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IFIT1 interferon induced protein with tetratricopeptide repeats 1 [ Homo sapiens (human) ]

Gene ID: 3434, updated on 3-Nov-2024

Summary

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Official Symbol
IFIT1provided by HGNC
Official Full Name
interferon induced protein with tetratricopeptide repeats 1provided by HGNC
Primary source
HGNC:HGNC:5407
See related
Ensembl:ENSG00000185745 MIM:147690; AllianceGenome:HGNC:5407
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
C56; P56; G10P1; IFI56; ISG56; IFI-56; IFIT-1; IFNAI1; RNM561; IFI-56K
Summary
This gene encodes a protein containing tetratricopeptide repeats that was originally identified as induced upon treatment with interferon. The encoded protein may inhibit viral replication and translational initiation. This gene is located in a cluster on chromosome 10 with five other closely related genes. There is a pseudogene for this gene on chromosome 13. Alternatively spliced transcript variants encoding multiple isoforms have been observed. [provided by RefSeq, Aug 2012]
Expression
Ubiquitous expression in adrenal (RPKM 10.7), spleen (RPKM 10.7) and 25 other tissues See more
Orthologs
all
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Genomic context

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See IFIT1 in Genome Data Viewer
Location:
10q23.31
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (89392623..89406487)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (90276467..90290330)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (91152380..91166244)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3746 Neighboring gene interferon induced protein with tetratricopeptide repeats 6, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr10:91151215-91151376 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3747 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3748 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3749 Neighboring gene interferon induced protein with tetratricopeptide repeats 1B Neighboring gene uncharacterized LOC107984251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3750 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3751 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3752 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:91181772-91182971 Neighboring gene interferon induced protein with tetratricopeptide repeats 5 Neighboring gene solute carrier family 16 member 12 Neighboring gene SLC16A12 antisense RNA 1

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 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 inhibitory action of P56 on select functions of E1 mediates interferon's effect on human papillomavirus DNA replication. Saikia P, et al. J Virol, 2010 Dec. PMID 20926571, Free PMC Article
  2. Antiviral effects of IFIT1 in human cytomegalovirus-infected fetal astrocytes. Zhang L, et al. J Med Virol, 2017 Apr. PMID 27589693, Free PMC Article
  3. Identification of Interferon-Stimulated Gene Proteins That Inhibit Human Parainfluenza Virus Type 3. Rabbani MA, et al. J Virol, 2016 Dec 15. PMID 27707917, Free PMC Article
  4. IFIT1 polymorphisms predict interferon-α treatment efficiency for hepatitis B virus infection. Xie DY, et al. World J Gastroenterol, 2016 Nov 28. PMID 27956805, Free PMC Article
  5. Human IFIT1 Inhibits mRNA Translation of Rubulaviruses but Not Other Members of the Paramyxoviridae Family. Young DF, et al. J Virol, 2016 Oct 15. PMID 27512068, Free PMC Article

See all (104) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. TLR3 signaling-induced interferon-stimulated gene 56 plays a role in the pathogenesis of rheumatoid arthritis.
    Title: TLR3 signaling-induced interferon-stimulated gene 56 plays a role in the pathogenesis of rheumatoid arthritis.
  2. IFIT1 modulates the proliferation, migration and invasion of pancreatic cancer cells via Wnt/beta-catenin signaling.
    Title: IFIT1 modulates the proliferation, migration and invasion of pancreatic cancer cells via Wnt/β-catenin signaling.
  3. Kruppel-like factor 13 acts as a tumor suppressor in thyroid carcinoma by downregulating IFIT1.
    Title: Kruppel-like factor 13 acts as a tumor suppressor in thyroid carcinoma by downregulating IFIT1.
  4. Lysyl oxidase-like 2 promotes stemness and enhances antitumor effects of gefitinib in head and neck cancer via IFIT1 and IFIT3.
    Title: Lysyl oxidase-like 2 promotes stemness and enhances antitumor effects of gefitinib in head and neck cancer via IFIT1 and IFIT3.
  5. Comprehensive analysis of the prognosis and biological significance for IFIT family in skin cutaneous melanoma.
    Title: Comprehensive analysis of the prognosis and biological significance for IFIT family in skin cutaneous melanoma.
  6. ISG56 is involved in CXCL10 expression induced by TLR3 signaling in BEAS-2B bronchial epithelial cells.
    Title: ISG56 is involved in CXCL10 expression induced by TLR3 signaling in BEAS-2B bronchial epithelial cells.
  7. Intrahepatic immune changes after hepatitis c virus eradication by direct-acting antiviral therapy.
    Title: Intrahepatic immune changes after hepatitis c virus eradication by direct-acting antiviral therapy.
  8. Development of bis-ANS-based modified fluorescence titration assay for IFIT/RNA studies.
    Title: Development of bis-ANS-based modified fluorescence titration assay for IFIT/RNA studies.
  9. IFIT1 and IFITM3 were overexpressed in head and neck squamous cell carcinoma and indicated poor prognoses for patients with head and neck squamous cell carcinoma.
    Title: Expression and Prognostic Value of IFIT1 and IFITM3 in Head and Neck Squamous Cell Carcinoma.
  10. The results uncovered a large ensemble of RNA secondary structures of diverse size and shape in the different viruses, which showed little correspondence to the phylogeny of the viruses. Unexpectedly, the 50UTR of several viral genomes in this family did not fold into any structure, suggesting either their extreme sensitivity to IFIT1 or the existence of alternative viral mechanisms of subverting IFIT1 function.
    Title: In silico structure analysis of alphaviral RNA genomes shows diversity in the evasion of IFIT1-mediated innate immunity.
Submit: New GeneRIF Correction See all GeneRIFs (42)

