TRAF3IP1 TRAF3 interacting protein 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TRAF3IP1provided by HGNC
Official Full Name: TRAF3 interacting protein 1provided by HGNC
Primary source: HGNC:HGNC:17861
See related: Ensembl:ENSG00000204104 MIM:607380; AllianceGenome:HGNC:17861
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: IFT54; MIPT3; SLSN9; FAP116; MIP-T3; CFAP116
Summary: The protein encoded by this gene interacts with TNF receptor-associated factor 3, tethering it to cytoskeletal microtubules. The encoded protein is also an inhibitor of the innate type I IFN response. Defects in this gene are a cause of Senior-Loken syndrome 9. [provided by RefSeq, Mar 2017]
Expression: Broad expression in testis (RPKM 8.2), thyroid (RPKM 4.0) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q37.3

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (238320518..238400900)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (238810296..238891033)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (239229159..239309541)

Chromosome 2 - NC_000002.12 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

[1]H, [13]C, and [15]N resonance assignments and solution structure of the N-terminal divergent calponin homology (NN-CH) domain of human intraflagellar transport protein 54.
Title: (1)H, (13)C, and (15)N resonance assignments and solution structure of the N-terminal divergent calponin homology (NN-CH) domain of human intraflagellar transport protein 54.
Mutations in TRAF3IP1 are identified in patients with nephronophthisis and retinal degeneration. The identified mutations result in mild ciliary defects in patients and reveal a role of IFT54 as a negative regulator of microtubule stability via MAP4.
Title: Mutations in TRAF3IP1/IFT54 reveal a new role for IFT proteins in microtubule stabilization.
MIP-T3 functions as a negative regulator of the innate type I interferon response by preventing TRAF3 from forming protein complexes with critical downstream transducers and effectors of antiviral response.
Title: MIP-T3 is a negative regulator of innate type I IFN response.
Data show that MIP-T3 protein level is highly regulated; mainly mediated by the ubiquitin-proteasome system.
Title: The C-terminus of MIP-T3 protein is required for ubiquitin-proteasome-mediated degradation in human cells.
The interaction of MIP-T3 with both actin filaments and microtubule suggested that MIP-T3 may play an important role in regulation of cytoskeleton dynamics in cells.
Title: Proteomic analysis reveals novel binding partners of MIP-T3 in human cells.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Observational study of gene-disease association. (HuGE Navigator)
Title: Genetic variants in TPMT and COMT are associated with hearing loss in children receiving cisplatin chemotherapy.
These results suggest that MIP-T3 is a novel inhibitor of IL-13 signaling and may be a useful molecule in ameliorating various conditions in which IL-13 plays a central role.
Title: MIP-T3 associates with IL-13Ralpha1 and suppresses STAT6 activation in response to IL-13 stimulation.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Senior-Loken syndrome 9 MedGen: C4225263 OMIM: 616629 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
GWAS findings for human iris patterns: associations with variants in genes that influence normal neuronal pattern development. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-78398 (e-PCR)
- UniSTS:169748

TRAF3IP1_9465 (e-PCR)
- UniSTS:468770

RH65470 (e-PCR)
- UniSTS:26968

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables microtubule binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cilium assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in cilium assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in intraciliary anterograde transport	NAS Non-traceable Author Statement more info	PubMed
involved_in intraciliary transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in kidney development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in morphogenesis of a polarized epithelium	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of defense response to virus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of protein phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of protein-containing complex assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of type I interferon production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of microtubule cytoskeleton organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of microtubule cytoskeleton organization	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in axoneme	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 base	IDA Inferred from Direct Assay more info	PubMed
located_in ciliary tip	IDA Inferred from Direct Assay more info	PubMed
located_in ciliary tip	TAS Traceable Author Statement more info
located_in ciliary transition zone	IDA Inferred from Direct Assay more info	PubMed
located_in cilium	NAS Non-traceable Author Statement more info	PubMed
located_in cilium	TAS Traceable Author Statement more info
part_of intraciliary transport particle B	IBA Inferred from Biological aspect of Ancestor more info
part_of intraciliary transport particle B	IPI Inferred from Physical Interaction more info	PubMed
part_of intraciliary transport particle B	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: TRAF3-interacting protein 1

Names: TNF receptor-associated factor 3 interacting protein 1; interleukin 13 receptor alpha 1-binding protein-1; intraflagellar transport protein 54 homolog; microtubule interacting protein that associates with TRAF3; microtubule-interacting protein associated with TRAF3

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.

Genomic

NG_053055.1 RefSeqGene

Range

5030..85409

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001139490.1 → NP_001132962.1 TRAF3-interacting protein 1 isoform 2

See identical proteins and their annotated locations for NP_001132962.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks two in-frame exons in the 5' coding region, compared to variant 1, and encodes a shorter isoform (2), compared to isoform 1.

Source sequence(s)

AF230877, AI356967, BC059174, BX482493

Consensus CDS

CCDS46557.1

UniProtKB/Swiss-Prot

Q8TDR0

Related

ENSP00000375851.3, ENST00000391993.7

Conserved Domains (1) summary

pfam10243
Location:49 → 619

MIP-T3; Microtubule-binding protein MIP-T3
NM_015650.4 → NP_056465.2 TRAF3-interacting protein 1 isoform 1

See identical proteins and their annotated locations for NP_056465.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC012485, AF230877, AF242456, AI356967, BC059174, BX482493

Consensus CDS

CCDS33415.1

UniProtKB/Swiss-Prot

Q6PCT1, Q7L8N9, Q8TDR0, Q9NRD6, Q9Y4Q1

Related

ENSP00000362424.4, ENST00000373327.5

Conserved Domains (2) summary

PHA03249
Location:376 → 522

PHA03249; DNA packaging tegument protein UL25; Provisional

pfam10243
Location:49 → 685

MIP-T3; Microtubule-binding protein MIP-T3

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

238320518..238400900

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011510944.3 → XP_011509246.1 TRAF3-interacting protein 1 isoform X1

Conserved Domains (2) summary

PTZ00121
Location:126 → 715

PTZ00121; MAEBL; Provisional

PRK12678
Location:132 → 300

PRK12678; transcription termination factor Rho; Provisional
XM_017003789.2 → XP_016859278.1 TRAF3-interacting protein 1 isoform X2
XM_011510945.3 → XP_011509247.1 TRAF3-interacting protein 1 isoform X3

Conserved Domains (1) summary

pfam10243
Location:49 → 706

MIP-T3; Microtubule-binding protein MIP-T3
XM_011510948.3 → XP_011509250.1 TRAF3-interacting protein 1 isoform X5

Conserved Domains (1) summary

pfam10243
Location:49 → 653

MIP-T3; Microtubule-binding protein MIP-T3
XM_006712414.3 → XP_006712477.1 TRAF3-interacting protein 1 isoform X6

Conserved Domains (1) summary

pfam10243
Location:49 → 618

MIP-T3; Microtubule-binding protein MIP-T3
XM_011510946.3 → XP_011509248.1 TRAF3-interacting protein 1 isoform X4

Conserved Domains (2) summary

PHA03249
Location:386 → 532

PHA03249; DNA packaging tegument protein UL25; Provisional

pfam10243
Location:49 → 695

MIP-T3; Microtubule-binding protein MIP-T3
XM_047443898.1 → XP_047299854.1 TRAF3-interacting protein 1 isoform X7
XM_011510950.3 → XP_011509252.1 TRAF3-interacting protein 1 isoform X8

Conserved Domains (1) summary

pfam10243
Location:42 → 341

MIP-T3; Microtubule-binding protein MIP-T3