Human Gene IRF5 (ENST00000402030.6) from GENCODE V44
  Description: Homo sapiens interferon regulatory factor 5 (IRF5), transcript variant 2, mRNA. (from RefSeq NM_032643)
RefSeq Summary (NM_001098630): 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].
Gencode Transcript: ENST00000402030.6
Gencode Gene: ENSG00000128604.21
Transcript (Including UTRs)
   Position: hg38 chr7:128,937,989-128,950,035 Size: 12,047 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg38 chr7:128,942,082-128,948,818 Size: 6,737 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:128,937,989-128,950,035)mRNA (may differ from genome)Protein (498 aa)
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-  Comments and Description Text from UniProtKB
  ID: IRF5_HUMAN
DESCRIPTION: RecName: Full=Interferon regulatory factor 5; Short=IRF-5;
FUNCTION: Transcription factor involved in the induction of interferons IFNA and INFB and inflammatory cytokines upon virus infection. Activated by TLR7 or TLR8 signaling.
SUBUNIT: Homodimer, when phosphorylated.
INTERACTION: Q7Z434:MAVS; NbExp=2; IntAct=EBI-3931258, EBI-995373; O43765:SGTA; NbExp=3; IntAct=EBI-3931258, EBI-347996;
SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Shuttles between the nucleus and the cytoplasm.
PTM: Phosphorylation of serine and threonine residues in a C- terminal autoinhibitory region, stimulates dimerization, transport into the nucleus, assembly with the coactivator CBP/p300 and initiation of transcription.
PTM: 'Lys-63'-linked polyubiquitination by TRAF6 is required for activation.
DISEASE: Genetic variations in IRF5 are associated with susceptibility to inflammatory bowel disease type 14 (IBD14) [MIM:612245]. IBD14 is a chronic, relapsing inflammation of the gastrointestinal tract with a complex etiology. It is subdivided into Crohn disease and ulcerative colitis phenotypes. Crohn disease may affect any part of the gastrointestinal tract from the mouth to the anus, but most frequently it involves the terminal ileum and colon. Bowel inflammation is transmural and discontinuous; it may contain granulomas or be associated with intestinal or perianal fistulas. In contrast, in ulcerative colitis, the inflammation is continuous and limited to rectal and colonic mucosal layers; fistulas and granulomas are not observed. Both diseases include extraintestinal inflammation of the skin, eyes, or joints.
DISEASE: Genetic variations in IRF5 are associated with susceptibility to systemic lupus erythematosus type 10 (SLEB10) [MIM:612251]. Systemic lupus erythematosus (SLE) is a chronic, inflammatory and often febrile multisystemic disorder of connective tissue. It affects principally the skin, joints, kidneys and serosal membranes. It is thought to represent a failure of the regulatory mechanisms of the autoimmune system.
DISEASE: Genetic variations in IRF5 are a cause of susceptibility to rheumatoid arthritis (RA) [MIM:180300]. It is a systemic inflammatory disease with autoimmune features and a complex genetic component. It primarily affects the joints and is characterized by inflammatory changes in the synovial membranes and articular structures, widespread fibrinoid degeneration of the collagen fibers in mesenchymal tissues, and by atrophy and rarefaction of bony structures.
SIMILARITY: Belongs to the IRF family.
SIMILARITY: Contains 1 IRF tryptophan pentad repeat DNA-binding domain.

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

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-  MalaCards Disease Associations
  MalaCards Gene Search: IRF5
Diseases sorted by gene-association score: systemic lupus erythematosus 10* (594), inflammatory bowel disease 14* (569), diffuse cutaneous systemic sclerosis* (43), primary biliary cholangitis* (18), limited scleroderma* (14), crohn's disease (9), macrophage activation syndrome (9), systemic lupus erythematosus (8), splenic marginal zone lymphoma (6), rheumatoid arthritis (5), epstein-barr virus-associated gastric carcinoma (5), lupus erythematosus (5), ulcerative colitis (4), colitis (4), hypersensitivity reaction type ii disease (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 49.78 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 197.80 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -28.5072-0.396 Picture PostScript Text
3' UTR -454.001217-0.373 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR019817 - Interferon_reg_fac_CS
IPR001346 - Interferon_reg_fact_DNA-bd_dom
IPR019471 - Interferon_reg_factor-3
IPR017855 - SMAD_dom-like
IPR008984 - SMAD_FHA_domain
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00605 - Interferon regulatory factor transcription factor
PF10401 - Interferon-regulatory factor 3

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3DSH - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q13568
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0042802 identical protein binding
GO:0043565 sequence-specific DNA binding
GO:0044212 transcription regulatory region DNA binding

Biological Process:
GO:0002376 immune system process
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0019221 cytokine-mediated signaling pathway
GO:0032494 response to peptidoglycan
GO:0032495 response to muramyl dipeptide
GO:0032727 positive regulation of interferon-alpha production
GO:0032728 positive regulation of interferon-beta production
GO:0032735 positive regulation of interleukin-12 production
GO:0043065 positive regulation of apoptotic process
GO:0045087 innate immune response
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0051607 defense response to virus
GO:0060333 interferon-gamma-mediated signaling pathway
GO:0060337 type I interferon signaling pathway

