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    ift88 intraflagellar transport 88 homolog [ Danio rerio (zebrafish) ]

    Gene ID: 321855, updated on 9-Dec-2024

    Summary

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    Official Symbol
    ift88provided by ZNC
    Official Full Name
    intraflagellar transport 88 homologprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-574
    See related
    Ensembl:ENSDARG00000027234 AllianceGenome:ZFIN:ZDB-GENE-030131-574
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    ttc10; fb37b11; polaris; wu:fb37b11; xx:zah8127
    Summary
    Predicted to enable kinesin binding activity. Acts upstream of or within with a positive effect on cilium assembly. Acts upstream of or within several processes, including cerebrospinal fluid circulation; photoreceptor cell maintenance; and plasma membrane bounded cell projection organization. Located in axoneme and ciliary basal body. Is expressed in forerunner cell group; head; nervous system; and pronephric duct. Orthologous to human IFT88 (intraflagellar transport 88). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See ift88 in Genome Data Viewer
    Location:
    chromosome: 9
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 9 NC_007120.7 (21365630..21383612, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 9 NC_007120.6 (21554755..21572712, complement)

    Chromosome 9 - NC_007120.7Genomic Context describing neighboring genes Neighboring gene EEF1A lysine methyltransferase 1 Neighboring gene interleukin 17d Neighboring gene crystallin, lambda 1 Neighboring gene gap junction protein beta 8

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Cilia in the developing zebrafish ear. Whitfield TT. Philos Trans R Soc Lond B Biol Sci, 2020 Feb 17. PMID 31884918, Free PMC Article
    2. OCRL1 modulates cilia length in renal epithelial cells. Rbaibi Y, et al. Traffic, 2012 Sep. PMID 22680056, Free PMC Article
    3. Olfactory Rod Cells: A Rare Cell Type in the Larval Zebrafish Olfactory Epithelium With a Large Actin-Rich Apical Projection. Cheung KY, et al. Front Physiol, 2021. PMID 33716772, Free PMC Article
    4. Genetic analysis of photoreceptor cell development in the zebrafish retina. Doerre G, et al. Mech Dev, 2002 Jan. PMID 11744374
    5. The cilia protein IFT88 is required for spindle orientation in mitosis. Delaval B, et al. Nat Cell Biol, 2011 Apr. PMID 21441926, Free PMC Article

    See all (72) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Data show that IFT88 depletion induces mitotic defects in human cultured cells, in kidney cells from the IFT88 mouse mutant Tg737(orpk) and in zebrafish embryos.
      Title: The cilia protein IFT88 is required for spindle orientation in mitosis.
    2. Zebrafish IFT mutants also exhibited no dramatic changes in the craniofacial skeleton, somite formation, or motor neuron patterning.
      Title: Zebrafish ift57, ift88, and ift172 intraflagellar transport mutants disrupt cilia but do not affect hedgehog signaling.
    3. The functions of polaris and pkd2 in LR patterning are conserved between zebrafish and mice and that Kupffer's vesicle functions as a ciliated organ of asymmetry.
      Title: Polaris and Polycystin-2 in dorsal forerunner cells and Kupffer's vesicle are required for specification of the zebrafish left-right axis.
    4. These studies reveal an essential role for IFT genes in vertebrate sensory neurons and implicate the molecular components of intraflagellar transport in degenerative disorders of these cells.
      Title: Intraflagellar transport genes are essential for differentiation and survival of vertebrate sensory neurons.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Process Evidence Code Pubs
    acts_upstream_of Notch signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within cellular response to light stimulus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within cerebrospinal fluid circulation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within_positive_effect cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within cilium organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within determination of left/right symmetry IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within determination of left/right symmetry IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within epithelial cilium movement involved in extracellular fluid movement IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within establishment of mitotic spindle orientation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within eye photoreceptor cell development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within gastrulation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within inner ear receptor cell stereocilium organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within intraciliary transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within non-motile cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within photoreceptor cell maintenance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of smoothened signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within proximal convoluted tubule development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of apoptosis involved in tissue homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in axoneme IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in ciliary basal body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cilium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    intraflagellar transport protein 88 homolog
    Names
    intraflagellar transport protein 88
    oval
    ovl
    tetratricopeptide repeat domain 10

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001001725.1 → NP_001001725.1  intraflagellar transport protein 88 homolog

      See identical proteins and their annotated locations for NP_001001725.1

      Status: PROVISIONAL

      Source sequence(s)
      AY491507
      UniProtKB/TrEMBL
      A0A8M2BEW9, Q6RUQ9
      Related
      ENSDARP00000034047.6, ENSDART00000038923.8
      Conserved Domains (4) summary
      COG0457
      Location:431 → 687
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      sd00006
      Location:485 → 513
      TPR; TPR repeat [structural motif]
      cd15832
      Location:229 → 260
      SNAP; TPR repeat [structural motif]
      cl24038
      Location:229 → 330
      SNAP; Soluble N-ethylmaleimide-sensitive factor (NSF) Attachment Protein family

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007120.7 Reference GRCz11 Primary Assembly

      Range
      21365630..21383612 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068223285.1 → XP_068079386.1  intraflagellar transport protein 88 homolog isoform X1

      UniProtKB/TrEMBL
      A0A8M9QF86, A0A8M9QJI0

    2. XM_068223288.1 → XP_068079389.1  intraflagellar transport protein 88 homolog isoform X4

      UniProtKB/TrEMBL
      A0A8M9Q4H3
      Related
      ENSDARP00000150029.1, ENSDART00000188129.1

    3. XM_068223289.1 → XP_068079390.1  intraflagellar transport protein 88 homolog isoform X5

      UniProtKB/TrEMBL
      A0A8M2BF03

    4. XM_068223286.1 → XP_068079387.1  intraflagellar transport protein 88 homolog isoform X2

      UniProtKB/TrEMBL
      A0A8M2BEY1
      Related
      ENSDARP00000101727.2, ENSDART00000110943.5

    5. XM_068223287.1 → XP_068079388.1  intraflagellar transport protein 88 homolog isoform X3

      UniProtKB/TrEMBL
      A0A8M9PRW8

    6. XM_021478606.2 → XP_021334281.1  intraflagellar transport protein 88 homolog isoform X1

      UniProtKB/TrEMBL
      A0A8M9QF86, A0A8M9QJI0
      Conserved Domains (2) summary
      sd00006
      Location:485 → 513
      TPR; TPR repeat [structural motif]
      cl26002
      Location:213 → 698
      TPR_11; TPR repeat

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394749.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      231325..249135 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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