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

Variation

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See Variation Viewer (GRCh37.p13)

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Vpr vpr HIV-1 Vpr antagonizes IFIT1 (ISG56) mRNA induction in TZM-bl STING cells (TZM-bl cells engineered to express TMEM173 (STING)); IFIT1 is involved in viral recognition innate sensing within cell PubMed
vpr HIV-1 Vpr upregulates the gene expression of IFIT1 in human monocyte-derived dendritic cells PubMed
vpr HIV-1 Vpr upregulates the gene expression of IFIT1 in human monocyte-derived macrophages PubMed
Vpu vpu The expression of IFIT1 is enhanced in Vpu-deficient HIV-1-infected cells as compared to that in wild-type-infected cells PubMed
capsid gag Infection with HIV-1 CA mutant N74D upregulates the expression of IFIT1 in primary human monocyte-derived macrophages PubMed

Go to the HIV-1, Human Interaction Database

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in antiviral innate immune response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in antiviral innate immune response IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in cellular response to exogenous dsRNA IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to type I interferon IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in defense response to virus IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in intracellular transport of viral protein in host cell IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of helicase activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of viral genome replication IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of viral genome replication IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in response to virus IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in response to virus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in host cell IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
interferon-induced protein with tetratricopeptide repeats 1
Names
interferon, alpha-inducible protein (MW 56kD)
interferon-induced 56 kDa protein
interferon-inducible mRNA 561

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_001270927.2 → NP_001257856.1  interferon-induced protein with tetratricopeptide repeats 1 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate exon in the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AK308688, AL353146, BU625391, DA822484
    Conserved Domains (3) summary
    sd00006
    Location:252 → 279
    TPR; TPR repeat [structural motif]
    pfam00515
    Location:438 → 470
    TPR_1; Tetratricopeptide repeat
    pfam13424
    Location:54 → 127
    TPR_12; Tetratricopeptide repeat

  2. NM_001270928.2 → NP_001257857.1  interferon-induced protein with tetratricopeptide repeats 1 isoform 3

    See identical proteins and their annotated locations for NP_001257857.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate internal exon and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1. Variants 3, 4, and 5 encode the same isoform (3).
    Source sequence(s)
    AL353146, BU625391, DA822484, DB180094
    Consensus CDS
    CCDS59220.1
    UniProtKB/Swiss-Prot
    P09914
    Conserved Domains (3) summary
    sd00006
    Location:221 → 248
    TPR; TPR repeat [structural motif]
    pfam00515
    Location:407 → 439
    TPR_1; Tetratricopeptide repeat
    pfam13424
    Location:23 → 96
    TPR_12; Tetratricopeptide repeat

  3. NM_001270929.2 → NP_001257858.1  interferon-induced protein with tetratricopeptide repeats 1 isoform 3

    See identical proteins and their annotated locations for NP_001257858.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an alternate internal exon and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1. Variants 3, 4, and 5 encode the same isoform (3).
    Source sequence(s)
    AL353146, BU625391, DB003897
    Consensus CDS
    CCDS59220.1
    UniProtKB/Swiss-Prot
    P09914
    Conserved Domains (3) summary
    sd00006
    Location:221 → 248
    TPR; TPR repeat [structural motif]
    pfam00515
    Location:407 → 439
    TPR_1; Tetratricopeptide repeat
    pfam13424
    Location:23 → 96
    TPR_12; Tetratricopeptide repeat

  4. NM_001270930.2 → NP_001257859.1  interferon-induced protein with tetratricopeptide repeats 1 isoform 3

    See identical proteins and their annotated locations for NP_001257859.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) contains an alternate internal exon and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1. Variants 3, 4, and 5 encode the same isoform (3).
    Source sequence(s)
    AL353146, BU625391, DA822484, DB474377
    Consensus CDS
    CCDS59220.1
    UniProtKB/Swiss-Prot
    P09914
    Related
    ENSP00000441968.1, ENST00000546318.2
    Conserved Domains (3) summary
    sd00006
    Location:221 → 248
    TPR; TPR repeat [structural motif]
    pfam00515
    Location:407 → 439
    TPR_1; Tetratricopeptide repeat
    pfam13424
    Location:23 → 96
    TPR_12; Tetratricopeptide repeat

  5. NM_001548.5 → NP_001539.3  interferon-induced protein with tetratricopeptide repeats 1 isoform 1

    See identical proteins and their annotated locations for NP_001539.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AK314588, AL353146, BU625391
    Consensus CDS
    CCDS31243.1
    UniProtKB/Swiss-Prot
    B3KS50, D3DR31, P09914, Q5T7J1, Q96QM5
    Related
    ENSP00000360869.3, ENST00000371804.4
    Conserved Domains (2) summary
    sd00006
    Location:252 → 279
    TPR; TPR repeat [structural motif]
    cl26002
    Location:55 → 466
    TPR_11; TPR repeat

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

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    89392623..89406487
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    90276467..90290330
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P09914.2 GenPept UniProtKB/Swiss-Prot:P09914

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