Format

Send to:

Choose Destination

Links from PubMed

    • Showing Current items.

    IRF5 interferon regulatory factor 5 [ Homo sapiens (human) ]

    Gene ID: 3663, updated on 25-May-2017
    Official Symbol
    IRF5provided by HGNC
    Official Full Name
    interferon regulatory factor 5provided by HGNC
    Primary source
    HGNC:HGNC:6120
    See related
    Ensembl:ENSG00000128604 MIM:607218; Vega:OTTHUMG00000158410
    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
    SLEB10
    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. Alternative promoter use and alternative splicing result in multiple transcript variants, and a 30-nt indel polymorphism (SNP rs60344245) can result in loss of a 10-aa segment. [provided by RefSeq, Dec 2016]
    Orthologs
    Location:
    7q32.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 7 NC_000007.14 (128937737..128950042)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (128577976..128590089)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375497 Neighboring gene kielin/chordin-like protein Neighboring gene filamin C pseudogene Neighboring gene transportin 3 Neighboring gene RNA, 7SL, cytoplasmic 306, pseudogene Neighboring gene ornithine decarboxylase pseudogene

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Inflammatory bowel disease 14
    MedGen: C2677100 OMIM: 612245 GeneReviews: Not available
    Compare labs
    Systemic lupus erythematosus 10
    MedGen: C2677097 OMIM: 612251 GeneReviews: Not available
    Compare labs

    NHGRI GWAS Catalog

    Description
    A genome-wide association study suggests contrasting associations in ACPA-positive versus ACPA-negative rheumatoid arthritis.
    NHGRI GWA Catalog
    A systemic sclerosis and systemic lupus erythematosus pan-meta-GWAS reveals new shared susceptibility loci.
    NHGRI GWA Catalog
    Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX.
    NHGRI GWA Catalog
    Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production.
    NHGRI GWA Catalog
    Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci.
    NHGRI GWA Catalog
    Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis.
    NHGRI GWA Catalog
    Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus.
    NHGRI GWA Catalog
    Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci.
    NHGRI GWA Catalog
    Genome-wide association study of systemic sclerosis identifies CD247 as a new susceptibility locus.
    NHGRI GWA Catalog
    Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis.
    NHGRI GWA Catalog
    Genome-wide pathway analysis of genome-wide association studies on systemic lupus erythematosus and rheumatoid arthritis.
    NHGRI GWA Catalog
    Genome-wide scan identifies TNIP1, PSORS1C1, and RHOB as novel risk loci for systemic sclerosis.
    NHGRI GWA Catalog
    GWAS identifies novel SLE susceptibility genes and explains the association of the HLA region.
    NHGRI GWA Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    NHGRI GWA Catalog
    Identification of novel genetic markers associated with clinical phenotypes of systemic sclerosis through a genome-wide association strategy.
    NHGRI GWA Catalog
    Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians.
    NHGRI GWA Catalog
    Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
    NHGRI GWA Catalog
    • 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 ...
    • 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...
    • Direct p53 effectors, organism-specific biosystem (from Pathway Interaction Database)
      Direct p53 effectors, organism-specific biosystem
      Direct p53 effectors
    • 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 ...
    • Regulation of toll-like receptor signaling pathway, organism-specific biosystem (from WikiPathways)
      Regulation of toll-like receptor signaling pathway, organism-specific biosystem
      Regulation of toll-like receptor signaling pathway
    • Senescence and Autophagy in Cancer, organism-specific biosystem (from WikiPathways)
      Senescence and Autophagy in Cancer, organism-specific biosystemSenescense and Autophagy Pathways in Cancer
    • Toll-like Receptor Signaling Pathway, organism-specific biosystem (from WikiPathways)
      Toll-like Receptor Signaling Pathway, organism-specific biosystemSpecific families of pattern recognition receptors are responsible for detecting microbial pathogens and generating innate immune responses. Toll-like receptors (TLRs) are membrane-bound receptors id...
    • Toll-like receptor signaling pathway, organism-specific biosystem (from KEGG)
      Toll-like receptor signaling pathway, organism-specific biosystemSpecific families of pattern recognition receptors are responsible for detecting microbial pathogens and generating innate immune responses. Toll-like receptors (TLRs) are membrane-bound receptors id...
    • Toll-like receptor signaling pathway, conserved biosystem (from KEGG)
      Toll-like receptor signaling pathway, conserved biosystemSpecific families of pattern recognition receptors are responsible for detecting microbial pathogens and generating innate immune responses. Toll-like receptors (TLRs) are membrane-bound receptors id...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    regulatory region DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    sequence-specific DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding IC
    Inferred by Curator
    more info
     
