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    Irf5 interferon regulatory factor 5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 296953, updated on 18-Apr-2019

    Summary

    Official Symbol
    Irf5provided by RGD
    Official Full Name
    interferon regulatory factor 5provided by RGD
    Primary source
    RGD:1310447
    See related
    Ensembl:ENSRNOG00000007437
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Expression
    Biased expression in Spleen (RPKM 111.6), Thymus (RPKM 32.7) and 9 other tissues See more
    Orthologs

    Genomic context

    See Irf5 in Genome Data Viewer
    Location:
    4q22
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (56804477..56816271)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 4 NC_005103.3 (56571823..56583434)

    Chromosome 4 - NC_005103.4Genomic Context describing neighboring genes Neighboring gene ATP6V1F neighbor Neighboring gene kielin cysteine rich BMP regulator Neighboring gene transportin 3 Neighboring gene uncharacterized LOC102552812

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    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 ...
    • 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...
    • Toll-like receptor signaling pathway, organism-specific biosystem (from WikiPathways)
      Toll-like receptor signaling pathway, organism-specific biosystem
      Toll-like receptor signaling pathway

    General gene information

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    identical protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    transcription regulatory region DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    cytokine-mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    defense response to virus IEA
    Inferred from Electronic Annotation
    more info
     
    defense response to virus ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    immune system process IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    positive regulation of apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of apoptotic process ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    response to muramyl dipeptide IEA
    Inferred from Electronic Annotation
    more info
     
    response to muramyl dipeptide ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    response to peptidoglycan IEA
    Inferred from Electronic Annotation
    more info
     
    response to peptidoglycan ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    Component Evidence Code Pubs
    cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    nucleus ISO
    Inferred from Sequence Orthology
    more info
    PubMed 

    General protein information

    Preferred Names
    interferon regulatory factor 5

    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.

    mRNA and Protein(s)

    1. NM_001106586.1NP_001100056.1  interferon regulatory factor 5

      See identical proteins and their annotated locations for NP_001100056.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473959
      UniProtKB/TrEMBL
      D3ZPU1
      Related
      ENSRNOP00000010001.5, ENSRNOT00000010001.6
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:247430
      IRF-3; Interferon-regulatory factor 3

    RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

    Reference Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005103.4 Reference Rnor_6.0 Primary Assembly

      Range
      56804477..56816271
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006236183.3XP_006236245.1  interferon regulatory factor 5 isoform X2

      Conserved Domains (2) summary
      pfam00605
      Location:23128
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:258441
      IRF-3; Interferon-regulatory factor 3
    2. XM_008762765.2XP_008760987.1  interferon regulatory factor 5 isoform X3

      See identical proteins and their annotated locations for XP_008760987.1

      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:251434
      IRF-3; Interferon-regulatory factor 3
    3. XM_006236184.3XP_006236246.1  interferon regulatory factor 5 isoform X3

      See identical proteins and their annotated locations for XP_006236246.1

      Related
      ENSRNOP00000069195.1, ENSRNOT00000085483.1
      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:251434
      IRF-3; Interferon-regulatory factor 3
    4. XM_006236185.3XP_006236247.1  interferon regulatory factor 5 isoform X3

      See identical proteins and their annotated locations for XP_006236247.1

      Conserved Domains (2) summary
      pfam00605
      Location:16121
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:251434
      IRF-3; Interferon-regulatory factor 3
    5. XM_006236180.2XP_006236242.1  interferon regulatory factor 5 isoform X1

      Conserved Domains (2) summary
      pfam00605
      Location:51156
      IRF; Interferon regulatory factor transcription factor
      pfam10401
      Location:286469
      IRF-3; Interferon-regulatory factor 3

    Alternate Rn_Celera

    Genomic

    1. AC_000072.1 Alternate Rn_Celera

      Range
      53236000..53247024
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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