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Irf9 interferon regulatory factor 9 [ Mus musculus (house mouse) ]

Gene ID: 16391, updated on 26-Jun-2024

Summary

Official Symbol
Irf9provided by MGI
Official Full Name
interferon regulatory factor 9provided by MGI
Primary source
MGI:MGI:107587
See related
Ensembl:ENSMUSG00000002325 AllianceGenome:MGI:107587
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
p48; Irf-9; Isgf3g
Summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in immune system process and regulation of transcription by RNA polymerase II. Predicted to be located in cytosol. Predicted to be active in nucleus. Is expressed in several structures, including alimentary system; central nervous system; genitourinary system; hemolymphoid system gland; and sensory organ. Human ortholog(s) of this gene implicated in immunodeficiency 65. Orthologous to human IRF9 (interferon regulatory factor 9). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in spleen adult (RPKM 24.9), thymus adult (RPKM 20.8) and 27 other tissues See more
Orthologs
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Genomic context

See Irf9 in Genome Data Viewer
Location:
14 C3; 14 28.19 cM
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 14 NC_000080.7 (55841442..55847487)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (55603985..55610030)

Chromosome 14 - NC_000080.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E5440 Neighboring gene CapStarr-seq enhancer MGSCv37_chr14:56210161-56210270 Neighboring gene proteasome (prosome, macropain) activator subunit 2 (PA28 beta) Neighboring gene ring finger protein 31 Neighboring gene CapStarr-seq enhancer MGSCv37_chr14:56222707-56223021 Neighboring gene REC8 meiotic recombination protein Neighboring gene importin 4

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Chemically induced (ENU) (1) 
  • Endonuclease-mediated (2) 
  • Targeted (1)  1 citation

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
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 ISO
Inferred from Sequence Orthology
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables sequence-specific double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables transcription cis-regulatory region binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in immune system process IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within type I interferon production IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
part_of ISGF3 complex ISO
Inferred from Sequence Orthology
more info
 
located_in cytosol ISO
Inferred from Sequence Orthology
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 

General protein information

Preferred Names
interferon regulatory factor 9
Names
IFN-alpha-responsive transcription factor subunit
ISGF-3 gamma
ISGF3 p48 subunit
interferon dependent positive acting transcription factor 3 gamma
interferon-stimulated gene factor 3 gamma
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_001159417.1NP_001152889.1  interferon regulatory factor 9 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC174678, BB860586, BY761438, CK788642, CN531811, U51992
    Consensus CDS
    CCDS49496.1
    UniProtKB/TrEMBL
    E9PZJ2
    Related
    ENSMUSP00000120525.2, ENSMUST00000134863.8
    Conserved Domains (2) summary
    pfam00605
    Location:77181
    IRF; Interferon regulatory factor transcription factor
    pfam10401
    Location:277443
    IRF-3; Interferon-regulatory factor 3
  2. NM_001159418.1NP_001152890.1  interferon regulatory factor 9 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region, compared to variant 1, resulting in an isoform (2) with a distinct and shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC174678, BY761438, U51992
    Consensus CDS
    CCDS49497.1
    UniProtKB/TrEMBL
    E9Q8M6
    Related
    ENSMUSP00000119477.2, ENSMUST00000138037.2
    Conserved Domains (2) summary
    pfam00605
    Location:29133
    IRF; Interferon regulatory factor transcription factor
    pfam10401
    Location:229395
    IRF-3; Interferon-regulatory factor 3
  3. NM_008394.3NP_032420.1  interferon regulatory factor 9 isoform 3

    See identical proteins and their annotated locations for NP_032420.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon in the 5' coding region and uses a downstream translational start codon, compared to variant 1. The resulting isoform (3) is shorter at the N-terminus, compared to isoform 1.
    Source sequence(s)
    AC174678, BY761438, CN531811, U51992
    Consensus CDS
    CCDS27119.1
    UniProtKB/Swiss-Prot
    Q61179
    UniProtKB/TrEMBL
    Q3UKQ7
    Related
    ENSMUSP00000120359.2, ENSMUST00000130697.8
    Conserved Domains (2) summary
    pfam00605
    Location:11115
    IRF; Interferon regulatory factor transcription factor
    pfam10401
    Location:212375
    IRF-3; Interferon-regulatory factor 3

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000080.7 Reference GRCm39 C57BL/6J

    Range
    55841442..55847487
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)