    Component Evidence Code Pubs
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    interferon regulatory factor 5

    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_012306.1 RefSeqGene

      Range
      4998..17103
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001098627.3NP_001092097.2  interferon regulatory factor 5 isoform b

      See identical proteins and their annotated locations for NP_001092097.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice site in the coding region, compared to variant 9. The encoded isoform (b) is shorter, compared to isoform d. Variants 2, 3, and 6 encode the same isoform.
      Source sequence(s)
      AL713733, AY504946, BC004201, CA444548, DC427600, U51127
      Consensus CDS
      CCDS5808.1
      UniProtKB/Swiss-Prot
      Q13568
      Related
      ENSP00000419149.1, OTTHUMP00000212910, ENST00000473745.5, OTTHUMT00000350942
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:248431
      IRF-3; Interferon-regulatory factor 3
    2. NM_001098629.2NP_001092099.1  interferon regulatory factor 5 isoform d

      See identical proteins and their annotated locations for NP_001092099.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, compared to variant 9. Variants 5 and 9 encode the same isoform.
      Source sequence(s)
      AK293654, AL713733, AY693665, BC004139, CA444548, U51127
      Consensus CDS
      CCDS43645.1
      UniProtKB/Swiss-Prot
      Q13568
      UniProtKB/TrEMBL
      A0A024R763, B7Z1M2
      Related
      ENSP00000349770.5, OTTHUMP00000212905, ENST00000357234.9, OTTHUMT00000350935
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:264447
      IRF-3; Interferon-regulatory factor 3
    3. NM_001098630.2NP_001092100.1  interferon regulatory factor 5 isoform b

      See identical proteins and their annotated locations for NP_001092100.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and uses an alternate in-frame splice site, compared to variant 9. The encoded isoform (b) is shorter, compared to isoform d. Variants 2, 3, and 6 encode the same isoform.
      Source sequence(s)
      AK293654, AL713733, AY693666, CA444548, U51127
      Consensus CDS
      CCDS5808.1
      UniProtKB/Swiss-Prot
      Q13568
      UniProtKB/TrEMBL
      B7Z1M2
      Related
      ENSP00000385352.2, OTTHUMP00000212904, ENST00000402030.6, OTTHUMT00000350934
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:248431
      IRF-3; Interferon-regulatory factor 3
    4. NM_001242452.2NP_001229381.1  interferon regulatory factor 5 isoform e

      See identical proteins and their annotated locations for NP_001229381.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) differs in the 5' UTR and lacks an alternate in-frame exon, compared to variant 9. The encoded isoform (e) is shorter, compared to isoform d.
      Source sequence(s)
      AK293654, AL713733, AY693666, CA444548, U51127
      Consensus CDS
      CCDS56512.1
      UniProtKB/Swiss-Prot
      Q13568
      UniProtKB/TrEMBL
      B7Z1M2
      Related
      ENSP00000419950.1, OTTHUMP00000212907, ENST00000477535.5, OTTHUMT00000350938
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:162345
      IRF-3; Interferon-regulatory factor 3
    5. NM_001347928.1NP_001334857.1  interferon regulatory factor 5 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: represents the longest transcript. Variants 5 and 9 encode the same isoform. This variant represents use of an upstream long terminal repeat (LTR) promoter and exon sequence and results in oncogenic overexpression in Hodgkin lymphoma. (PMID: 26279299)
      Source sequence(s)
      AC025594, CA444548, KP843528
      UniProtKB/Swiss-Prot
      Q13568
      UniProtKB/TrEMBL
      A0A024R763, A0A0G2USB5
    6. NM_032643.4NP_116032.1  interferon regulatory factor 5 isoform b

