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ift88

intraflagellar transport 88 homolog

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GeneInformationForm
GeneName ift88
Aliases ENSDARG:ENSDARG00000027234; fb37b11, xx:zah8127, wu:fb37b11, polaris, ttc10, ovl, oval, intraflagellar transport protein 88
Description intraflagellar transport 88 homolog
GenomicLocation chromosome 9 22398978-22416834 reverse strand
ExternalIDs Entrez:321855; EMBL:AY491507; UniGene:2900; ZFIN:ZDB-GENE-030131-574;
TranscriptID ENSDART:ENSDART00000038923; ENSDART:ENSDART00000132032; ENSDART:ENSDART00000110943
mRNA NCBI:NM_001001725
GeneDescription IFT refers to the movement of intraflagellar transport particle, a multisubunit protein complex that consists of atleast 17 IFT proteins that form two subcomplexes: complex A and complex B. IFT88 belongs to complex B and is involved in ciliary assembly.
GeneFunction Bisgrove et al. (2005) reported the expression of polaris to be dependent on the T-box transcription factors no tail, suggesting its role in regulating ciliary structure and function.
GeneCloning The gene is contained in a BAC clone DKEY-51D17 (Vector: pIndigoBAC-536).
GeneStructure This gene encodes three transcripts: ENSDART00000038923 that contains 26 exons with the transcript length of 2,895 bps and The protein product (ENSDARP00000034047) consits 824 residues.(ENSDART00000110943) that contains 4 exons with the transcript length of 600 bps The protein product (ENSDARP00000101727) consits of 108 residues.
Protein ENSDARP00000034047 ENSDARP00000122577 ENSDARP00000101727
ProteinDomainandFamilies has domain InterPro:IPR001440; InterPro:IPR013026; InterPro:IPR006597; InterPro:IPR013105; InterPro:IPR011990;
Motifs has motif Prosite:PS50005; Prosite:PS50293; PFAM:PF00515; PFAM:PF07719;
Expression ArrayExpress:ENSDARG00000027234;
GeneOntology GO:0005622; GO:0005840; GO:0019861; GO:0005929; GO:0006412; GO:0035058; GO:0045494; GO:0042462; GO:0001539; GO:0042384; GO:0007368; GO:0003735; GO:0005488;
Orthologs Entrez:8100;
VariationAndRepeats ss252400833 ss252400833 ss252400833 ss252400836
DisordersAndMutations ZFINID:ZDB-GENO-090605-79;ZFINID:ZDB-GENO-100512-4;ZFINID:ZDB-GENO-080301-1;ZFINID:ZDB-GENO-080730-2;ZFINID:ZDB-GENO-980410-147;ZFINID:ZDB-GENO-110203-15;ZFINID:ZDB-GENO-080108-5;ZFINID:ZDB-GENO-080108-2;Tsujikawa et al. (2004) showed a mutation of zebrafish oval locus (ovl), that affects a component of the ciliary transport (IFT) mechanism, the IFT88 polypeptide. In mutant retina, cilia were generated but not maintained, producing the absence of photoreceptor outer segments. The loss of cilia was also observed in auditory air cells and olfactory sensory neurons. Bisgrove et al. (2005) designed translation- and splice-blocking morpholino antisense oligonucleotides to knock down polaris or pkd2 in zebrafish that resulted in the misexpression of left-side-specific genes, including southpaw, leftyl and lefty2, and randomization of heart and gut looping. Their analysis of polaris and pkd2 expression levels in zebrafish laterality mutants suggested the role of T-box transcription factors no-tail (ntl) and spadetail (Spt) in the regulation of these genes in Dorsal forerunner cells(DFC).Krock et al. (2008) compared the retinal phenotypes of IFT57 and IFT88 mutant zebrafish and observed the failure of IFT88 mutants to form outer segments, whereas IFT57 mutants formed short outer segments with reduced amounts of opsin. Both IFT57 and IFT88 mutants exhibited holes within the photoreceptor layer, which is the indicative of cell death, whereas other cell types within the retina were unaffected. Cell death specifically within the outer nuclear layer indicated that photoreceptors are the only cell type within the retina whose survival was affected by the loss of IFT proteins.
