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IRF4 interferon regulatory factor 4 [ Homo sapiens (human) ]

Gene ID: 3662, updated on 17-Jun-2019

Summary

Official Symbol
IRF4provided by HGNC
Official Full Name
interferon regulatory factor 4provided by HGNC
Primary source
HGNC:HGNC:6119
See related
Ensembl:ENSG00000137265 MIM:601900
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
MUM1; LSIRF; SHEP8; NF-EM5
Summary
The protein encoded by this gene belongs to the IRF (interferon regulatory factor) family of transcription factors, characterized by an unique tryptophan pentad repeat DNA-binding domain. The IRFs are important in the regulation of interferons in response to infection by virus, and in the regulation of interferon-inducible genes. This family member is lymphocyte specific and negatively regulates Toll-like-receptor (TLR) signaling that is central to the activation of innate and adaptive immune systems. A chromosomal translocation involving this gene and the IgH locus, t(6;14)(p25;q32), may be a cause of multiple myeloma. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2010]
Expression
Broad expression in lymph node (RPKM 13.5), bone marrow (RPKM 12.6) and 14 other tissues See more
Orthologs

Genomic context

See IRF4 in Genome Data Viewer
Location:
6p25.3
Exon count:
10
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (391739..411443)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (391739..411443)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723922 Neighboring gene uncharacterized LOC107986553 Neighboring gene dual specificity phosphatase 22 Neighboring gene uncharacterized LOC105374875 Neighboring gene exocyst complex component 2 Neighboring gene HUS1 checkpoint clamp component B

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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Skin/hair/eye pigmentation, variation in, 8
MedGen: C2673265 OMIM: 611724 GeneReviews: Not available
not available

NHGRI GWAS Catalog

Description
A genome-wide association study identifies multiple susceptibility loci for chronic lymphocytic leukemia.
NHGRI GWA Catalog
A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation.
NHGRI GWA Catalog
A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia.
NHGRI GWA Catalog
Common variation at 6p21.31 (BAK1) influences the risk of chronic lymphocytic leukemia.
NHGRI GWA Catalog
Genetic determinants of hair, eye and skin pigmentation in Europeans.
NHGRI GWA Catalog
Genetics of rheumatoid arthritis contributes to biology and drug discovery.
NHGRI GWA Catalog
Genome-wide association studies identify several new loci associated with pigmentation traits and skin cancer risk in European Americans.
NHGRI GWA Catalog
Genome-wide association study identifies multiple risk loci for chronic lymphocytic leukemia.
NHGRI GWA Catalog
Genome-wide association study of serum albumin:globulin ratio in Korean populations.
NHGRI GWA Catalog
Identification of common variants influencing risk of the tauopathy progressive supranuclear palsy.
NHGRI GWA Catalog
Multiple common variants for celiac disease influencing immune gene expression.
NHGRI GWA Catalog
Web-based, participant-driven studies yield novel genetic associations for common traits.
NHGRI GWA Catalog

Pathways from BioSystems

  • Apoptosis, organism-specific biosystem (from WikiPathways)
    Apoptosis, organism-specific biosystemApoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and ...
  • B Cell Receptor Signaling Pathway, organism-specific biosystem (from WikiPathways)
    B Cell Receptor Signaling Pathway, organism-specific biosystemThe functional B-cell receptor is a multi-protein complex consisting of an antigen binding subunit and a signaling subunit. The antigen binding subunit is the membrane bound immunoglobulin and the si...
  • Calcineurin-regulated NFAT-dependent transcription in lymphocytes, organism-specific biosystem (from Pathway Interaction Database)
    Calcineurin-regulated NFAT-dependent transcription in lymphocytes, organism-specific biosystem
    Calcineurin-regulated NFAT-dependent transcription in lymphocytes
  • Cytokine Signaling in Immune system, organism-specific biosystem (from REACTOME)
    Cytokine Signaling in Immune system, organism-specific biosystemCytokines are small proteins that regulate and mediate immunity, inflammation, and hematopoiesis. They are secreted in response to immune stimuli, and usually act briefly, locally, at very low concen...
  • Development of pulmonary dendritic cells and macrophage subsets, organism-specific biosystem (from WikiPathways)
    Development of pulmonary dendritic cells and macrophage subsets, organism-specific biosystemDevelopment of pulmonary DC and macrophage subsets. This model of pulmonary DC and macrophage subset differentiation in mice summarizes recent findings suggesting early lineage commitment of cDCs in ...
  • IL4-mediated signaling events, organism-specific biosystem (from Pathway Interaction Database)
    IL4-mediated signaling events, organism-specific biosystem
    IL4-mediated signaling events
  • 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...
  • Interferon Signaling, organism-specific biosystem (from REACTOME)
    Interferon Signaling, organism-specific biosystemInterferons (IFNs) are cytokines that play a central role in initiating immune responses, especially antiviral and antitumor effects. There are three types of IFNs:Type I (IFN-alpha, -beta and others...
  • Interferon alpha/beta signaling, organism-specific biosystem (from REACTOME)
    Interferon alpha/beta signaling, organism-specific biosystemType I interferons (IFNs) are composed of various genes including IFN alpha (IFNA), beta (IFNB), omega, epsilon, and kappa. In humans the IFNA genes are composed of more than 13 subfamily genes, wher...
  • Interferon gamma signaling, organism-specific biosystem (from REACTOME)
    Interferon gamma signaling, organism-specific biosystemInterferon-gamma (IFN-gamma) belongs to the type II interferon family and is secreted by activated immune cells-primarily T and NK cells, but also B-cells and APC. INFG exerts its effect on cells by ...
  • Interleukin-4 and 13 signaling, organism-specific biosystem (from REACTOME)
    Interleukin-4 and 13 signaling, organism-specific biosystemInterleukin-4 (IL4) is a principal regulatory cytokine during the immune response, crucially important in allergy and asthma (Nelms et al. 1999). When resting T cells are antigen-activated and expand...
  • Preimplantation Embryo, organism-specific biosystem (from WikiPathways)
    Preimplantation Embryo, organism-specific biosystemThe source of this pathway is RNA-Seq data from single-cell pre-implantation embryos (Supplemental Table 1): http://www.nature.com/nsmb/journal/v20/n9/full/nsmb.2660.html Analysis options for runnin...
  • Signaling by Interleukins, organism-specific biosystem (from REACTOME)
    Signaling by Interleukins, organism-specific biosystemInterleukins are low molecular weight proteins that bind to cell surface receptors and act in an autocrine and/or paracrine fashion. They were first identified as factors produced by leukocytes but a...
  • T-Cell antigen Receptor (TCR) Signaling Pathway, organism-specific biosystem (from WikiPathways)
    T-Cell antigen Receptor (TCR) Signaling Pathway, organism-specific biosystemThe T-cell antigen receptor (TCR) complex is composed of a ligand-binding subunit, the ? and ? chains, and a signaling subunit, namely the CD3?, ? and ? chains and the TCR? chain. This complex partic...
  • Th17 cell differentiation, organism-specific biosystem (from KEGG)
    Th17 cell differentiation, organism-specific biosystemInterleukin (IL)-17-producing helper T (Th17) cells serve as a subset of CD4+ T cells involved in epithelial cell- and neutrophil mediated immune responses against extracellular microbes and in the p...
  • Th17 cell differentiation, conserved biosystem (from KEGG)
    Th17 cell differentiation, conserved biosystemInterleukin (IL)-17-producing helper T (Th17) cells serve as a subset of CD4+ T cells involved in epithelial cell- and neutrophil mediated immune responses against extracellular microbes and in the p...
  • Type II interferon signaling (IFNG), organism-specific biosystem (from WikiPathways)
    Type II interferon signaling (IFNG), organism-specific biosystemAdapted from Raza et al. (2008). This pathway is initiated by IFNG binding to its receptor and a subsequent phosphorylation cascade involving a number of the JAK and STAT family of proteins. Several ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
T cell activation NAS
Non-traceable Author Statement
more info
PubMed 
T-helper 17 cell lineage commitment ISS
Inferred from Sequence or Structural Similarity
more info
 
