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IRF9 interferon regulatory factor 9 [ Homo sapiens (human) ]

Gene ID: 10379, updated on 5-Mar-2024

Summary

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Official Symbol
IRF9provided by HGNC
Official Full Name
interferon regulatory factor 9provided by HGNC
Primary source
HGNC:HGNC:6131
See related
Ensembl:ENSG00000213928 MIM:147574; AllianceGenome:HGNC:6131
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
p48; IRF-9; ISGF3; ISGF3G
Summary
This gene encodes a member of the interferon regulatory factor (IRF) family, a group of transcription factors with diverse roles, including virus-mediated activation of interferon, and modulation of cell growth, differentiation, apoptosis, and immune system activity. Members of the IRF family are characterized by a conserved N-terminal DNA-binding domain containing tryptophan (W) repeats. Mutations in this gene result in Immunodeficiency 65. [provided by RefSeq, Jul 2020]
Annotation information
Note: This gene has been reviewed for its involvement in coronavirus biology, and is involved in immune response or antiviral activity.
Expression
Ubiquitous expression in spleen (RPKM 55.3), appendix (RPKM 34.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
14q12
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (24161265..24166565)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (18359574..18364874)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (24630474..24635774)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5626 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8190 Neighboring gene microRNA 7703 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:24616442-24616942 Neighboring gene proteasome activator subunit 2 Neighboring gene ring finger protein 31 Neighboring gene RNA, 5S ribosomal pseudogene 383 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8191 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8192 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:24640701-24641201 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8193 Neighboring gene REC8 meiotic recombination protein Neighboring gene importin 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:24657018-24657228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5630 Neighboring gene transmembrane 9 superfamily member 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:24664227-24664926

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. Evolution and emergence of primate-specific interferon regulatory factor 9. Drury S, et al. J Med Virol, 2023 Feb. PMID 36691924, Free PMC Article
  2. Positive selection-driven fixation of a hominin-specific amino acid mutation related to dephosphorylation in IRF9. Chen J, et al. BMC Ecol Evol, 2022 Nov 10. PMID 36357830, Free PMC Article
  3. Pseudorabies Virus DNA Polymerase Processivity Factor UL42 Inhibits Type I IFN Response by Preventing ISGF3-ISRE Interaction. Zhang R, et al. J Immunol, 2021 Jul 15. PMID 34272232
  4. IRF9 Affects the TNF-Induced Phenotype of Rheumatoid-Arthritis Fibroblast-Like Synoviocytes via Regulation of the SIRT-1/NF-κB Signaling Pathway. Jiang F, et al. Cells Tissues Organs, 2020. PMID 32772027
  5. Interferon Regulatory Factor 9 Structure and Regulation. Paul A, et al. Front Immunol, 2018. PMID 30147694, Free PMC Article

See all (95) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ISGF3 and STAT2/IRF9 Control Basal and IFN-Induced Transcription through Genome-Wide Binding of Phosphorylated and Unphosphorylated Complexes to Common ISRE-Containing ISGs.
    Title: ISGF3 and STAT2/IRF9 Control Basal and IFN-Induced Transcription through Genome-Wide Binding of Phosphorylated and Unphosphorylated Complexes to Common ISRE-Containing ISGs.
  2. Twist1-IRF9 Interaction Is Necessary for IFN-Stimulated Gene Anti-Zika Viral Infection.
    Title: Twist1-IRF9 Interaction Is Necessary for IFN-Stimulated Gene Anti-Zika Viral Infection.
  3. Evolution and emergence of primate-specific interferon regulatory factor 9.
    Title: Evolution and emergence of primate-specific interferon regulatory factor 9.
  4. Positive selection-driven fixation of a hominin-specific amino acid mutation related to dephosphorylation in IRF9.
    Title: Positive selection-driven fixation of a hominin-specific amino acid mutation related to dephosphorylation in IRF9.
  5. Aberrant inflammatory responses to type I interferon in STAT2 or IRF9 deficiency.
    Title: Aberrant inflammatory responses to type I interferon in STAT2 or IRF9 deficiency.
  6. IRF9 and XAF1 as Diagnostic Markers of Primary Sjogren Syndrome.
    Title: IRF9 and XAF1 as Diagnostic Markers of Primary Sjogren Syndrome.
  7. SCD2-mediated cooperative activation of IRF3-IRF9 regulatory circuit controls type I interferon transcriptome in CD4(+) T cells.
    Title: SCD2-mediated cooperative activation of IRF3-IRF9 regulatory circuit controls type I interferon transcriptome in CD4(+) T cells.
  8. Increased IRF9-STAT2 Signaling Leads to Adaptive Resistance toward Targeted Therapy in Melanoma by Restraining GSDME-Dependent Pyroptosis.
    Title: Increased IRF9-STAT2 Signaling Leads to Adaptive Resistance toward Targeted Therapy in Melanoma by Restraining GSDME-Dependent Pyroptosis.
  9. Pseudorabies Virus DNA Polymerase Processivity Factor UL42 Inhibits Type I IFN Response by Preventing ISGF3-ISRE Interaction.
    Title: Pseudorabies Virus DNA Polymerase Processivity Factor UL42 Inhibits Type I IFN Response by Preventing ISGF3-ISRE Interaction.
  10. SARS-CoV-2 Spike Targets USP33-IRF9 Axis via Exosomal miR-148a to Activate Human Microglia.
    Title: SARS-CoV-2 Spike Targets USP33-IRF9 Axis via Exosomal miR-148a to Activate Human Microglia.
Submit: New GeneRIF Correction See all GeneRIFs (53)

