Human Gene IRF9 (ENST00000396864.8) from GENCODE V44
  Description: Homo sapiens interferon regulatory factor 9 (IRF9), transcript variant 2, mRNA. (from RefSeq NM_006084)
RefSeq Summary (NM_006084): 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].
Gencode Transcript: ENST00000396864.8
Gencode Gene: ENSG00000213928.10
Transcript (Including UTRs)
   Position: hg38 chr14:24,161,265-24,166,565 Size: 5,301 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg38 chr14:24,162,145-24,166,196 Size: 4,052 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:24,161,265-24,166,565)mRNA (may differ from genome)Protein (393 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: IRF9_HUMAN
DESCRIPTION: RecName: Full=Interferon regulatory factor 9; Short=IRF-9; AltName: Full=IFN-alpha-responsive transcription factor subunit; AltName: Full=ISGF3 p48 subunit; AltName: Full=Interferon-stimulated gene factor 3 gamma; Short=ISGF-3 gamma; AltName: Full=Transcriptional regulator ISGF3 subunit gamma;
FUNCTION: Transcription regulatory factor that mediates signaling by type I IFNs (IFN-alpha and IFN-beta). Following type I IFN binding to cell surface receptors, Jak kinases (TYK2 and JAK1) are activated, leading to tyrosine phosphorylation of STAT1 and STAT2. The phosphorylated STATs dimerize, associate with IRF9/ISGF3G to form a complex termed ISGF3 transcription factor, that enters the nucleus. ISGF3 binds to the IFN stimulated response element (ISRE) to activate the transcription of interferon stimulated genes, which drive the cell in an antiviral state.
SUBUNIT: Interacts with STAT2 in the cytoplasm. Forms a complex with heterodimer STAT1/STAT2.
INTERACTION: P48551:IFNAR2; NbExp=6; IntAct=EBI-626526, EBI-958408; P52630:STAT2; NbExp=4; IntAct=EBI-626526, EBI-1546963;
SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Translocated into the nucleus upon activation by IFN-alpha/beta.
INDUCTION: By IFN-alpha and IFNB1/IFN-beta.
SIMILARITY: Belongs to the IRF family.
SIMILARITY: Contains 1 IRF tryptophan pentad repeat DNA-binding domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: IRF9
Diseases sorted by gene-association score: skin papilloma (7), hepatitis c (6)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 19.18 RPKM in Spleen
Total median expression: 269.27 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -20.9075-0.279 Picture PostScript Text
3' UTR -72.40369-0.196 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR019817 - Interferon_reg_fac_CS
IPR001346 - Interferon_reg_fact_DNA-bd_dom
IPR019471 - Interferon_reg_factor-3
IPR017855 - SMAD_dom-like
IPR008984 - SMAD_FHA_domain
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00605 - Interferon regulatory factor transcription factor
PF10401 - Interferon-regulatory factor 3

ModBase Predicted Comparative 3D Structure on Q00978
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001047 core promoter binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0044212 transcription regulatory region DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0007166 cell surface receptor signaling pathway
GO:0051607 defense response to virus
GO:0060333 interferon-gamma-mediated signaling pathway
GO:0060337 type I interferon signaling pathway

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AK074144 - Homo sapiens mRNA for FLJ00217 protein.
LF384990 - JP 2014500723-A/192493: Polycomb-Associated Non-Coding RNAs.
MA620567 - JP 2018138019-A/192493: Polycomb-Associated Non-Coding RNAs.
AK308347 - Homo sapiens cDNA, FLJ98295.
AK295467 - Homo sapiens cDNA FLJ61271 complete cds, highly similar to Transcriptional regulator ISGF3 subunit gamma.
M87503 - Human IFN-responsive transcription factor subunit mRNA, complete cds.
BC035716 - Homo sapiens interferon regulatory factor 9, mRNA (cDNA clone MGC:46151 IMAGE:5588434), complete cds.
EU446692 - Synthetic construct Homo sapiens clone IMAGE:100070344; IMAGE:100011901; FLH258770.01L interferon-stimulated transcription factor 3, gamma 48kDa (ISGF3G) gene, encodes complete protein.
KJ893020 - Synthetic construct Homo sapiens clone ccsbBroadEn_02414 IRF9 gene, encodes complete protein.
U92994 - Homo sapiens clone DT1P1f5 mRNA, CAG repeat region.
JD215098 - Sequence 196122 from Patent EP1572962.
JD304948 - Sequence 285972 from Patent EP1572962.
JD314912 - Sequence 295936 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04630 - Jak-STAT signaling pathway

BioCarta from NCI Cancer Genome Anatomy Project
h_ranklPathway - Bone Remodelling
h_ifnaPathway - IFN alpha signaling pathway

Reactome (by CSHL, EBI, and GO)

Protein Q00978 (Reactome details) participates in the following event(s):

R-HSA-909725 Interaction of IRF9 with p-STAT2:p-STAT1
R-HSA-909721 Translocation of ISGF3 complex to nucleus
R-HSA-1015699 ISGF3 binds the ISRE promoter elements in IFN-stimulated genes
R-HSA-909733 Interferon alpha/beta signaling
R-HSA-877300 Interferon gamma signaling
R-HSA-913531 Interferon Signaling
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: D3DS61, ENST00000396864.1, ENST00000396864.2, ENST00000396864.3, ENST00000396864.4, ENST00000396864.5, ENST00000396864.6, ENST00000396864.7, IRF9_HUMAN, ISGF3G, NM_006084, Q00978, uc058zzb.1, uc058zzb.2
UCSC ID: ENST00000396864.8
RefSeq Accession: NM_006084
Protein: Q00978 (aka IRF9_HUMAN)
CCDS: CCDS9615.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.