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NUP42/YDR192C 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: 844859 to 843567 CDS: 844859 - 843567 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
NUP42	YDR192C	RIP1, UIP1	ORF, Verified	S000002600
See Nomenclature Note.
Description
Subunit of the nuclear pore complex (NPC) that localizes exclusively to the cytoplasmic side; involved in RNA export, most likely at a terminal step; interacts with Gle1p

GO Annotations [TOP] [NEXT]
Molecular Function Annotation(s) Reference(s) Evidence Assigned By structural molecule activity Fabre E and Hurt E (1997) Yeast genetics to dissect the nuclear pore complex and nucleocytoplasmic trafficking. Annu Rev Genet 31:277-313      TAS : Traceable Author Statement Assigned on 2001-01-18 SGD
Biological Process Annotation(s) Reference(s) Evidence Assigned By NLS-bearing substrate import into nucleus Fabre E and Hurt E (1997) Yeast genetics to dissect the nuclear pore complex and nucleocytoplasmic trafficking. Annu Rev Genet 31:277-313      TAS : Traceable Author Statement Assigned on 2001-01-18 SGD mRNA export from nucleus Fabre E and Hurt E (1997) Yeast genetics to dissect the nuclear pore complex and nucleocytoplasmic trafficking. Annu Rev Genet 31:277-313      TAS : Traceable Author Statement Assigned on 2001-01-18 SGD mRNA transport GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0509 Assigned on 2007-05-23 UniProtKB mRNA-binding (hnRNP) protein import into nucleus Fabre E and Hurt E (1997) Yeast genetics to dissect the nuclear pore complex and nucleocytoplasmic trafficking. Annu Rev Genet 31:277-313      TAS : Traceable Author Statement Assigned on 2001-01-18 SGD nuclear pore organization Fabre E and Hurt E (1997) Yeast genetics to dissect the nuclear pore complex and nucleocytoplasmic trafficking. Annu Rev Genet 31:277-313      TAS : Traceable Author Statement Assigned on 2001-01-18 SGD protein export from nucleus Fabre E and Hurt E (1997) Yeast genetics to dissect the nuclear pore complex and nucleocytoplasmic trafficking. Annu Rev Genet 31:277-313      TAS : Traceable Author Statement 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 rRNA export from nucleus Fabre E and Hurt E (1997) Yeast genetics to dissect the nuclear pore complex and nucleocytoplasmic trafficking. Annu Rev Genet 31:277-313      TAS : Traceable Author Statement Assigned on 2001-01-18 SGD ribosomal protein import into nucleus Fabre E and Hurt E (1997) Yeast genetics to dissect the nuclear pore complex and nucleocytoplasmic trafficking. Annu Rev Genet 31:277-313      TAS : Traceable Author Statement Assigned on 2001-01-18 SGD snRNA export from nucleus Fabre E and Hurt E (1997) Yeast genetics to dissect the nuclear pore complex and nucleocytoplasmic trafficking. Annu Rev Genet 31:277-313      TAS : Traceable Author Statement Assigned on 2001-01-18 SGD snRNP protein import into nucleus Fabre E and Hurt E (1997) Yeast genetics to dissect the nuclear pore complex and nucleocytoplasmic trafficking. Annu Rev Genet 31:277-313      TAS : Traceable Author Statement Assigned on 2001-01-18 SGD tRNA export from nucleus Fabre E and Hurt E (1997) Yeast genetics to dissect the nuclear pore complex and nucleocytoplasmic trafficking. Annu Rev Genet 31:277-313      TAS : Traceable Author Statement Assigned on 2001-01-18 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 transmembrane transport GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0811 Assigned on 2009-10-01 UniProtKB 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 membrane GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0472 Assigned on 2008-06-16 UniProtKB nuclear pore Fabre E and Hurt E (1997) Yeast genetics to dissect the nuclear pore complex and nucleocytoplasmic trafficking. Annu Rev Genet 31:277-313      IDA : Inferred from Direct Assay Assigned on 2001-01-18 SGD GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0906 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-0185 Assigned on 2009-05-06 UniProtKB nucleus GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0539 Assigned on 2009-06-29 UniProtKB

Pathways [TOP] [NEXT]
No pathways available

Summary Paragraph [TOP] [NEXT]

