Ift88 intraflagellar transport 88 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ift88provided by RGD
Official Full Name: intraflagellar transport 88provided by RGD
Primary source: RGD:1309717
See related: EnsemblRapid:ENSRNOG00000009278 AllianceGenome:RGD:1309717
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Ttc10
Summary: Predicted to enable kinesin binding activity. Involved in response to silicon dioxide. Located in outer acrosomal membrane and trans-Golgi network. Biomarker of silicosis. Orthologous to human IFT88 (intraflagellar transport 88). [provided by Alliance of Genome Resources, Oct 2024]
Expression: Biased expression in Testes (RPKM 44.9), Thymus (RPKM 40.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 15p12

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	15	NC_086033.1 (35685678..35786875)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	15	NC_051350.1 (31573325..31666068)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	15	NC_005114.4 (37690417..37786855)

Chromosome 15 - NC_086033.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Intraflagellar transport protein 88 interacts with polycystin 2 to regulate mechanosensitive hedgehog signaling in mandibular condylar chondrocytes.
Title: Intraflagellar transport protein 88 interacts with polycystin 2 to regulate mechanosensitive hedgehog signaling in mandibular condylar chondrocytes.
Tg737 regulates a Wnt/beta-catenin/Snail-HNF4alpha negative feedback circuit, thereby blocking EMT and the malignant transformation of liver stem cells to liver cancer stem cells.
Title: Tg737 regulates epithelial-mesenchymal transition and cancer stem cell properties via a negative feedback circuit between Snail and HNF4α during liver stem cell malignant transformation.
Data show that inactivation of Tg737 (Ift88, Ttc10) may play an important role in malignant transformation of fetal liver stem/progenitor cells.
Title: Tg737 inhibition results in malignant transformation in fetal liver stem/progenitor cells by promoting cell-cycle progression and differentiation arrest.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

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

Process	Evidence Code	Pubs
acts_upstream_of_or_within Notch signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within animal organ morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within anterior/posterior pattern specification	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within brain development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cardiac muscle cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cardiac septum morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cilium assembly	ISO Inferred from Sequence Orthology more info
involved_in cilium assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cilium movement	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cochlea development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cytoplasmic microtubule organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within determination of left/right symmetry	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within dorsal/ventral pattern formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic digit morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within endothelial cell morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within epidermal stem cell homeostasis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within epidermis development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within eye development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within forebrain development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within forebrain morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within heart development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within heart formation	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in intraciliary transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of keratinocyte proliferation	ISO Inferred from Sequence Orthology more info
involved_in kidney development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within kidney development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within limb development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within liver development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lung development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lung vasculature development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of epithelial cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of keratinocyte proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within nervous system development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neural precursor cell proliferation	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within pancreas development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cilium assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of insulin-like growth factor receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within primary palate development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein localization	ISO Inferred from Sequence Orthology more info
involved_in regulation of autophagosome assembly	ISO Inferred from Sequence Orthology more info
involved_in regulation of cilium assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of fat cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of feeding behavior	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of odontogenesis of dentin-containing tooth	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of protein processing	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to fluid shear stress	ISO Inferred from Sequence Orthology more info
involved_in response to silicon dioxide	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within smoothened signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within sperm axoneme assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within spermatid nucleus elongation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within spinal cord dorsal/ventral patterning	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within telencephalon development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in acrosomal membrane	ISO Inferred from Sequence Orthology more info
located_in axonemal basal plate	ISO Inferred from Sequence Orthology more info
located_in axoneme	ISO Inferred from Sequence Orthology more info
is_active_in centriole	IBA Inferred from Biological aspect of Ancestor more info
located_in centriole	ISO Inferred from Sequence Orthology more info
located_in centrosome	ISO Inferred from Sequence Orthology more info
is_active_in ciliary basal body	IBA Inferred from Biological aspect of Ancestor more info
located_in ciliary basal body	ISO Inferred from Sequence Orthology more info
is_active_in ciliary base	IBA Inferred from Biological aspect of Ancestor more info
located_in ciliary base	ISO Inferred from Sequence Orthology more info
located_in ciliary tip	ISO Inferred from Sequence Orthology more info
located_in cilium	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
part_of intraciliary transport particle B	ISO Inferred from Sequence Orthology more info
located_in kinocilium	ISO Inferred from Sequence Orthology more info
located_in manchette	ISO Inferred from Sequence Orthology more info
located_in motile cilium	ISO Inferred from Sequence Orthology more info
is_active_in non-motile cilium	IBA Inferred from Biological aspect of Ancestor more info
located_in non-motile cilium	ISO Inferred from Sequence Orthology more info
located_in outer acrosomal membrane	IDA Inferred from Direct Assay more info	PubMed
located_in photoreceptor connecting cilium	ISO Inferred from Sequence Orthology more info
located_in sperm flagellum	ISO Inferred from Sequence Orthology more info
located_in sperm head-tail coupling apparatus	ISO Inferred from Sequence Orthology more info
located_in trans-Golgi network	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 88 homolog; 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_001107266.1 → NP_001100736.1 intraflagellar transport protein 88 homolog

