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

Gene ID: 26146, updated on 5-Mar-2024

Summary

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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
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Genomic context

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See TRAF3IP1 in Genome Data Viewer
Location:
2q37.3
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (238320518..238400900)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (238810296..238891033)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (239229159..239309541)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:239147110-239147678 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12492 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:239149579-239150084 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:239150085-239150590 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:239154789-239155988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:239156797-239157297 Neighboring gene hes family bHLH transcription factor 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:239172424-239172924 Neighboring gene period circadian regulator 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:239179613-239180112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:239187958-239188582 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:239190897-239191397 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:239192245-239192744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:239196189-239196711 Neighboring gene uncharacterized LOC112268433 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:239196796-239197690 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17380 Neighboring gene MPRA-validated peak4101 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:239223693-239224192 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12495 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17381 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:239276069-239276272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:239317872-239318404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:239318939-239319470 Neighboring gene RNA, U6 small nuclear 234, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:239330367-239331026 Neighboring gene uncharacterized LOC124908002 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:239334149-239334684 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12497 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12498

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. The C-terminus of MIP-T3 protein is required for ubiquitin-proteasome-mediated degradation in human cells. Guo CW, et al. FEBS Lett, 2011 May 6. PMID 21510943
  2. The T cell IFT20 interactome reveals new players in immune synapse assembly. Galgano D, et al. J Cell Sci, 2017 Mar 15. PMID 28154159, Free PMC Article
  3. MIP-T3, a novel protein linking tumor necrosis factor receptor-associated factor 3 to the microtubule network. Ling L, et al. J Biol Chem, 2000 Aug 4. PMID 10791955
  4. GWAS findings for human iris patterns: associations with variants in genes that influence normal neuronal pattern development. Larsson M, et al. Am J Hum Genet, 2011 Aug 12. PMID 21835309, Free PMC Article
  5. MIP-T3 associates with IL-13Ralpha1 and suppresses STAT6 activation in response to IL-13 stimulation. Niu Y, et al. FEBS Lett, 2003 Aug 28. PMID 12935900

See all (36) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
Submit: New GeneRIF Correction

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
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EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • DKFZp434F124

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 centrosome 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

  1. NG_053055.1 RefSeqGene

    Range
    5030..85409
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    238320518..238400900
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. XM_017003789.2 → XP_016859278.1  TRAF3-interacting protein 1 isoform X2

  3. 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

  4. 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

  5. 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

  6. 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

  7. XM_047443898.1 → XP_047299854.1  TRAF3-interacting protein 1 isoform X7

  8. 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

RNA

  1. XR_922902.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    238810296..238891033
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054341334.1 → XP_054197309.1  TRAF3-interacting protein 1 isoform X1

  2. XM_054341335.1 → XP_054197310.1  TRAF3-interacting protein 1 isoform X2

  3. XM_054341336.1 → XP_054197311.1  TRAF3-interacting protein 1 isoform X3

  4. XM_054341338.1 → XP_054197313.1  TRAF3-interacting protein 1 isoform X5

  5. XM_054341339.1 → XP_054197314.1  TRAF3-interacting protein 1 isoform X6

  6. XM_054341337.1 → XP_054197312.1  TRAF3-interacting protein 1 isoform X4

  7. XM_054341340.1 → XP_054197315.1  TRAF3-interacting protein 1 isoform X7

  8. XM_054341341.1 → XP_054197316.1  TRAF3-interacting protein 1 isoform X8

RNA

  1. XR_008486320.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TDR0.1 GenPept UniProtKB/Swiss-Prot:Q8TDR0

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