA : Inferred from Direct Assay Assigned on 2005-09-28 SGD Noguchi E, et al. (1997) Yrb2p, a Nup2p-related yeast protein, has a functional overlap with Rna1p, a yeast Ran-GTPase-activating protein. Mol Cell Biol 17(4):2235-46        IDA : Inferred from Direct Assay Assigned on 2005-09-28 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 forYRB2/YIL063C for YRB2 1) Taura T, et al. (1997) Yrb2p is a nuclear protein that interacts with Prp20p, a yeast Rcc1 homologue. J Biol Chem 272(50):31877-84        2) Taura T, et al. (1998) A member of the Ran-binding protein family, Yrb2p, is involved in nuclear protein export. Proc Natl Acad Sci U S A 95(13):7427-32        3) Noguchi E, et al. (1997) Yrb2p, a Nup2p-related yeast protein, has a functional overlap with Rna1p, a yeast Ran-GTPase-activating protein. Mol Cell Biol 17(4):2235-46        4) Maurer P, et al. (2001) The nuclear export receptor Xpo1p forms distinct complexes with NES transport substrates and the yeast Ran binding protein 1 (Yrb1p). Mol Biol Cell 12(3):539-49

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for YRB2/YIL063C

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for YRB2/YIL063C

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 MSETNGG C-term IVKSVPK Length(aa) 327 MW(Da) 36,054 pI 6.64 Amino Acid Composition (full length) GCG tools: PepPlot, Helical Wheel, PepStruct Transcript Translation Calculations Codon Bias 0.067   Codon Adaptation Index 0.170   Frequency of Optimal Codons 0.466   Hydropathicity of Protein -1.048   Aromaticity Score 0.049	10 20 30 40 50 | | | | | MSETNGGNAARENSEVKQTAVENPIDKLDGTPKRPREKDQDEQAEETSDK SEAPNKNDEEKKEEGKKDQEPSHKKIKVDDGKTVESGIVEDDKKEDKFVF GAASKFGTGFGVAKKDTKDGDATTSTESLPASDSKTKKPFAFGSGLSFGS GFNILKNKTENNSESEKKATDVDKDKVHSGSEQLANASEDTKDKPKPLKL QKQEVKSGEESEECIYQVNAKLYQLSNIKEGWKERGVGIIKINKSKDDVE KTRIVMRSRGILKVILNIQLVKGFTVQKGFTGSLQSEKFIRLLAVDDNGD PAQYAIKTGKKETTDELYNIIVKSVPK*

Protein Structures from PDB: proteins of known structure with sequence similarity to YRB2/YIL063C, based on Smith-Waterman analysis. [TOP] [NEXT]

PDB protein structure(s) homologous to YRB2 Homolog Source (per PDB) Protein Alignment: YRB2 vs. Homolog External Links P-Value %Identical %Similar Alignment 2crf ( Chain: A) Solution structure of the ran_bp1 domain of ran-binding protein-3 PDB_Info PDB_Structure Homo sapiens 1.1e-07 33 36 View alignment SCOP MMDB CATH 1rrp ( Chain: B, D) Structure of the ran-gppnhp-ranbd1 complex PDB_Info PDB_Structure Homo sapiens Chain B = 2.8e-05 35 27 View alignment SCOP MMDB CATH Chain D = 2.8e-05 35 27 View alignment 1k5d ( Chain: B, E, K, H) Crystal structure of ran-gppnhp-ranbp1-rangap complex PDB_Info PDB_Structure Homo sapiens | Schizosaccharomyces pombe Chain B = 0.000569 32 36 View alignment SCOP MMDB CATH Chain E = 0.000569 32 36 View alignment Chain K = 0.000569 32 36 View alignment Chain H = 0.000569 32 36 View alignment 1k5g ( Chain: K, B, E, H) Crystal structure of ran-gdp-alfx-ranbp1-rangap complex PDB_Info PDB_Structure Homo sapiens | Schizosaccharomyces pombe Chain K = 0.000569 32 36 View alignment SCOP MMDB CATH Chain B = 0.000569 32 36 View alignment Chain E = 0.000569 32 36 View alignment Chain H = 0.000569 32 36 View alignment 1xke ( Chain: A) Solution structure of the second ran-binding domain from human ranbp2 PDB_Info PDB_Structure Homo sapiens 0.001700 33 28 View alignment SCOP MMDB CATH

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
YRB2	Taura T, et al. (1997) Yrb2p is a nuclear protein that interacts with Prp20p, a yeast Rcc1 homologue. J Biol Chem 272(50):31877-84        Noguchi E, et al. (1997) Yrb2p, a Nup2p-related yeast protein, has a functional overlap with Rna1p, a yeast Ran-GTPase-activating protein. Mol Cell Biol 17(4):2235-46