SUMMARY PARAGRAPH for NUP42/YDR192C for NUP42 NUP42 encodes a nuclear pore protein first identified as interacting with the effector domain of HIV-1 Rev expressed in yeast (1, 2). Transport of macromolecules between the nucleus and the cytoplasm of eukaryotic cells occurs through the nuclear pore complex (NPC), a large macromolecular complex that spans the nuclear envelope (reviewed in 2, 3, 4, 5). The structure of the vertebrate NPC has been studied extensively; recent reviews include 6, 7, 8, and 9. The yeast NPC shares several features with the vertebrate NPC, despite being smaller and less elaborate (10, 11). Many yeast nuclear pore proteins, or nucleoporins, have been identified by a variety of genetic approaches (reviewed in 2, 3, 12, 13, 14). Nup42p interacts with the RNA export factor Gle1p (15) and with the nuclear pore proteins Nup100p and Gle2p (2). Nup42p is not essential for viability, but is required for the export of heat shock mRNA following stress (16, 2). Nup42p contains FG repeats (2), but deleting the repeats has no effect on mRNA export (17). Last Updated: 1999-07-27

Basic References [TOP]

BASIC INFORMATION REFERENCES forNUP42/YDR192C for NUP42 1) Stutz F, et al. (1995) Identification of a novel nuclear pore-associated protein as a functional target of the HIV-1 Rev protein in yeast. Cell 82(3):495-506        2) Fabre E and Hurt E (1997) Yeast genetics to dissect the nuclear pore complex and nucleocytoplasmic trafficking. Annu Rev Genet 31:277-313      3) Wente SR, et al. (1997) "The nucleus and nucleocytoplasmic transport in Saccharomyces cerevisiae." Pp. 471-546 in The Molecular and Cellular Biology of the Yeast Saccharomyces: Cell Cycle and Cell Biology, edited by Pringle JR, Broach JR and Jones EW. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press    4) Pemberton LF, et al. (1998) Transport routes through the nuclear pore complex. Curr Opin Cell Biol 10(3):392-9      5) Izaurralde E and Adam S (1998) Transport of macromolecules between the nucleus and the cytoplasm. RNA 4(4):351-64      6) Hinshaw JE (1994) Architecture of the nuclear pore complex and its involvement in nucleocytoplasmic transport. Biochem Pharmacol 47(1):15-20      7) Pante N and Aebi U (1996) Molecular dissection of the nuclear pore complex. Crit Rev Biochem Mol Biol 31(2):153-99      8) Davis LI (1995) The nuclear pore complex. Annu Rev Biochem 64:865-96      9) Pante N and Aebi U (1994) Toward the molecular details of the nuclear pore complex. J Struct Biol 113(3):179-89      10) Rout MP and Blobel G (1993) Isolation of the yeast nuclear pore complex. J Cell Biol 123(4):771-83      11) 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        12) Doye V and Hurt E (1997) From nucleoporins to nuclear pore complexes. Curr Opin Cell Biol 9(3):401-11      13) Doye V and Hurt EC (1995) Genetic approaches to nuclear pore structure and function. Trends Genet 11(6):235-41        14) Newmeyer DD (1993) The nuclear pore complex and nucleocytoplasmic transport. Curr Opin Cell Biol 5(3):395-407      15) Murphy R and Wente SR (1996) An RNA-export mediator with an essential nuclear export signal. Nature 383(6598):357-60      16) Saavedra CA, et al. (1997) Yeast heat shock mRNAs are exported through a distinct pathway defined by Rip1p. Genes Dev 11(21):2845-56        17) Stutz F, et al. (1997) The yeast nucleoporin rip1p contributes to multiple export pathways with no essential role for its FG-repeat region. Genes Dev 11(21):2857-68        18) Strahm Y, et al. (1999) The RNA export factor Gle1p is located on the cytoplasmic fibrils of the NPC and physically interacts with the FG-nucleoporin Rip1p, the DEAD-box protein Rat8p/Dbp5p and a new protein Ymr 255p. EMBO J 18(20):5761-77        19) Rout MP, et al. (2000) The yeast nuclear pore complex: composition, architecture, and transport mechanism. J Cell Biol 148(4):635-51