RelatedPubMedArticles Bisgrove, B. W.; Snarr, B. S.; Emrazian, A.; Yost, H. J.: Polaris and Polycystin-2 in dorsal forerunner cells and Kupffer's vesicle are required for specification of the zebrafish left-right axis. Dev Biol. 2005 Nov 15;287(2):274-88. Epub 2005 Oct 7. PMID:16216239 Krock, B. L.; Perkins, B. D.: The intraflagellar transport protein IFT57 is required for cilia maintenance and regulates IFT-particle-kinesin-II dissociation in vertebrate photoreceptors. J Cell Sci. 2008 Jun 1;121(Pt 11):1907-15. PMID:18492793 Tsujikawa, M.; Malicki, J.: Intraflagellar transport genes are essential for differentiation and survival of vertebrate sensory neurons. Neuron. 2004 Jun 10;42(5):703-16. PMID:15182712 Insinna, C.; Pathak, N.; Perkins, B.; Drummond, I.; Besharse, J. C.: The homodimeric kinesin, Kif17, is essential for vertebrate photoreceptor sensory outer segment development. Dev Biol. 2008 Apr 1;316(1):160-70. Epub 2008 Jan 31. PMID:18304522 NCBI Resource Coordinators.: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 41(Database issue):D8-D20. 2013. PMID:23193264
Kersey, P. J.; Allen, J. E.; Christensen, M.; et al.: Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res. 2013. PMID:24163254
Sigrist, C. J. A.; de, Castro, E; Cerutti, L; Cuche, B. A.; Hulo, N.; Bridge, A.; Bougueleret, L. Xenarios, I.: New and continuing developments at PROSITE. Nucleic Acids Res. doi: 10.1093/nar/gks1067. 2012. PMID:23161676
Punta, M.; Coggill, P. C.; Eberhardt, et al.: The Pfam protein families database. Nucleic Acids Res. 40(Database Issue):D290-D301. 2012. PMID:22127870
Hunter, S.; Jones P.; Mitchell A.; et al.: Interpro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. doi: 10.1093/nar/gkr948. 2011. PMID:22096229
Carbon, S.; Ireland, A.; Mungall, C. J.; Shu, S.; Marshall, B.; Lewis, S.; AMIGO Hub; Web Presence Working Group.: AMIGO: online access to ontology and annotation data. Bioinformatics. 25(2):288-9. 2009. PMID:19033274
Ashburner, M.; Ball, C. A.; Blake, J. A.; et al. The Gene Ontology Consortium.: Gene ontology: tool for the unification of biology. Nat. Genet. 25(1):25-9. 2000. PMID:10802651
Sherry, S. T.; Ward, M. H.; Kholodov, M.; Baker, J.; Phan, L.; Smigielski, E. M.; Sirotkin, K.: dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 1;29(1):308-11. 2001. PMID:11125122
Bradford, Y.; Conlin, T.; Dunn, N.; et al.: ZFIN: enhancements and updates to the zebrafish model organism database. Nucleic Acids Res. 39(suppl 1):D822-D829. 2011. PMID:21036866
Kapushesky, M.; Adamusiak, T.; Burdett, T.; et al.: Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments. Nucleic Acids Res. 40(Database isue):D1077-81. 2012. PMID:22064864

Web resources:
NCBI: http://www.ncbi.nlm.nih.gov/
PFAM: http://pfam.sanger.ac.uk/
PROSITE: http://prosite.expasy.org/
Interpro: http://www.ebi.ac.uk/interpro/
ZFIN: http://zfin.org/
Expression Atlas (EMBL): http://www.ebi.ac.uk/gxa/
Ensembl: http://asia.ensembl.org/Danio_rerio/
Database of Single Nucleotide Polymorphisms (dbSNP). Bethesda (MD): National Center for Biotechnology Information, National Library of Medicine.: http://www.ncbi.nlm.nih.gov/SNP/
PRINTS from Genomenet: http://www.genome.jp/
European Nucleotide Archive: http://www.ebi.ac.uk/ena/home
UNIGENE: http://www.ncbi.nlm.nih.gov/unigene/
AMIGO Gene Ontology: http://amigo.geneontology.org
Topic revision: r2 - 2013-06-20 - MeghnaSingh
 
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