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IFI16 interferon gamma inducible protein 16 [ Homo sapiens (human) ]

Gene ID: 3428, updated on 18-Nov-2018

Summary

Official Symbol
IFI16provided by HGNC
Official Full Name
interferon gamma inducible protein 16provided by HGNC
Primary source
HGNC:HGNC:5395
See related
Ensembl:ENSG00000163565 MIM:147586; Vega:OTTHUMG00000037108
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
PYHIN2; IFNGIP1
Summary
This gene encodes a member of the HIN-200 (hematopoietic interferon-inducible nuclear antigens with 200 amino acid repeats) family of cytokines. The encoded protein contains domains involved in DNA binding, transcriptional regulation, and protein-protein interactions. The protein localizes to the nucleoplasm and nucleoli, and interacts with p53 and retinoblastoma-1. It modulates p53 function, and inhibits cell growth in the Ras/Raf signaling pathway. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2011]
Expression
Ubiquitous expression in lymph node (RPKM 45.3), appendix (RPKM 41.3) and 24 other tissues See more
Orthologs

Genomic context

See IFI16 in Genome Data Viewer
Location:
1q23.1
Exon count:
14
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (158999970..159055155)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (158979682..159024945)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene olfactory receptor family 6 subfamily N member 1 Neighboring gene myeloid cell nuclear differentiation antigen Neighboring gene pyrin and HIN domain family member 5, pseudogene Neighboring gene pyrin and HIN domain family member 1 Neighboring gene pyrin domain containing 5 Neighboring gene uncharacterized LOC105371461 Neighboring gene absent in melanoma 2 Neighboring gene RAD1 pseudogene 2

Genomic regions, transcripts, and products

Expression

  • 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association and population genetic analysis of C-reactive protein in African American and Hispanic American women.
NHGRI GWA Catalog
GWAS of blood cell traits identifies novel associated loci and epistatic interactions in Caucasian and African-American children.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Nef nef Production of infectious triple deletion vpr/vpu/nef HIV-1 mutant is suppressed, indicating that Nef may antagonize restriction activity of IFI16 against production of infectious wild-type HIV-1 PubMed
Pr55(Gag) gag HIV-1 Gag interacts with IfI16 as demonstrated by proximity dependent biotinylation proteomics PubMed
Tat tat Microarray analysis indicates HIV-1 Tat upregulates the interferon-responsive gene expression of many proteins, including IFI16, in immature dendritic cells, an effect that likely facilitates the expansion of HIV-1 infection PubMed
Vpr vpr Production of infectious triple deletion vpr/vpu/nef HIV-1 mutant is suppressed, indicating that Vpr may antagonize restriction activity of IFI16 against production of infectious wild-type HIV-1 PubMed
Vpu vpu Production of infectious triple deletion vpr/vpu/nef HIV-1 mutant is suppressed, indicating that Vpu may antagonize restriction activity of IFI16 against production of infectious wild-type HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Cytosolic sensors of pathogen-associated DNA, organism-specific biosystem (from REACTOME)
    Cytosolic sensors of pathogen-associated DNA, organism-specific biosystemPresence of pathogen-associated DNA in cytosol induces type I IFN production. Several intracellular receptors have been implicated to some degree. These include DNA-dependent activator of interferon ...
  • IRF3-mediated induction of type I IFN, organism-specific biosystem (from REACTOME)
    IRF3-mediated induction of type I IFN, organism-specific biosystemTANK-binding kinase 1 (TBK1) and interferon regulatory factor 3 (IRF3) are central regulators of type-I interferon induction during bacterial or viral infection. TBK1 was found to form complexes with...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • NOD-like receptor signaling pathway, organism-specific biosystem (from KEGG)
    NOD-like receptor signaling pathway, organism-specific biosystemSpecific families of pattern recognition receptors are responsible for detecting various pathogens and generating innate immune responses. The intracellular NOD-like receptor (NLR) family contains mo...
  • NOD-like receptor signaling pathway, conserved biosystem (from KEGG)
    NOD-like receptor signaling pathway, conserved biosystemSpecific families of pattern recognition receptors are responsible for detecting various pathogens and generating innate immune responses. The intracellular NOD-like receptor (NLR) family contains mo...
  • STING mediated induction of host immune responses, organism-specific biosystem (from REACTOME)
    STING mediated induction of host immune responses, organism-specific biosystemSTING (stimulator of IFN genes; also known as MITA/ERIS/MPYS/TMEM173) is an endoplasmic reticulum (ER) resident, which is required for effective type I IFN production in response to nucleic acids. In...
  • Senescence and Autophagy in Cancer, organism-specific biosystem (from WikiPathways)
    Senescence and Autophagy in Cancer, organism-specific biosystemSenescense and Autophagy Pathways in Cancer