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for NUP42/YDR192C

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for NUP42/YDR192C

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 MSAFGNP C-term PPPALVA Length(aa) 430 MW(Da) 42,778 pI 10.73 Amino Acid Composition (full length) GCG tools: PepPlot, Helical Wheel, PepStruct Transcript Translation Calculations Codon Bias -0.002   Codon Adaptation Index 0.092   Frequency of Optimal Codons 0.384   Hydropathicity of Protein -0.407   Aromaticity Score 0.088

10 20 30 40 50 | | | | | MSAFGNPFTSGAKPNLSNTSGINPFTNNAASTNNMGGSAFGRPSFGTANT MTGGTTTSAFGMPQFGTNTGNTGNTSISAFGNTSNAAKPSAFGAPAFGSS APINVNPPSTTSAFGAPSFGSTGFGAMAATSNPFGKSPGSMGSAFGQPAF GANKTAIPSSSVSNSNNSAFGAASNTPLTTTSPFGSLQQNASQNASSTSS AFGKPTFGAATNTQSPFGTIQNTSTSSGTGVSPFGTFGTNSNNKSPFSNL QSGAGAGSSPFGTTTSKANNNNNVGSSAFGTTNNQSPFSGGSGGTFGSAS NLNKNTNGNFQSSFGNKGFSFGITPQNDANKVSQSNPSFGQTMPNTDPNI SLKSNGNATSFGFGQQQMNATNVNANTATGKIRFVQGLSSEKDGILELAD LAEETLKIFRANKFELGLVPDIPPPPALVA*

Protein Structures from PDB: proteins of known structure with sequence similarity to NUP42/YDR192C, based on Smith-Waterman analysis. [TOP] [NEXT]