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  KP843529 - UNVERIFIED: Homo sapiens isolate LTR-TSS-1 interferon regulatory factor 5-like (IRF5) mRNA, partial sequence.
KP843530 - Homo sapiens isolate LTR-TSS-2 interferon regulatory factor 5 (IRF5) mRNA, partial cds.
KP843531 - UNVERIFIED: Homo sapiens isolate LTR-TSS-3 interferon regulatory factor 5-like (IRF5) mRNA, partial sequence.
KP843532 - Homo sapiens isolate LTR-TSS-4 interferon regulatory factor 5 (IRF5) mRNA, partial cds.
KP843533 - Homo sapiens isolate LTR-TSS-5 interferon regulatory factor 5 (IRF5) mRNA, partial cds.
KP843527 - Homo sapiens isolate LTR-1 interferon regulatory factor 5 (IRF5) mRNA, partial cds.
KP843528 - Homo sapiens isolate LTR-2 interferon regulatory factor 5 (IRF5) mRNA, partial cds.
KP843534 - Homo sapiens isolate L2-TSS-1 interferon regulatory factor 5 (IRF5) mRNA, partial cds.
LF212014 - JP 2014500723-A/19517: Polycomb-Associated Non-Coding RNAs.
MA447591 - JP 2018138019-A/19517: Polycomb-Associated Non-Coding RNAs.
KP843535 - Homo sapiens isolate E-TSS-1 interferon regulatory factor 5 (IRF5) mRNA, partial cds.
KP843536 - Homo sapiens isolate D-TSS-1 interferon regulatory factor 5 (IRF5) mRNA, partial cds.
EU258897 - Homo sapiens clone HMR5L6 IRF-5 variant 12 mRNA, partial cds, alternatively spliced.
LF207060 - JP 2014500723-A/14563: Polycomb-Associated Non-Coding RNAs.
MA442637 - JP 2018138019-A/14563: Polycomb-Associated Non-Coding RNAs.
KP843537 - Homo sapiens isolate A-TSS-1 interferon regulatory factor 5 (IRF5) mRNA, partial cds.
KP843538 - Homo sapiens isolate A-TSS-2 interferon regulatory factor 5 (IRF5) mRNA, partial cds.
AK293654 - Homo sapiens cDNA FLJ53720 complete cds, highly similar to Interferon regulatory factor 5.
AY693665 - Homo sapiens interferon regulatory factor 5 variant 5 (IRF5) mRNA, complete cds, alternatively spliced.
AY693668 - Homo sapiens interferon regulatory factor 5 variant 8 (IRF5) mRNA, complete cds, alternatively spliced.
DQ995492 - Homo sapiens IRF5 mRNA, exon 1A and 5' UTR.
U51127 - Human interferon regulatory factor 5 (Humirf5) mRNA, complete cds.
KP843539 - Homo sapiens isolate A-TSS-3 interferon regulatory factor 5 (IRF5) mRNA, partial cds.
AK297083 - Homo sapiens cDNA FLJ60671 complete cds, highly similar to Interferon regulatory factor 5.
AY504947 - Homo sapiens interferon regulatory factor 5 variant 4 (IRF5) mRNA, complete cds, alternatively spliced.
AY693666 - Homo sapiens interferon regulatory factor 5 variant 6 (IRF5) mRNA, complete cds, alternatively spliced.
KP843540 - Homo sapiens isolate A-TSS-4 interferon regulatory factor 5 (IRF5) mRNA, partial cds.
KP843541 - Homo sapiens isolate A-TSS-5 interferon regulatory factor 5 (IRF5) mRNA, partial cds.
AY693667 - Homo sapiens interferon regulatory factor 5 variant 7 (IRF5) mRNA, complete cds, alternatively spliced.
KP843542 - Homo sapiens isolate A-TSS-6 interferon regulatory factor 5 (IRF5) mRNA, partial cds.
EU258896 - Homo sapiens clone HMR5L4 IRF-5 variant 12 mRNA, partial cds, alternatively spliced.
AY693669 - Homo sapiens interferon regulatory factor 5 variant 9 (IRF5) mRNA, complete cds, alternatively spliced.
BC004139 - Homo sapiens interferon regulatory factor 5, mRNA (cDNA clone MGC:1715 IMAGE:2963923), complete cds.
BC004201 - Homo sapiens interferon regulatory factor 5, mRNA (cDNA clone MGC:3698 IMAGE:2963923), complete cds.
DQ277633 - Homo sapiens interferon regulatory factor 5 variant 10 (IRF5) mRNA, complete cds, alternatively spliced.
KP843543 - Homo sapiens isolate F-TSS-1 interferon regulatory factor 5 (IRF5) mRNA, partial cds.
KP843544 - Homo sapiens isolate F-TSS-2 interferon regulatory factor 5 (IRF5) mRNA, partial cds.
EU258898 - Homo sapiens clone HMR5U4 IRF-5 variant 12 mRNA, partial cds, alternatively spliced.