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC9466

Gene Ontology Provided by GOA

Process Evidence Code Pubs
activation of cysteine-type endopeptidase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
activation of innate immune response IDA
Inferred from Direct Assay
more info
PubMed 
autophagy IEA
Inferred from Electronic Annotation
more info
 
cell proliferation NAS
Non-traceable Author Statement
more info
PubMed 
cellular response to glucose starvation IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to interferon-beta IEA
Inferred from Electronic Annotation
more info
 
cellular response to ionizing radiation IDA
Inferred from Direct Assay
more info
PubMed 
defense response to virus IDA
Inferred from Direct Assay
more info
PubMed 
defense response to virus IMP
Inferred from Mutant Phenotype
more info
PubMed 
hemopoiesis NAS
Non-traceable Author Statement
more info
PubMed 
inflammatory response IEA
Inferred from Electronic Annotation
more info
 
innate immune response IEA
Inferred from Electronic Annotation
more info
 
intrinsic apoptotic signaling pathway by p53 class mediator IMP
Inferred from Mutant Phenotype
more info
PubMed 
intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator IDA
Inferred from Direct Assay
more info
PubMed 
monocyte differentiation IDA
Inferred from Direct Assay
more info
PubMed 
myeloid cell differentiation NAS
Non-traceable Author Statement
more info
PubMed 
negative regulation of DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of cysteine-type endopeptidase activity IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of innate immune response IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of viral genome replication IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cytokine production TAS
Traceable Author Statement
more info
PubMed 
positive regulation of interleukin-1 beta production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of type I interferon production TAS
Traceable Author Statement
more info
 
regulation of autophagy IEP
Inferred from Expression Pattern
more info
PubMed 
regulation of gene expression, epigenetic IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
colocalizes_with cytosol IPI
Inferred from Physical Interaction
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
membrane HDA PubMed 
nuclear speck IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
gamma-interferon-inducible protein 16
Names
IFI16 beta isoform
interferon-gamma induced protein IFI 16
interferon-inducible myeloid differentiation transcriptional activator

NCBI Reference Sequences (RefSeq)

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_029141.2 RefSeqGene

    Range
    14923..60186
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001206567.1NP_001193496.1  gamma-interferon-inducible protein 16 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an in-frame exon in the 5' coding region and has an additional in-frame exon in the 3' coding region, compared to variant 2. The additional exon is described as exon 7a in PMID:9718316. The resulting isoform (1) is of the same size but lacks a segment in the N-terminal region and has an additional segment in the C-terminal region, compared to isoform 2. Note the CDS was annotated to initiate translation from an in-frame downstream AUG, as it is flanked by a strong Kozak signal, and is better conserved than the upstream AUG located 4 codons upstream.
    Source sequence(s)
    AK296228, BM806453, DA945454, DB273519, M63838
    Consensus CDS
    CCDS58039.1
    UniProtKB/Swiss-Prot
    Q16666
    Related
    ENSP00000352740.3, OTTHUMP00000249915, ENST00000359709.7, OTTHUMT00000421721
    Conserved Domains (3) summary
    cd08305
    Location:1083
    Pyrin; Pyrin: a protein-protein interaction domain
    pfam02760
    Location:145313
    HIN; HIN-200/IF120x domain
    pfam06583
    Location:343545
    Neogenin_C; Neogenin C-terminus
  2. NM_001364867.1NP_001351796.1  gamma-interferon-inducible protein 16 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) encodes the longest isoform (3, also known as IFI 16A).
    Source sequence(s)
    AL359753
    Conserved Domains (3) summary
    cd08305
    Location:1083
    Pyrin; Pyrin: a protein-protein interaction domain
    pfam02760
    Location:201369
    HIN; HIN-200/IF120x domain
    cl25751
    Location:100215
    DUF4045; Domain of unknown function (DUF4045)
  3. NM_005531.2NP_005522.2  gamma-interferon-inducible protein 16 isoform 2

    See identical proteins and their annotated locations for NP_005522.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) consists of 11 exons and encodes isoform 2 (also known as isoform B, PMIDs:9718316 and 12588705). Note the CDS was annotated to initiate translation from an in-frame downstream AUG, as it is flanked by a strong Kozak signal, and is better conserved than the upstream AUG located 4 codons upstream.
    Source sequence(s)
    AL359753, BC017059, BM993134, DA990524, M63838
    Consensus CDS
    CCDS1180.3
    UniProtKB/Swiss-Prot
    Q16666
    Related
    ENSP00000357113.4, OTTHUMP00000035192, ENST00000368131.8, OTTHUMT00000090101
    Conserved Domains (2) summary
    cd08305
    Location:1083
    Pyrin; Pyrin: a protein-protein interaction domain
    pfam02760
    Location:201369
    HIN; HIN-200/IF120x domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    158999970..159055155
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005245127.4XP_005245184.1  gamma-interferon-inducible protein 16 isoform X1

    Related
    ENSP00000295809.7, OTTHUMP00000249914, ENST00000295809.11
  2. XM_017001149.2XP_016856638.1  gamma-interferon-inducible protein 16 isoform X2

    Conserved Domains (2) summary
    cd08305
    Location:1487
    Pyrin; Pyrin: a protein-protein interaction domain
    pfam02760
    Location:205373
    HIN; HIN-200/IF120x domain
  3. XM_006711290.2XP_006711353.1  gamma-interferon-inducible protein 16 isoform X2

    Related
    ENSP00000404325.2, OTTHUMP00000035197, ENST00000448393.6
    Conserved Domains (2) summary
    cd08305
    Location:1487
    Pyrin; Pyrin: a protein-protein interaction domain
    pfam02760
    Location:205373
    HIN; HIN-200/IF120x domain
  4. XM_017001150.2XP_016856639.1  gamma-interferon-inducible protein 16 isoform X3

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