PDB protein structure(s) homologous to NUP42 Homolog Source (per PDB) Protein Alignment: NUP42 vs. Homolog External Links P-Value %Identical %Similar Alignment 3gtq ( Chain: A) DNA-directed RNA polym PDB_Info PDB_Structure Unknown 0.000289 23 33 View alignment SCOP MMDB CATH 3gtg ( Chain: A) DNA-directed RNA polym PDB_Info PDB_Structure Unknown 0.000289 23 33 View alignment SCOP MMDB CATH 3hoy ( Chain: A) DNA-directed RNA polym PDB_Info PDB_Structure Unknown 0.000289 23 33 View alignment SCOP MMDB CATH 2nvz ( Chain: A) Rna polymerase ii elongation complex with utp, updated 11/2006 PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 2ja6 ( Chain: A) Cpd lesion containing rna polymerase ii elongation complex b PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 3gtm ( Chain: A) DNA-directed RNA polym PDB_Info PDB_Structure Unknown 0.000289 23 33 View alignment SCOP MMDB CATH 3how ( Chain: A) DNA-directed RNA polym PDB_Info PDB_Structure Unknown 0.000289 23 33 View alignment SCOP MMDB CATH 2ja7 ( Chain: A, M) Cpd lesion containing rna polymerase ii elongation complex c PDB_Info PDB_Structure Saccharomyces cerevisiae Chain A = 0.000289 23 33 View alignment SCOP MMDB CATH Chain M = 0.000289 23 33 View alignment 2ja5 ( Chain: A) Cpd lesion containing rna polymerase ii elongation complex a PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 3hoz ( Chain: A) DNA-directed RNA polym PDB_Info PDB_Structure Unknown 0.000289 23 33 View alignment SCOP MMDB CATH 2nvx ( Chain: A) Rna polymerase ii elongation complex in 5 mm mg+2 with 2'- dutp PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 3gtk ( Chain: A) DNA-directed RNA polym PDB_Info PDB_Structure Unknown 0.000289 23 33 View alignment SCOP MMDB CATH 3hov ( Chain: A) DNA-directed RNA polym PDB_Info PDB_Structure Unknown 0.000289 23 33 View alignment SCOP MMDB CATH 2nvy ( Chain: A) Rna polymerase ii form ii in 150 mm mn+2 PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 1i3q ( Chain: A) Rna polymerase ii crystal form i at 3.1 a resolution PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 2vum ( Chain: A) Alpha-amanitin inhibited complete rna polymerase ii elongation complex PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 1nik ( Chain: A) Wild type rna polymerase ii PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 2nvt ( Chain: A) Rna polymerase ii elongation complex in 150 mm mg+2 with gmpcpp PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 3gtl ( Chain: A) DNA-directed RNA polym PDB_Info PDB_Structure Unknown 0.000289 23 33 View alignment SCOP MMDB CATH 1twg ( Chain: A) Rna polymerase ii complexed with ctp PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 3i4n ( Chain: A) DNA-directed RNA polym PDB_Info PDB_Structure Unknown 0.000289 23 33 View alignment SCOP MMDB CATH 2nvq ( Chain: A) Rna polymerase ii elongation complex in 150 mm mg+2 with 2'dutp PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 1twa ( Chain: A) Rna polymerase ii complexed with atp PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 1y1y ( Chain: A) Rna polymerase ii-tfiis-dna/rna complex PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 3gtp ( Chain: A) DNA-directed RNA polym PDB_Info PDB_Structure Unknown 0.000289 23 33 View alignment SCOP MMDB CATH 3gto ( Chain: A) DNA-directed RNA polym PDB_Info PDB_Structure Unknown 0.000289 23 33 View alignment SCOP MMDB CATH 1r9s ( Chain: A) Rna polymerase ii strand separated elongation complex, matched nucleotide PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 1twc ( Chain: A) Rna polymerase ii complexed with gtp PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 3cqz ( Chain: A) Crystal structure of 10 subunit rna polymerase ii in complex with the inhibitor alpha-amanitin PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 1r9t ( Chain: A) Rna polymerase ii strand separated elongation complex, mismatched nucleotide PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 1twf ( Chain: A) Rna polymerase ii complexed with utp at 2.3 a resolution PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 1y1w ( Chain: A) Complete rna polymerase ii elongation complex PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 1y77 ( Chain: A) Complete rna polymerase ii elongation complex with substrate analogue gmpcpp PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 1r5u ( Chain: A) Rna polymerase ii tfiib complex PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 1wcm ( Chain: A) Complete 12-subunit rna polymerase ii at 3.8 ang PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 3fki ( Chain: A) -subunit rna polymerase ii refined with zn-sad data PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 2e2h ( Chain: A) Rna polymerase ii elongation complex at 5 mm mg2+ with gtp PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 2e2j ( Chain: A) Rna polymerase ii elongation complex in 5 mm mg+2 with gmpcpp PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 2ja8 ( Chain: A) Cpd lesion containing rna polymerase ii elongation complex d PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 1k83 ( Chain: A) Crystal structure of yeast rna polymerase ii complexed with the inhibitor alpha amanitin PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 2r7z ( Chain: A) Cisplatin lesion containing rna polymerase ii elongation complex PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 1i50 ( Chain: A) Rna polymerase ii crystal form ii at 2.8 a resolution PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 3hou ( Chain: A, M) DNA-directed RNA polym PDB_Info PDB_Structure Unknown Chain A = 0.000289 23 33 View alignment SCOP MMDB CATH Chain M = 0.000289 23 33 View alignment 1twh ( Chain: A) Rna polymerase ii complexed with 2'datp PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 2yu9 ( Chain: A) Rna polymerase ii elongation complex in 150 mm mg+2 with utp PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 2r93 ( Chain: A) Elongation complex of rna polymerase ii with a hepatitis delta virus-derived rna stem loop PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 2b63 ( Chain: A) Complete rna polymerase ii-rna inhibitor complex PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 1nt9 ( Chain: A) Complete 12-subunit rna polymerase ii PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 1pqv ( Chain: A) Rna polymerase ii-tfiis complex PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 3h3v ( Chain: B) DNA-directed RNA polym PDB_Info PDB_Structure Unknown 0.000289 23 33 View alignment SCOP MMDB CATH 2e2i ( Chain: A) Rna polymerase ii elongation complex in 5 mm mg+2 with 2'- dgtp PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 3i4m ( Chain: A) DNA-directed RNA polym PDB_Info PDB_Structure Unknown 0.000289 23 33 View alignment SCOP MMDB CATH 3gtj ( Chain: A) DNA-directed RNA polym PDB_Info PDB_Structure Unknown 0.000289 23 33 View alignment SCOP MMDB CATH 2r92 ( Chain: A) Elongation complex of rna polymerase ii with artificial rdrp scaffold PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 2b8k ( Chain: A) -subunit rna polymerase ii PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 1i6h ( Chain: A) Rna polymerase ii elongation complex PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 3hox ( Chain: A) DNA-directed RNA polym PDB_Info PDB_Structure Unknown 0.000289 23 33 View alignment SCOP MMDB CATH 1sfo ( Chain: A) Rna polymerase ii strand separated elongation complex PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 1y1v ( Chain: A) Refined rna polymerase ii-tfiis complex PDB_Info PDB_Structure Saccharomyces cerevisiae 0.000289 23 33 View alignment SCOP MMDB CATH 3h0g ( Chain: A, M) DNA-directed RNA polym PDB_Info PDB_Structure Unknown Chain A = 0.003599 22 34 View alignment SCOP MMDB CATH Chain M = 0.003599 22 34 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	Reference
NUP42	SGD (2007) Information without a citation in SGD