      See identical proteins and their annotated locations for NP_116032.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and uses an alternate in-frame splice site, compared to variant 9. The encoded isoform (b) is shorter, compared to isoform d. Variants 2, 3, and 6 encode the same isoform.
      Source sequence(s)
      AL713733, BC004139, CA444548, U51127
      Consensus CDS
      CCDS5808.1
      UniProtKB/Swiss-Prot
      Q13568
      Related
      ENSP00000249375.4, ENST00000249375.8
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:248431
      IRF-3; Interferon-regulatory factor 3

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p7 Primary Assembly

      Range
      128937737..128950042
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011516160.1XP_011514462.1  interferon regulatory factor 5 isoform X1

      See identical proteins and their annotated locations for XP_011514462.1

      UniProtKB/Swiss-Prot
      Q13568
      UniProtKB/TrEMBL
      A0A024R763
      Related
      ENSP00000418037.2, ENST00000489702.6
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:264447
      IRF-3; Interferon-regulatory factor 3
    2. XM_011516161.1XP_011514463.1  interferon regulatory factor 5 isoform X2

      See identical proteins and their annotated locations for XP_011514463.1

      UniProtKB/Swiss-Prot
      Q13568
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:254437
      IRF-3; Interferon-regulatory factor 3
    3. XM_011516162.1XP_011514464.1  interferon regulatory factor 5 isoform X3

      See identical proteins and their annotated locations for XP_011514464.1

      UniProtKB/Swiss-Prot
      Q13568
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:238421
      IRF-3; Interferon-regulatory factor 3
    4. XM_006715974.2XP_006716037.1  interferon regulatory factor 5 isoform X1

      See identical proteins and their annotated locations for XP_006716037.1

      UniProtKB/Swiss-Prot
      Q13568
      UniProtKB/TrEMBL
      A0A024R763
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:264447
      IRF-3; Interferon-regulatory factor 3
    5. XM_011516164.1XP_011514466.1  interferon regulatory factor 5 isoform X3

      See identical proteins and their annotated locations for XP_011514466.1

      UniProtKB/Swiss-Prot
      Q13568
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:238421
      IRF-3; Interferon-regulatory factor 3
    6. XM_011516158.2XP_011514460.1  interferon regulatory factor 5 isoform X1

      See identical proteins and their annotated locations for XP_011514460.1

      UniProtKB/Swiss-Prot
      Q13568
      UniProtKB/TrEMBL
      A0A024R763
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:264447
      IRF-3; Interferon-regulatory factor 3
    7. XM_011516163.2XP_011514465.1  interferon regulatory factor 5 isoform X3

      See identical proteins and their annotated locations for XP_011514465.1

      UniProtKB/Swiss-Prot
      Q13568
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:238421
      IRF-3; Interferon-regulatory factor 3
    8. XM_005250317.3XP_005250374.1  interferon regulatory factor 5 isoform X1

      See identical proteins and their annotated locations for XP_005250374.1

      UniProtKB/Swiss-Prot
      Q13568
      UniProtKB/TrEMBL
      A0A024R763
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:264447
      IRF-3; Interferon-regulatory factor 3
    9. XM_011516159.2XP_011514461.1  interferon regulatory factor 5 isoform X1

      See identical proteins and their annotated locations for XP_011514461.1

      UniProtKB/Swiss-Prot
      Q13568
      UniProtKB/TrEMBL
      A0A024R763
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:264447
      IRF-3; Interferon-regulatory factor 3

    Alternate CHM1_1.1

    Genomic

    1. NC_018918.2 Alternate CHM1_1.1

      Range
      128511263..128523404
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Support Center