Mapping Notes

Date	Note
1996-09-21	Edition 13: Identified by homology to Yrb1p (Yeast Ran-Binding protein 1). Yrb2p has Ran-Binding domain. Cherry JM, et al. (1996) "Genetic and Physical Maps of Saccharomyces cerevisiae (Edition 13)". Pp. 361-364 in 1996 Yeast Genetics and Molecular Biology Meeting Program and Abstracts. Bethesda, MD: The Genetics Society of America

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
YIL063C	SGD Systematic Sequence
854747	NCBI: Gene ID
NP_012201.1	NCBI: RefSeq protein version ID
NP_012201.1	NCBI: RefSeq protein version ID
6322126	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) 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
27 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 |BUD23 |DED1 |EAP1 |ENO1 |ENP2 |FCF1 |FCF2 |FUN12 |HAS1 |MORE
Mutants/Phenotypes Strains/Constructs	Breslow DK, et al. (2008) A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Nat Methods 5(8):711-8	|AAR2 |ABD1 |ABF1 |ACC1 |ACP1 |ADE13 |AFG2 |ALA1 |ALG1 |ALG13 |ALG14 |ALG2 |ALG7 |ALR1 |MORE
Non-Fungal Related Genes/Proteins	Casanova M, et al. (2008) Inhibition of active nuclear transport is an intrinsic trigger of programmed cell death in trypanosomatids. Cell Death Differ 15(12):1910-20	|CRM1 |GSP1 |NTF2 |RNA1 |SEC13 |SRM1
Function/Process Genetic Interactions Mutants/Phenotypes Protein Sequence Features Strains/Constructs	Hayashi N, et al. (2007) Mutations in Ran system affected telomere silencing in Saccharomyces cerevisiae. Biochem Biophys Res Commun 363(3):788-94	|RNA1 |SIR3 |SIT4
Protein Processing/Modification/Regulation Regulation of	Smolka MB, et al. (2007) Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases. Proc Natl Acad Sci U S A 104(25):10364-9	|CEP3 |CPR5 |CTF4 |DEF1 |DUN1 |EXO1 |HPC2 |ITC1 |MEC1 |MLP1 |NET1 |NPL3 |NSP1 |NUP1 |MORE
Reviews	Taddei A (2007) Active genes at the nuclear pore complex. Curr Opin Cell Biol 19(3):305-310	|ASM4 |CDC31 |DBP5 |GAL1 |GFD1 |GLE1 |GLE2 |HSP104 |HTZ1 |INO1 |KAP120 |KAP122 |KAP123 |KAP95 |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	Seiser RM, et al. (2006) Ltv1 is required for efficient nuclear export of the ribosomal small subunit in Saccharomyces cerevisiae. Genetics 174(2):679-91	|CRM1 |ITS1-1 |ITS1-2 |LTV1 |RPS3 |YAR1
Mutants/Phenotypes	Luna R, et al. (2005) Interdependence between transcription and mRNP processing and export, and its impact on genetic stability. Mol Cell 18(6):711-22	|BRR6 |CAF20 |CCR4 |CDC40 |CFT1 |CRM1 |DBP1 |DBP5 |DBP7 |DCP1 |FIP1 |GBP2 |GLE1 |HRB1 |MORE
Genetic Interactions Protein Sequence Features Protein-protein Interactions Strains/Constructs	Wang Y, et al. (2005) Saccharomyces cerevisiae GTPase complex: Gtr1p-Gtr2p regulates cell-proliferation through Saccharomyces cerevisiae Ran-binding protein, Yrb2p. Biochem Biophys Res Commun 336(2):639-45	|GTR1 |GTR2 |RNA1 |SRM1
Protein Physical Properties Protein Sequence Features	Denning DP, et al. (2003) Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded. Proc Natl Acad Sci U S A 100(5):2450-5	|ASM4 |CDC31 |GLE1 |GLE2 |NDC1 |NIC96 |NSP1 |NUP1 |NUP100 |NUP116 |NUP120 |NUP133 |NUP145 |NUP157 |MORE
Function/Process Mutants/Phenotypes Strains/Constructs	Moy TI and Silver PA (2002) Requirements for the nuclear export of the small ribosomal subunit. J Cell Sci 115(Pt 14):2985-95	|CRM1
Function/Process Mutants/Phenotypes Strains/Constructs	Hood JK, et al. (2001) The Saccharomyces cerevisiae cyclin Clb2p is targeted to multiple subcellular locations by cis- and trans-acting determinants. J Cell Sci 114(Pt 3):589-97	|CDC28 |CLB1 |CLB2 |GSP1 |KAP123 |KAP95 |RNA1 |SRP1 |YRB1
Fungal Related Genes/Proteins Non-Fungal Related Genes/Proteins Reviews	Kunzler M and Hurt E (2001) Targeting of Ran: variation on a common theme? J Cell Sci 114(Pt 18):3233-41	|DIS3 |GSP1 |MOG1 |NTF2 |NUP2 |RNA1 |SRM1 |YRB1
