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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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