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MIP6/YHR015W 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   ChrVIII: 134547 to 136526 CDS: 134547 - 136526 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
MIP6	YHR015W		ORF, Verified	S000001057
Description
Putative RNA-binding protein, interacts with Mex67p, which is a component of the nuclear pore involved in nuclear mRNA export

GO Annotations [TOP] [NEXT]
Molecular Function Annotation(s) Reference(s) Evidence Assigned By RNA binding Segref A, et al. (1997) Mex67p, a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. EMBO J 16(11):3256-71        ISS : Inferred from Sequence or structural Similarity Assigned on 2002-08-20 SGD GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0694 Assigned on 2007-05-23 UniProtKB nucleic acid binding DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.      IEA : Inferred from Electronic Annotation with EBI:IPR000504 Assigned on 2007-05-23 UniProtKB nucleotide binding DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.      IEA : Inferred from Electronic Annotation with EBI:IPR012677 Assigned on 2007-05-23 UniProtKB
Biological Process Annotation(s) Reference(s) Evidence Assigned By mRNA export from nucleus Segref A, et al. (1997) Mex67p, a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. EMBO J 16(11):3256-71        IPI : Inferred from Physical Interaction Assigned on 2002-08-20 SGD translational termination 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 cytoplasm GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0963 Assigned on 2009-03-04 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 2009-03-04 UniProtKB nuclear pore Segref A, et al. (1997) Mex67p, a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. EMBO J 16(11):3256-71        IPI : Inferred from Physical Interaction Assigned on 2002-08-20 SGD

Pathways [TOP] [NEXT]
No pathways available

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

Basic References [TOP]
BASIC INFORMATION REFERENCES forMIP6/YHR015W for MIP6 1) Segref A, et al. (1997) Mex67p, a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. EMBO J 16(11):3256-71

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for MIP6/YHR015W

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for MIP6/YHR015W

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 MPNSHGN C-term ESLGFTV Length(aa) 659 MW(Da) 75,919 pI 10.24 Amino Acid Composition (full length) GCG tools: PepPlot, Helical Wheel, PepStruct Transcript Translation Calculations Codon Bias -0.021   Codon Adaptation Index 0.136   Frequency of Optimal Codons 0.415   Hydropathicity of Protein -0.634   Aromaticity Score 0.094

10 20 30 40 50 | | | | | MPNSHGNVLNNISLNSKQNPRSISKSCPNDKDARQKSFKTISAQALVRVQ GAGYKLGDVKLKDAEVKEKNSLKKYDCKNATQEKKEQEQVFEKTVAKGSV QKYITKTSKTNSLFIGNLKSTVTEEMLRKIFKRYQSFESAKVCRDFLTKK SLGYGYLNFKDKNDAESARKEFNYTVFFGQEVKIMPSMKNTLFRKNIGTN VFFSNLPLENPQLTTRSFYLIMIEYGNVLSCLLERRKNIGFVYFDNDISA RNVIKKYNNQEFFGNKIICGLHFDKEVRTRPEFTKRKKMIGSDIVIEDEL LASNNLSDNARSKTILVKNLPSDTTQEEVLDYFSTIGPIKSVFISEKQAN TPHKAFVTYKNEEESKKAQKCLNKTIFKNHTIWVGPGKDKPVHNQIGTNK KTKVYLKNLSFNCNKEFISQLCLQEKIRFSEIKITNYNSLNWTFCGHVEC FSRSDAERLFNILDRRLIGSSLVEASWSKNNDNILNEIDYDDGNNNENYK KLINISSMMRFRTQELSAHQKGLTSQFQQVVSPFSSYSNSYTNMNSLVAT PMKPHPAFNLITNTVDEKLHQPKRTKQENAEILESLKKIINRNLQRISIS GLNKEENLRSISEFIFDVFWEHDSERLSHFLLMTNTSLESQKILQKQVTR AAESLGFTV*

Protein Structures from PDB: proteins of known structure with sequence similarity to MIP6/YHR015W, based on Smith-Waterman analysis. [TOP] [NEXT]