Cellular Location Function/Process Fungal Related Genes/Proteins Protein-protein Interactions	Maurer P, et al. (2001) The nuclear export receptor Xpo1p forms distinct complexes with NES transport substrates and the yeast Ran binding protein 1 (Yrb1p). Mol Biol Cell 12(3):539-49	|CRM1 |CSE1 |GSP1 |RNA1 |YRB1
Function/Process Substrates/Ligands/Cofactors	Ciufo LF and Brown JD (2000) Nuclear export of yeast signal recognition particle lacking Srp54p by the Xpo1p/Crm1p NES-dependent pathway. Curr Biol 10(20):1256-64	|CRM1 |SCR1 |SEC65 |SRP14 |SRP21 |SRP54 |SRP68 |SRP72
Function/Process Genetic Interactions Mutants/Phenotypes Strains/Constructs	Jones AL, et al. (2000) SAC3 may link nuclear protein export to cell cycle progression. Proc Natl Acad Sci U S A 97(7):3224-9	|CRM1 |NSP1 |SAC3 |SDS23 |SDS24
Cellular Location Protein Physical Properties Strains/Constructs Techniques and Reagents	Rout MP, et al. (2000) The yeast nuclear pore complex: composition, architecture, and transport mechanism. J Cell Biol 148(4):635-51	|AIM4 |ASM4 |BMS1 |BUD20 |CTR9 |GLE1 |GLE2 |HAS1 |KAP120 |KAP122 |KAP123 |KAP95 |KRR1 |MEX67 |MORE
Cell Cycle Phase Involved Function/Process Fungal Related Genes/Proteins Genetic Interactions Mutants/Phenotypes Protein-protein Interactions Strains/Constructs	Noguchi E, et al. (1999) Disruption of the YRB2 gene retards nuclear protein export, causing a profound mitotic delay, and can be rescued by overexpression of XPO1/CRM1. J Biochem 125(3):574-85	|CDC28 |CDC5 |CRM1 |GSP1 |MAD1 |MAD3 |YRB1
Cellular Location Function/Process Genetic Interactions Mutants/Phenotypes Protein Sequence Features Protein-protein Interactions Strains/Constructs	Taura T, et al. (1998) A member of the Ran-binding protein family, Yrb2p, is involved in nuclear protein export. Proc Natl Acad Sci U S A 95(13):7427-32	|CRM1
Non-Fungal Related Genes/Proteins Techniques and Reagents	Yang Q, et al. (1998) Three-dimensional architecture of the isolated yeast nuclear pore complex: functional and evolutionary implications. Mol Cell 1(2):223-34	|GLE1 |NIC96 |NSP1 |NUP1 |NUP100 |NUP116 |NUP120 |NUP133 |NUP145 |NUP157 |NUP159 |NUP170 |NUP188 |NUP2 |MORE
Reviews	Fabre E and Hurt E (1997) Yeast genetics to dissect the nuclear pore complex and nucleocytoplasmic trafficking. Annu Rev Genet 31:277-313	|ACC1 |ASM4 |CBC2 |GLE1 |GLE2 |GSP1 |HRP1 |KAP104 |KAP123 |KAP95 |LOS1 |MEX67 |MTR2 |MTR3 |MORE
Cellular Location Function/Process Fungal Related Genes/Proteins Genetic Interactions Mutants/Phenotypes Protein-protein Interactions Strains/Constructs	Noguchi E, et al. (1997) Yrb2p, a Nup2p-related yeast protein, has a functional overlap with Rna1p, a yeast Ran-GTPase-activating protein. Mol Cell Biol 17(4):2235-46	|GSP1 |NUP2 |RNA1 |SRM1 |YRB1
Cellular Location Function/Process Genetic Interactions Protein Physical Properties Protein Sequence Features Protein-protein Interactions	Taura T, et al. (1997) Yrb2p is a nuclear protein that interacts with Prp20p, a yeast Rcc1 homologue. J Biol Chem 272(50):31877-84	|GSP1 |SRM1 |YRB1
Cell Cycle Phase Involved Cellular Location	Winey M, et al. (1997) Nuclear pore complex number and distribution throughout the Saccharomyces cerevisiae cell cycle by three-dimensional reconstruction from electron micrographs of nuclear envelopes. Mol Biol Cell 8(11):2119-32	|NIC96 |NSP1 |NUP1 |NUP100 |NUP116 |NUP120 |NUP133 |NUP145 |NUP157 |NUP159 |NUP170 |NUP188 |NUP2 |NUP42 |MORE
Protein Sequence Features Protein-protein Interactions	Noguchi E, et al. (1996) Dis3, implicated in mitotic control, binds directly to Ran and enhances the GEF activity of RCC1. EMBO J 15(20):5595-605	|DIS3 |GSP1 |SRM1 |YRB1
Alias Function/Process Fungal Related Genes/Proteins Non-Fungal Related Genes/Proteins	Dingwall C, et al. (1995) A family of Ran binding proteins that includes nucleoporins. Proc Natl Acad Sci U S A 92(16):7525-9	|GSP1 |NUP2 |YRB1

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