cytokine-mediated signaling pathway TAS
Traceable Author Statement
more info
 
defense response to protozoan ISS
Inferred from Sequence or Structural Similarity
more info
 
histone H3 acetylation IEA
Inferred from Electronic Annotation
more info
 
histone H4 acetylation IEA
Inferred from Electronic Annotation
more info
 
immune system process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
interferon-gamma-mediated signaling pathway TAS
Traceable Author Statement
more info
 
myeloid dendritic cell differentiation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of toll-like receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
positive regulation of DNA binding IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cold-induced thermogenesis ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
positive regulation of interleukin-10 biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interleukin-13 biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interleukin-2 biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interleukin-4 biosynthetic process 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, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
regulation of T-helper cell differentiation NAS
Non-traceable Author Statement
more info
PubMed 
type I interferon signaling pathway TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cytosol TAS
Traceable Author Statement
more info
 
membrane HDA PubMed 
nuclear nucleosome IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IC
Inferred by Curator
more info
PubMed 

General protein information

Preferred Names
interferon regulatory factor 4
Names
lymphocyte-specific interferon regulatory factor
multiple myeloma oncogene 1

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_027728.1 RefSeqGene

    Range
    5001..24705
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001195286.2NP_001182215.1  interferon regulatory factor 4 isoform 2

    See identical proteins and their annotated locations for NP_001182215.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame acceptor splice site at an internal coding exon compared to variant 1, resulting in an isoform (2) that is 1 aa shorter than isoform 1.
    Source sequence(s)
    AL512308, AL589962, AW197089, BG230623, BM551611, KF458069, U52682, U63738
    UniProtKB/Swiss-Prot
    Q15306
    Conserved Domains (2) summary
    pfam00605
    Location:23128
    IRF; Interferon regulatory factor transcription factor
    pfam10401
    Location:249417
    IRF-3; Interferon-regulatory factor 3
  2. NM_002460.4NP_002451.2  interferon regulatory factor 4 isoform 1

    See identical proteins and their annotated locations for NP_002451.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AL512308, AL589962, AW197089, BC015752, BG230623, BM551611, KF458069, U52682, U63738
    Consensus CDS
    CCDS4469.1
    UniProtKB/Swiss-Prot
    Q15306
    Related
    ENSP00000370343.4, ENST00000380956.9
    Conserved Domains (2) summary
    pfam00605
    Location:23128
    IRF; Interferon regulatory factor transcription factor
    pfam10401
    Location:250418
    IRF-3; Interferon-regulatory factor 3

RNA

  1. NR_046000.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an alternate 3' splice pattern, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL512308, AL589962, AW197089, D78261, KF458069, U52682

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    391739..411443
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006715090.2XP_006715153.1  interferon regulatory factor 4 isoform X1

    See identical proteins and their annotated locations for XP_006715153.1

    Conserved Domains (2) summary
    pfam00605
    Location:23128
    IRF; Interferon regulatory factor transcription factor
    pfam10401
    Location:214382
    IRF-3; Interferon-regulatory factor 3

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NR_036585.1: Suppressed sequence

    Description
    NR_036585.1: This RefSeq was permanently suppressed because currently there is support for the transcript.
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