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

Summary

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
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 10q23.31

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (89392623..89406487)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (90276467..90290330)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (91152380..91166244)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
Beyond the well-studied role of cytosolic IFIT1 in restricting viral replication, data demonstrate a function for nuclear IFIT1 in differential transcriptional regulation of separate branches of the LPS-induced gene program.
Title: IFIT1 Exerts Opposing Regulatory Effects on the Inflammatory and Interferon Gene Programs in LPS-Activated Human Macrophages.
HEV RNA-dependent RNA polymerase (RdRp) binds to IFIT1, thereby protecting the viral RNA from IFIT1-mediated translation inhibition.
Title: Hepatitis E virus polymerase binds to IFIT1 to protect the viral RNA from IFIT1-mediated translation inhibition.

Submit: New GeneRIF Correction See all GeneRIFs (40)

Phenotypes

Go to the top of the page Help

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

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

Go to the top of the page Help

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

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

RH17956 (e-PCR)
- UniSTS:24381

RH123621 (e-PCR)
- UniSTS:136040

GDB:193862 (e-PCR)
- UniSTS:155770

IFIT1__6442 (e-PCR)
- UniSTS:463996

PMC135632P1 (e-PCR)
- UniSTS:270758

RH77911 (e-PCR)
- UniSTS:83631

G15877 (e-PCR)
- UniSTS:24570

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

Go to the top of the page Help

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)

Go to the top of the page Help

NEW Try the new Transcript table

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_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
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
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
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
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