Alias Name(s)	Reference
UIP1	Takahashi Y, et al. (2000) Yeast Ulp1, an Smt3-specific protease, associates with nucleoporins. J Biochem 128(5):723-5

Nomenclature History Notes

Date	Note
2004-06-10	RIP1 has been used in the literature to refer to both RIP1/YEL024, which encodes a Rieske iron-sulfur protein, and NUP42/YDR192C, which encodes a nuclear pore complex subunit.

Mapping Notes

Date	Note
1998-11-10	Edition 15: NUP42 has also been called RIP1, not to be confused with RIP1 encoding Rieske iron-sulfur protein Cherry JM, et al. (1998) "Genetic and Physical Maps of Saccharomyces cerevisiae (Edition 15)". Pp. 414-420 in 1998 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
YDR192C	SGD Systematic Sequence
851774	NCBI: Gene ID
NP_010478.1	NCBI: RefSeq protein version ID
NP_010478.1	NCBI: RefSeq protein version ID
6320399	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
48 curated references; 0 references not yet curated
Protein-protein Interactions Strains/Constructs	Alberti S, et al. (2009) A systematic survey identifies prions and illuminates sequence features of prionogenic proteins. Cell 137(1):146-58	|AIM3 |AKL1 |ASM4 |AZF1 |CAF40 |CBK1 |CCR4 |CLA4 |CYC8 |DDR48 |DEF1 |ENT1 |ENT2 |EPL1 |MORE
Protein-protein Interactions	Beliakova-Bethell N, et al. (2009) Ty3 nuclear entry is initiated by viruslike particle docking on GLFG nucleoporins. J Virol 83(22):11914-25	|NSP1 |NUP100 |NUP116 |NUP120 |NUP133 |NUP145 |NUP159 |NUP49 |NUP57 |YGR109W-A |YGR109W-B |YIL080W |YIL082W |YIL082W-A
Genetic Interactions Mutants/Phenotypes Strains/Constructs	Hung NJ, et al. (2008) Arx1 Is a Nuclear Export Receptor for the 60S Ribosomal Subunit in Yeast. Mol Biol Cell 19(2):735-44	|ARX1 |CRM1 |GLE2 |MEX67 |MTR2 |NIC96 |NMD3 |NSP1 |NUP100 |NUP116 |NUP120 |NUP133 |NUP57 |NUP82 |MORE
Reviews	Hurt JA and Silver PA (2008) mRNA nuclear export and human disease. Dis Model Mech 1(2-3):103-8	|DBP5 |GLE1 |MEX67 |MTR2 |SUB2 |YRA1
Mutants/Phenotypes	McCue PP and Phang JM (2008) Identification of Human Intracellular Targets of the Medicinal Herb St. John's Wort by Chemical-Genetic Profiling in Yeast. J Agric Food Chem 56(22):11011-11017	|ABD1 |ACS1 |ADP1 |AHC1 |APN2 |ASR1 |ATP5 |BCK2 |BFR1 |CBP6 |CHK1 |CIN8 |CRR1 |CTF19 |MORE
Protein-protein Interactions	Neuber A, et al. (2008) Nuclear export receptor Xpo1/Crm1 is physically and functionally linked to the spindle pole body in budding yeast. Mol Cell Biol 28(17):5348-58	|CRM1 |GSP1 |HPA3 |LTV1 |NUP49 |SGM1 |SLA2 |SPC110 |SPC72 |YAP1
Mutants/Phenotypes	Thomsen R, et al. (2008) General, rapid, and transcription-dependent fragmentation of nucleolar antigens in S. cerevisiae mRNA export mutants. RNA 14(4):706-16	|ASM4 |HPR1 |HSP104 |MEX67 |MFT1 |NOP1 |NOP58 |NSR1 |NUP100 |NUP120 |NUP133 |NUP159 |NUP188 |NUP2 |MORE
Cellular Location Computational analysis Protein Physical Properties Protein-protein Interactions Protein/Nucleic Acid Structure	Alber F, et al. (2007) Determining the architectures of macromolecular assemblies. Nature 450(7170):683-94	|ASM4 |GLE1 |GLE2 |NDC1 |NIC96 |NSP1 |NUP1 |NUP100 |NUP116 |NUP120 |NUP133 |NUP145 |NUP157 |NUP159 |MORE
Cellular Location Evolution Protein/Nucleic Acid Structure	Alber F, et al. (2007) The molecular architecture of the nuclear pore complex. Nature 450(7170):695-701	|ASM4 |GLE1 |GLE2 |NDC1 |NIC96 |NSP1 |NUP1 |NUP100 |NUP116 |NUP120 |NUP133 |NUP145 |NUP157 |NUP159 |MORE
Evolution Fungal Related Genes/Proteins Protein Sequence Features Protein/Nucleic Acid Structure	Denning DP and Rexach MF (2007) Rapid evolution exposes the boundaries of domain structure and function in natively unfolded FG nucleoporins. Mol Cell Proteomics 6(2):272-82	|ASM4 |NSP1 |NUP1 |NUP100 |NUP116 |NUP159 |NUP2 |NUP49 |NUP53 |NUP57 |NUP60
Reviews	Kohler A and Hurt E (2007) Exporting RNA from the nucleus to the cytoplasm. Nat Rev Mol Cell Biol 8(10):761-73	|ARC1 |ARX1 |CDC31 |CEX1 |CRM1 |DBP5 |GLE1 |GLE2 |HTZ1 |LOS1 |MEX67 |MLP1 |MLP2 |MTR2 |MORE
