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

Summary

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; plasma membrane bounded cell projection organization; and tissue homeostasis. 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, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 9

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	9	NC_007120.7 (21365632..21383589, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	9	NC_007120.6 (21554755..21572712, complement)

Chromosome 9 - NC_007120.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.

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General gene information

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Markers

AI437044 (e-PCR)
- UniSTS:206597

fb37b11.x1 (e-PCR)
- UniSTS:190509

fb37b11.x1 (e-PCR)
- UniSTS:190510

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables kinesin binding	IBA Inferred from Biological aspect of Ancestor more info

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
involved_in inner ear receptor cell stereocilium organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within inner ear receptor cell stereocilium organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intraciliary transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within intraciliary transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in kidney development	IBA Inferred from Biological aspect of Ancestor more info
involved_in non-motile cilium assembly	IBA Inferred from Biological aspect of Ancestor more info
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
is_active_in centriole	IBA Inferred from Biological aspect of Ancestor more info
is_active_in ciliary basal body	IBA Inferred from Biological aspect of Ancestor more info
located_in ciliary basal body	IDA Inferred from Direct Assay more info	PubMed
is_active_in ciliary base	IBA Inferred from Biological aspect of Ancestor more info
located_in cilium	IDA Inferred from Direct Assay more info	PubMed
is_active_in non-motile cilium	IBA Inferred from Biological aspect of Ancestor more info

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)

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

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: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007120.7 Reference GRCz11 Primary Assembly

Range

21365632..21383589 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_021478605.1 → XP_021334280.1 intraflagellar transport protein 88 homolog isoform X1

UniProtKB/TrEMBL

A0A8M9QJI0

Conserved Domains (2) summary

sd00006
Location:487 → 515

TPR; TPR repeat [structural motif]

cl26002
Location:213 → 700

TPR_11; TPR repeat
XM_021478606.1 → XP_021334281.1 intraflagellar transport protein 88 homolog isoform X2

UniProtKB/TrEMBL

A0A8M9QF86

Conserved Domains (2) summary

sd00006
Location:485 → 513

TPR; TPR repeat [structural motif]

cl26002
Location:213 → 698

TPR_11; TPR repeat
XM_021478608.1 → XP_021334283.1 intraflagellar transport protein 88 homolog isoform X5

UniProtKB/TrEMBL

A0A8M9Q4H3

Related

ENSDARP00000150029.1, ENSDART00000188129.1

Conserved Domains (2) summary

sd00006
Location:487 → 515

TPR; TPR repeat [structural motif]

cl26002
Location:213 → 700

TPR_11; TPR repeat
XM_005167530.4 → XP_005167587.1 intraflagellar transport protein 88 homolog isoform X6

UniProtKB/TrEMBL

A0A8M2BF03

Conserved Domains (5) summary

COG0457
Location:435 → 689

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

sd00006
Location:487 → 515

TPR; TPR repeat [structural motif]

cd15832
Location:229 → 260

SNAP; TPR repeat [structural motif]

pfam13414
Location:238 → 296

TPR_11; TPR repeat

cl24038
Location:229 → 330

SNAP; Soluble N-ethylmaleimide-sensitive factor (NSF) Attachment Protein family
XM_005167528.4 → XP_005167585.1 intraflagellar transport protein 88 homolog isoform X3

See identical proteins and their annotated locations for XP_005167585.1

UniProtKB/TrEMBL

A0A8M2BEY1

Related

ENSDARP00000101727.2, ENSDART00000110943.5

Conserved Domains (5) summary

COG0457
Location:435 → 689

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

sd00006
Location:487 → 515

TPR; TPR repeat [structural motif]

cd15832
Location:229 → 260

SNAP; TPR repeat [structural motif]

pfam13414
Location:238 → 303

TPR_11; TPR repeat

cl24038
Location:229 → 330

SNAP; Soluble N-ethylmaleimide-sensitive factor (NSF) Attachment Protein family
XM_021478607.1 → XP_021334282.1 intraflagellar transport protein 88 homolog isoform X4

UniProtKB/TrEMBL

A0A8M9PRW8

Conserved Domains (2) summary

sd00006
Location:487 → 515

TPR; TPR repeat [structural motif]

cl26002
Location:213 → 700

TPR_11; TPR repeat
XM_021478604.1 → XP_021334279.1 intraflagellar transport protein 88 homolog isoform X1

UniProtKB/TrEMBL

A0A8M9QJI0

Conserved Domains (2) summary

sd00006
Location:487 → 515

TPR; TPR repeat [structural motif]

cl26002
Location:213 → 700

TPR_11; TPR repeat
XM_005167531.3 → XP_005167588.1 intraflagellar transport protein 88 homolog isoform X7

UniProtKB/TrEMBL

A0A8M2BEW9

Conserved Domains (5) summary

COG0457
Location:435 → 689

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

sd00006
Location:487 → 515

TPR; TPR repeat [structural motif]

cd15832
Location:229 → 260

SNAP; TPR repeat [structural motif]

pfam13414
Location:238 → 303

TPR_11; TPR repeat

cl24038
Location:229 → 330

SNAP; Soluble N-ethylmaleimide-sensitive factor (NSF) Attachment Protein family