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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
    mouse all
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    Genomic context

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    See IRF9 in Genome Data Viewer
    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
    		Compare labs

    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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