Cellular Location Function/Process Protein Sequence Features Protein-protein Interactions	Patel SS, et al. (2007) Natively unfolded nucleoporins gate protein diffusion across the nuclear pore complex. Cell 129(1):83-96	|GLE1 |GLE2 |KAP95 |NDC1 |NIC96 |NSP1 |NUP1 |NUP100 |NUP116 |NUP120 |NUP157 |NUP159 |NUP170 |NUP192 |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
Genetic Interactions Strains/Constructs	Alcazar-Roman AR, et al. (2006) Inositol hexakisphosphate and Gle1 activate the DEAD-box protein Dbp5 for nuclear mRNA export. Nat Cell Biol 8(7):711-6	|DBP5 |DHH1 |GLE1 |IPK1
Regulation of Transcription	Buck MJ and Lieb JD (2006) A chromatin-mediated mechanism for specification of conditional transcription factor targets. Nat Genet 38(12):1446-51	|ACA1 |ACS1 |ADE3 |ADH1 |AGP1 |AIM38 |ANP1 |AQY1 |ASC1 |AST2 |ATG19 |AZF1 |BDF1 |BSC3 |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
Computational analysis Non-Fungal Related Genes/Proteins Protein Sequence Features Protein/Nucleic Acid Structure Strains/Constructs	Devos D, et al. (2006) Simple fold composition and modular architecture of the nuclear pore complex. Proc Natl Acad Sci U S A 103(7):2172-7	|ASM4 |NDC1 |NIC96 |NSP1 |NUP1 |NUP100 |NUP116 |NUP120 |NUP133 |NUP145 |NUP157 |NUP159 |NUP170 |NUP188 |MORE
Genetic Interactions Mutants/Phenotypes	Weirich CS, et al. (2006) Activation of the DExD/H-box protein Dbp5 by the nuclear-pore protein Gle1 and its coactivator InsP6 is required for mRNA export. Nat Cell Biol 8(7):668-76	|ARG82 |DBP5 |GLE1 |IPK1 |NUP159 |PLC1
Protein-protein Interactions	Estruch F, et al. (2005) Physical and genetic interactions link the yeast protein Zds1p with mRNA nuclear export. J Biol Chem 280(10):9691-7	|CEG1 |DBP5 |GFD1 |MEX67 |TIF1 |TIF3 |ZDS1 |ZDS2
Non-Fungal Related Genes/Proteins	Kendirgi F, et al. (2005) Interaction between the shuttling mRNA export factor Gle1 and the nucleoporin hCG1: a conserved mechanism in the export of Hsp70 mRNA. Mol Biol Cell 16(9):4304-15	|GLE1
Genetic Interactions Mutants/Phenotypes	Izawa S, et al. (2004) Gle2p is essential to induce adaptation of the export of bulk poly(A)+ mRNA to heat shock in Saccharomyces cerevisiae. J Biol Chem 279(34):35469-78	|GLE2
Mutants/Phenotypes Strains/Constructs	Kuperwasser N, et al. (2004) Nonsense-mediated decay does not occur within the yeast nucleus. RNA 10(12):1907-15	|NAM7 |SSA4
Genetic Interactions Mutants/Phenotypes Strains/Constructs	Miller AL, et al. (2004) Cytoplasmic inositol hexakisphosphate production is sufficient for mediating the Gle1-mRNA export pathway. J Biol Chem 279(49):51022-32	|GLE1 |GLE2 |IPK1 |MSS4 |NUP116 |NUP159
Alias Function/Process Mutants/Phenotypes Strains/Constructs	Rollenhagen C, et al. (2004) The nuclear pore complex and the DEAD box protein Rat8p/Dbp5p have nonessential features which appear to facilitate mRNA export following heat shock. Mol Cell Biol 24(11):4869-79	|DBP5 |GLE1
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
Protein-protein Interactions	Pyhtila B and Rexach M (2003) A gradient of affinity for the karyopherin Kap95p along the yeast nuclear pore complex. J Biol Chem 278(43):42699-709	|GSP1 |KAP95 |NUP1 |NUP100 |SRP1
Function/Process Protein-protein Interactions Techniques and Reagents	Allen NP, et al. (2001) Proteomic analysis of nucleoporin interacting proteins. J Biol Chem 276(31):29268-74	|GSP1 |KAP95 |NUP1 |NUP100 |NUP116 |NUP2 |NUP49 |NUP57 |NUP60 |NUP84 |SRP1
Alias Function/Process Substrates/Ligands/Cofactors	Jensen TH, et al. (2001) A block to mRNA nuclear export in S. cerevisiae leads to hyperadenylation of transcripts that accumulate at the site of transcription. Mol Cell 7(4):887-98	|DBP5 |GLE1 |HSP104 |MEX67 |MTR2 |NUP159 |SSA4
Reviews	Vasu SK and Forbes DJ (2001) Nuclear pores and nuclear assembly. Curr Opin Cell Biol 13(3):363-75	|ASM4 |CDC31 |GLE1 |GLE2 |MLP1 |MLP2 |NDC1 |NIC96 |NSP1 |NUP1 |NUP100 |NUP116 |NUP120 |NUP133 |MORE
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
Function/Process Mutants/Phenotypes Strains/Constructs Substrates/Ligands/Cofactors	Stage-Zimmermann T, et al. (2000) Factors affecting nuclear export of the 60S ribosomal subunit in vivo. Mol Biol Cell 11(11):3777-89	|CRM1 |CSE1 |DBP5 |FAL1 |GLE1 |GLE2 |KAP104 |KAP120 |KAP123 |KAP95 |MEX67 |MSN5 |MTR10 |MTR2 |MORE