DQ277634 - Homo sapiens interferon regulatory factor 5 variant 11 (IRF5) mRNA, complete cds, alternatively spliced.
AY504946 - Homo sapiens interferon regulatory factor 5 variant 3 (IRF5) mRNA, complete cds, alternatively spliced.
KP843545 - Homo sapiens isolate G-TSS-1 interferon regulatory factor 5 (IRF5) mRNA, partial cds.
AB527523 - Synthetic construct DNA, clone: pF1KB5925, Homo sapiens IRF5 gene for interferon regulatory factor 5, without stop codon, in Flexi system.
EU176684 - Synthetic construct Homo sapiens clone IMAGE:100011482; FLH184894.01L; RZPDo839D01145D interferon regulatory factor 5 (IRF5) gene, encodes complete protein.
DQ893637 - Synthetic construct clone IMAGE:100006267; FLH184898.01X; RZPDo839D01146D interferon regulatory factor 5 (IRF5) gene, encodes complete protein.
CU678588 - Synthetic construct Homo sapiens gateway clone IMAGE:100019684 5' read IRF5 mRNA.
KJ891487 - Synthetic construct Homo sapiens clone ccsbBroadEn_00881 IRF5 gene, encodes complete protein.
JQ950681 - Homo sapiens interferon regulatory factor 5 transcript variant 13 (IRF5) mRNA, exons 2 through 5 and partial cds, alternatively spliced.
EU258895 - Homo sapiens clone HMJ9V2 IRF-5 variant 12 mRNA, partial cds, alternatively spliced.
JQ950683 - Homo sapiens interferon regulatory factor 5 transcript variant 15 (IRF5) mRNA, exons 2, 3, 6, 7 and partial cds, alternatively spliced.
JQ950684 - Homo sapiens interferon regulatory factor 5 transcript variant 16 (IRF5) mRNA, exons 2, 3, 6 and partial cds, alternatively spliced.
JQ950682 - Homo sapiens interferon regulatory factor 5 transcript variant 14 (IRF5) mRNA, exons 3 through 5 and partial cds, alternatively spliced.
JQ950685 - Homo sapiens interferon regulatory factor 5 transcript variant 17 (IRF5) mRNA, exons 4 through 6 and partial cds, alternatively spliced.
JD535081 - Sequence 516105 from Patent EP1572962.
JD475851 - Sequence 456875 from Patent EP1572962.
JD401388 - Sequence 382412 from Patent EP1572962.
JD545333 - Sequence 526357 from Patent EP1572962.
JD565702 - Sequence 546726 from Patent EP1572962.
JD042741 - Sequence 23765 from Patent EP1572962.
JD339643 - Sequence 320667 from Patent EP1572962.
JD195350 - Sequence 176374 from Patent EP1572962.
JD125866 - Sequence 106890 from Patent EP1572962.
JD492551 - Sequence 473575 from Patent EP1572962.
JD334990 - Sequence 316014 from Patent EP1572962.
JD434663 - Sequence 415687 from Patent EP1572962.
JD280937 - Sequence 261961 from Patent EP1572962.
AL713733 - Homo sapiens mRNA; cDNA DKFZp667H0110 (from clone DKFZp667H0110).
JD229233 - Sequence 210257 from Patent EP1572962.
JD526693 - Sequence 507717 from Patent EP1572962.
JD210930 - Sequence 191954 from Patent EP1572962.
JD555126 - Sequence 536150 from Patent EP1572962.
JD564552 - Sequence 545576 from Patent EP1572962.
JD330048 - Sequence 311072 from Patent EP1572962.
JD110643 - Sequence 91667 from Patent EP1572962.
JD158590 - Sequence 139614 from Patent EP1572962.
JD366170 - Sequence 347194 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04620 - Toll-like receptor signaling pathway

BioCarta from NCI Cancer Genome Anatomy Project
h_pcafpathway - The information-processing pathway at the IFN-beta enhancer

Reactome (by CSHL, EBI, and GO)

Protein Q13568 (Reactome details) participates in the following event(s):

R-HSA-909733 Interferon alpha/beta signaling
R-HSA-877300 Interferon gamma signaling
R-HSA-913531 Interferon Signaling
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: A4D1J8, A8DUA8, A8DUA9, E7EQ16, ENST00000402030.1, ENST00000402030.2, ENST00000402030.3, ENST00000402030.4, ENST00000402030.5, IRF5_HUMAN, NM_032643, Q13568, Q64GB1, Q64GB2, Q6RCM8, Q9BQF0, uc003voh.1, uc003voh.2, uc003voh.3, uc003voh.4
UCSC ID: ENST00000402030.6
RefSeq Accession: NM_001098630
Protein: Q13568 (aka IRF5_HUMAN)
CCDS: CCDS5808.1, CCDS43645.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.