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
Immunodeficiency 65, susceptibility to viral infections
MedGen: C5231441 OMIM: 618648 GeneReviews: Not available
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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

Potential readthrough

Included gene: RNF31

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity TAS
Traceable Author Statement
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell surface receptor signaling pathway TAS
Traceable Author Statement
more info
 PubMed 
involved_in defense response to virus IEA
Inferred from Electronic Annotation
more info
  
involved_in immune system process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of ISGF3 complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in cytoplasm TAS
Traceable Author Statement
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
interferon regulatory factor 9
Names
IFN-alpha-responsive transcription factor subunit
ISGF-3 gamma
ISGF3 p48 subunit
interferon-stimulated gene factor 3 gamma
interferon-stimulated transcription factor 3, gamma (48kD)
interferon-stimulated transcription factor 3, gamma 48kDa
transcriptional regulator ISGF3 subunit gamma

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_001385400.1 → NP_001372329.1  interferon regulatory factor 9 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AL136295
    Consensus CDS
    CCDS91853.1
    UniProtKB/TrEMBL
    A0A8V8TMJ8, A0A8V8TN13
    Related
    ENSP00000514071.1, ENST00000698995.1
    Conserved Domains (2) summary
    pfam00605
    Location:11 → 115
    IRF; Interferon regulatory factor transcription factor
    pfam10401
    Location:227 → 340
    IRF-3; Interferon-regulatory factor 3

  2. NM_001385401.1 → NP_001372330.1  interferon regulatory factor 9 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AL136295
    Consensus CDS
    CCDS91854.1
    UniProtKB/TrEMBL
    A0A8V8TN47, H0YNP4
    Related
    ENSP00000454095.2, ENST00000560275.6
    Conserved Domains (2) summary
    pfam00605
    Location:11 → 115
    IRF; Interferon regulatory factor transcription factor
    pfam10401
    Location:227 → 390
    IRF-3; Interferon-regulatory factor 3

  3. NM_001385402.1 → NP_001372331.1  interferon regulatory factor 9 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AL136295
    Consensus CDS
    CCDS91855.1
    UniProtKB/TrEMBL
    A0A8V8TP83
    Related
    ENSP00000514183.1, ENST00000699178.1
    Conserved Domains (1) summary
    pfam00605
    Location:11 → 115
    IRF; Interferon regulatory factor transcription factor

  4. NM_006084.5 → NP_006075.3  interferon regulatory factor 9 isoform 2

    See identical proteins and their annotated locations for NP_006075.3

    Status: VALIDATED

    Source sequence(s)
    AL136295, BI497082, BI919023
    Consensus CDS
    CCDS9615.1
    UniProtKB/Swiss-Prot
    D3DS61, Q00978
    UniProtKB/TrEMBL
    A0A8V8TN47
    Related
    ENSP00000380073.3, ENST00000396864.8
    Conserved Domains (2) summary
    pfam00605
    Location:11 → 115
    IRF; Interferon regulatory factor transcription factor
    pfam10401
    Location:218 → 382
    IRF-3; Interferon-regulatory factor 3

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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    24161265..24166565
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654722.1 Reference GRCh38.p14 PATCHES

    Range
    462243..467543
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    18359574..18364874
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q00978.1 GenPept UniProtKB/Swiss-Prot:Q00978

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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