Fungal Related Genes/Proteins Genetic Interactions	Strasser K, et al. (2000) Binding of the Mex67p/Mtr2p heterodimer to FXFG, GLFG, and FG repeat nucleoporins is essential for nuclear mRNA export. J Cell Biol 150(4):695-706	|GLE2 |MEX67 |MTR2 |NSP1 |NUP116 |NUP159
Alias Function/Process Protein-protein Interactions Strains/Constructs	Takahashi Y, et al. (2000) Yeast Ulp1, an Smt3-specific protease, associates with nucleoporins. J Biochem 128(5):723-5	|CDC3 |GLE1 |SMT3 |SYN8 |UIP3 |UIP4 |UIP5 |ULP1
Alias Function/Process Genetic Interactions Mutants/Phenotypes Protein-protein Interactions Regulatory Role Substrates/Ligands/Cofactors	Vainberg IE, et al. (2000) Nuclear export of heat shock and non-heat-shock mRNA occurs via similar pathways. Mol Cell Biol 20(11):3996-4005	|GLE1 |MTR2 |NUP159 |RNA1 |SRM1
Alias Function/Process Protein-protein Interactions	Hodge CA, et al. (1999) Rat8p/Dbp5p is a shuttling transport factor that interacts with Rat7p/Nup159p and Gle1p and suppresses the mRNA export defect of xpo1-1 cells. EMBO J 18(20):5778-88	|CRM1 |DBP5 |GFD1 |GLE1 |GSP1 |MEX67 |NUP159
Alias Function/Process Mutants/Phenotypes Strains/Constructs	Krebber H, et al. (1999) Uncoupling of the hnRNP Npl3p from mRNAs during the stress-induced block in mRNA export. Genes Dev 13(15):1994-2004	|CRM1 |MTR10 |NPL3 |NUP159
Alias Cellular Location Cross-species Expression Function/Process Mutants/Phenotypes Non-Fungal Related Genes/Proteins Protein-protein Interactions Strains/Constructs	Strahm Y, et al. (1999) The RNA export factor Gle1p is located on the cytoplasmic fibrils of the NPC and physically interacts with the FG-nucleoporin Rip1p, the DEAD-box protein Rat8p/Dbp5p and a new protein Ymr 255p. EMBO J 18(20):5761-77	|DBP5 |GFD1 |GLE1
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
Protein-protein Interactions Regulation of	Neville M, et al. (1997) The importin-beta family member Crm1p bridges the interaction between Rev and the nuclear pore complex during nuclear export. Curr Biol 7(10):767-75	|CRM1 |CUP1-1 |CUP1-2 |KAP104 |MTR10 |NUP145 |NUP49 |NUP57
Alias Cellular Location Function/Process Mutants/Phenotypes Protein Sequence Features Protein-protein Interactions Strains/Constructs	Saavedra CA, et al. (1997) Yeast heat shock mRNAs are exported through a distinct pathway defined by Rip1p. Genes Dev 11(21):2845-56	|GLE1 |GSP1 |NPL3 |NUP120 |NUP145 |NUP159 |NUP2 |SSA1 |SSA4
Alias Mutants/Phenotypes	Stade K, et al. (1997) Exportin 1 (Crm1p) is an essential nuclear export factor. Cell 90(6):1041-50	|CRM1
Function/Process Genetic Interactions Mutants/Phenotypes Protein Sequence Features	Stutz F, et al. (1997) The yeast nucleoporin rip1p contributes to multiple export pathways with no essential role for its FG-repeat region. Genes Dev 11(21):2857-68	|GLE1
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 |NUP49 |MORE
Alias Protein-protein Interactions	Murphy R and Wente SR (1996) An RNA-export mediator with an essential nuclear export signal. Nature 383(6598):357-60	|GLE1 |NUP100
Alias Protein-protein Interactions	Murphy R, et al. (1996) GLE2, a Saccharomyces cerevisiae homologue of the Schizosaccharomyces pombe export factor RAE1, is required for nuclear pore complex structure and function. Mol Biol Cell 7(12):1921-37	|GLE2 |NUP100 |NUP145 |SRP1
Protein-protein Interactions	Stutz F, et al. (1996) A role for nucleoporin FG repeat domains in export of human immunodeficiency virus type 1 Rev protein and RNA from the nucleus. Mol Cell Biol 16(12):7144-50	|NUP100 |NUP116 |NUP145 |NUP159 |NUP49 |NUP57
Alias Cellular Location Function/Process Fungal Related Genes/Proteins Mutants/Phenotypes Protein-protein Interactions Strains/Constructs	Stutz F, et al. (1995) Identification of a novel nuclear pore-associated protein as a functional target of the HIV-1 Rev protein in yeast. Cell 82(3):495-506

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