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

    Gene ID: 3663, updated on 8-Jul-2021

    Summary

    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
    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]
    Expression
    Broad expression in spleen (RPKM 8.6), lymph node (RPKM 6.5) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See IRF5 in Genome Data Viewer
    Location:
    7q32.1
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 7 NC_000007.14 (128937032..128950038)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (128577086..128590092)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene filamin C pseudogene Neighboring gene Sharpr-MPRA regulatory region 2205 Neighboring gene transportin 3 Neighboring gene RNA, 7SL, cytoplasmic 306, pseudogene Neighboring gene ornithine decarboxylase pseudogene

    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 Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    A genome-wide association study suggests contrasting associations in ACPA-positive versus ACPA-negative rheumatoid arthritis.
    GeneReviews: Not available
    A systemic sclerosis and systemic lupus erythematosus pan-meta-GWAS reveals new shared susceptibility loci.
    GeneReviews: Not available
    Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX.
    GeneReviews: Not available
    Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production.
    GeneReviews: Not available
    Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci.
    GeneReviews: Not available
    Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis.
    GeneReviews: Not available
    Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus.
    GeneReviews: Not available
    Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci.
    GeneReviews: Not available
    Genome-wide association study of systemic sclerosis identifies CD247 as a new susceptibility locus.
    GeneReviews: Not available
    Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis.
    GeneReviews: Not available
    Genome-wide pathway analysis of genome-wide association studies on systemic lupus erythematosus and rheumatoid arthritis.
    GeneReviews: Not available
    Genome-wide scan identifies TNIP1, PSORS1C1, and RHOB as novel risk loci for systemic sclerosis.
    GeneReviews: Not available
    GWAS identifies novel SLE susceptibility genes and explains the association of the HLA region.
    GeneReviews: Not available
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    GeneReviews: Not available
    Identification of novel genetic markers associated with clinical phenotypes of systemic sclerosis through a genome-wide association strategy.
    GeneReviews: Not available
    Inflammatory bowel disease 14
    MedGen: C2677100 OMIM: 612245 GeneReviews: Not available
    Compare labs
    Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians.
    GeneReviews: Not available
    Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
    GeneReviews: Not available
    Systemic lupus erythematosus 10
    MedGen: C2677097 OMIM: 612251 GeneReviews: Not available
    Compare labs

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    interferon regulatory factor 5

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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
      4988..17099
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001098627.4NP_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, ENST00000473745.5
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:248431
      IRF-3; Interferon-regulatory factor 3
    2. NM_001098629.3NP_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)
      AC025594, AK293654, AL713733, AY693665, BC004139, CA444548, U51127
      Consensus CDS
      CCDS43645.1
      UniProtKB/Swiss-Prot
      Q13568
      UniProtKB/TrEMBL
      B7Z1M2, C9JAU6
      Related
      ENSP00000349770.5, ENST00000357234.10
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:264447
      IRF-3; Interferon-regulatory factor 3
    3. NM_001098630.3NP_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)
      AC025594, AK293654, AL713733, AY693666, CA444548, U51127
      Consensus CDS
      CCDS5808.1
      UniProtKB/Swiss-Prot
      Q13568
      UniProtKB/TrEMBL
      B7Z1M2
      Related
      ENSP00000385352.2, ENST00000402030.6
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:248431
      IRF-3; Interferon-regulatory factor 3
    4. NM_001242452.3NP_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)
      AC025594, AK293654, AL713733, AY693666, CA444548, U51127
      Consensus CDS
      CCDS56512.1
      UniProtKB/Swiss-Prot
      Q13568
      UniProtKB/TrEMBL
      B7Z1M2
      Related
      ENSP00000419950.1, ENST00000477535.5
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:162345
      IRF-3; Interferon-regulatory factor 3
    5. NM_001347928.2NP_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
      Consensus CDS
      CCDS43645.1
      UniProtKB/Swiss-Prot
      Q13568
      UniProtKB/TrEMBL
      A0A0G2USB5, C9JAU6
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:264447
      IRF-3; Interferon-regulatory factor 3
    6. NM_001364314.2NP_001351243.1  interferon regulatory factor 5 isoform d

      Status: REVIEWED

      Source sequence(s)
      AC025594
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:264447
      IRF-3; Interferon-regulatory factor 3
    7. NM_032643.5NP_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 Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p13 Primary Assembly

      Range
      128937032..128950038
      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
      C9JAU6
      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_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
      C9JAU6
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:264447
      IRF-3; Interferon-regulatory factor 3
    3. XM_011516158.3XP_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
      C9JAU6
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:264447
      IRF-3; Interferon-regulatory factor 3
    4. XM_011516159.3XP_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
      C9JAU6
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:264447
      IRF-3; Interferon-regulatory factor 3
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