See identical proteins and their annotated locations for NP_001100736.1

Status: PROVISIONAL

Source sequence(s)

CH474049

UniProtKB/TrEMBL

A0A096MJ06, A6KHC0

Related

ENSRNOP00000067945.3, ENSRNOT00000076839.3

Conserved Domains (5) summary

COG0457
Location:429 → 687

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

sd00006
Location:485 → 513

TPR; TPR repeat [structural motif]

cd15832
Location:515 → 548

SNAP; TPR repeat [structural motif]

pfam00515
Location:238 → 265

TPR_1; Tetratricopeptide repeat

cl24038
Location:501 → 721

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

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086033.1 Reference GRCr8

Range

35685678..35786875

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017599687.3 → XP_017455176.1 intraflagellar transport protein 88 homolog isoform X1

UniProtKB/TrEMBL

A0A096MJ06, A0A8I5ZPQ6

Conserved Domains (2) summary

TIGR02917
Location:213 → 698

PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein

sd00006
Location:485 → 513

TPR; TPR repeat [structural motif]
XM_006252067.5 → XP_006252129.1 intraflagellar transport protein 88 homolog isoform X1

See identical proteins and their annotated locations for XP_006252129.1

UniProtKB/TrEMBL

A0A096MJ06, A0A8I5ZPQ6

Conserved Domains (2) summary

TIGR02917
Location:213 → 698

PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein

sd00006
Location:485 → 513

TPR; TPR repeat [structural motif]
XM_006252066.5 → XP_006252128.1 intraflagellar transport protein 88 homolog isoform X1

See identical proteins and their annotated locations for XP_006252128.1

UniProtKB/TrEMBL

A0A096MJ06, A0A8I5ZPQ6

Related

ENSRNOP00000068425.3, ENSRNOT00000076608.4

Conserved Domains (2) summary

TIGR02917
Location:213 → 698

PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein

sd00006
Location:485 → 513

TPR; TPR repeat [structural motif]
XM_006252070.5 → XP_006252132.1 intraflagellar transport protein 88 homolog isoform X2

UniProtKB/TrEMBL

A0A096MJ06, D4ACI9

Related

ENSRNOP00000012988.5, ENSRNOT00000012988.9

Conserved Domains (2) summary

TIGR02917
Location:213 → 698

PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein

sd00006
Location:485 → 513

TPR; TPR repeat [structural motif]
XM_063274267.1 → XP_063130337.1 intraflagellar transport protein 88 homolog isoform X5
XM_039093318.2 → XP_038949246.1 intraflagellar transport protein 88 homolog isoform X3

UniProtKB/TrEMBL

A0A096MJ06

Conserved Domains (2) summary

TIGR02917
Location:135 → 620

PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein

sd00006
Location:407 → 435

TPR; TPR repeat [structural motif]
XM_039093319.2 → XP_038949247.1 intraflagellar transport protein 88 homolog isoform X4

Conserved Domains (2) summary

TIGR02917
Location:62 → 547

PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein

sd00006
Location:334 → 362

TPR; TPR repeat [structural motif]