PDB protein structure(s) homologous to MIP6 Homolog Source (per PDB) Protein Alignment: MIP6 vs. Homolog External Links P-Value %Identical %Similar Alignment 1cvj ( Chain: G, F, H, C, B, D, E, A) X-ray crystal structure of the poly(a)-binding protein in complex with polyadenylate rna PDB_Info PDB_Structure Homo sapiens Chain G = 1.4e-14 34 34 View alignment SCOP MMDB CATH Chain F = 1.4e-14 34 34 View alignment Chain H = 1.4e-14 34 34 View alignment Chain C = 1.4e-14 34 34 View alignment Chain B = 1.4e-14 34 34 View alignment Chain D = 1.4e-14 34 34 View alignment Chain E = 1.4e-14 34 34 View alignment Chain A = 1.4e-14 34 34 View alignment 1fnx ( Chain: H) Solution structure of the huc rbd1-rbd2 complexed with the au-rich element PDB_Info PDB_Structure Mus musculus 4.9e-08 28 38 View alignment SCOP MMDB CATH 1fxl ( Chain: A) Crystal structure of hud and au-rich element of the c-fos rna PDB_Info PDB_Structure Homo sapiens 7.2e-08 29 35 View alignment SCOP MMDB CATH 1g2e ( Chain: A) Crystal structure of hud and au-rich element of the tumor necrosis factor alpha rna PDB_Info PDB_Structure Homo sapiens 7.2e-08 29 35 View alignment SCOP MMDB CATH 1d8z ( Chain: A) Solution structure of the first rna-binding domain (rbd1) of hu antigen c (huc) PDB_Info PDB_Structure Mus musculus 0.001300 35 38 View alignment SCOP MMDB CATH 3sxl ( Chain: B, C, A) Sex-lethal rna recognition domains 1 and 2 from drosophila melanogaster PDB_Info PDB_Structure Drosophila melanogaster Chain B = 0.002200 26 35 View alignment SCOP MMDB CATH Chain C = 0.002200 26 35 View alignment Chain A = 0.002200 26 35 View alignment 1p1t ( Chain: A) Nmr structure of the n-terminal rrm domain of cleavage stimulation factor 64 kda subunit PDB_Info PDB_Structure Homo sapiens 0.002400 33 28 View alignment SCOP MMDB CATH 2jrs ( Chain: A) Solution nmr structure of caper rrm2 domain. northeast structural genomics target hr4730a PDB_Info PDB_Structure Homo sapiens 0.002501 35 39 View alignment SCOP MMDB CATH 1b7f ( Chain: B, A) Sxl-lethal protein/rna complex PDB_Info PDB_Structure Drosophila melanogaster Chain B = 0.004099 26 33 View alignment SCOP MMDB CATH Chain A = 0.004099 26 33 View alignment 2dnz ( Chain: A) Solution structure of the second rna binding domain of rna binding motif protein 23 PDB_Info PDB_Structure Homo sapiens 0.004598 30 44 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
MIP6	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 BLASTP BLASTN Design Primers FASTA aa FASTA nt Restriction Fragment Map Restriction Fragment Sizes Six-Frame Translation

Sequence from other databases
Sequence ID	Source
YHR015W	SGD Systematic Sequence
856408	NCBI: Gene ID
NP_011879.1	NCBI: RefSeq protein version ID
NP_011879.1	NCBI: RefSeq protein version ID
6321803	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]

DNA & RNA Details Topic Research Highlight Reference Contributor Other DNA & RNA Details Description: Specifically higher expression in carbon limited chemostat cultures versus carbon 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
5 curated references; 0 references not yet curated
Large-scale protein detection	Picotti P, et al. (2009) Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 138(4):795-806	|ACH1 |ACO1 |ADH1 |ADH2 |ADH4 |ALD6 |ASP1 |CCT7 |CCT8 |CDC7 |CIT1 |CIT2 |CMR2 |ENO1 |MORE
RNA Levels and Processing	Woo DK, et al. (2009) Multiple pathways of mitochondrial-nuclear communication in yeast: Intergenomic signaling involves ABF1 and affects a different set of genes than retrograde regulation. Biochim Biophys Acta 1789(2):135-45	|ABF1 |ACH1 |AGX1 |ALD3 |ARG4 |ARG7 |ARO4 |ATO2 |ATO3 |ATP14 |ATP16 |ATP17 |ATP19 |ATP2 |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
DNA/RNA Sequence Features RNA Levels and Processing	Karpichev IV and Small GM (1998) Global regulatory functions of Oaf1p and Pip2p (Oaf2p), transcription factors that regulate genes encoding peroxisomal proteins in Saccharomyces cerevisiae. Mol Cell Biol 18(11):6560-70	|ATF1 |CAT2 |CIN1 |CIT1 |CIT2 |CRC1 |CTA1 |CUP2 |DCI1 |DUS3 |ECI1 |EEB1 |FAA2 |FOX2 |MORE
DNA/RNA Sequence Features Protein-protein Interactions Strains/Constructs Techniques and Reagents	Segref A, et al. (1997) Mex67p, a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. EMBO J 16(11):3256-71	|MEX67 |NUP57 |NUP85

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