Human Gene IRF5 (uc003vog.3)
  Description: Homo sapiens interferon regulatory factor 5 (IRF5), transcript variant 5, mRNA.
RefSeq Summary (NM_001098629): 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].
Transcript (Including UTRs)
   Position: hg19 chr7:128,577,994-128,590,088 Size: 12,095 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr7:128,582,136-128,588,872 Size: 6,737 Coding Exon Count: 8 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:128,577,994-128,590,088)mRNA (may differ from genome)Protein (514 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDLynxMalacardsMGI
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): IRF5
CDC HuGE Published Literature: IRF5
Positive Disease Associations: Arthritis, Rheumatoid , Arthritis, Rheumatoid| , Autoimmune Diseases|Lupus Erythematosus, Systemic|Systemic lupus erythematosus , Liver Cirrhosis, Biliary , lupus erythematosus , Lupus Erythematosus, Systemic , rheumatoid arthritis , Scleroderma, Systemic , Scleroderma, Systemic|Systemic Scleroderma , Sclerosis , systemic lupus erythematosus , Wegener's granulomatosis- reduced risk
Related Studies:
  1. Arthritis, Rheumatoid
    Eli A Stahl et al. Nature genetics 2010, Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci., Nature genetics. [PubMed 20453842]
  2. Arthritis, Rheumatoid|
    K Shimane , et al. Annals of the rheumatic diseases 2009 68(3):377-83, A single nucleotide polymorphism in the IRF5 promoter region is associated with susceptibility to rheumatoid arthritis in the Japanese population., Annals of the rheumatic diseases 2009 68(3):377-83. [PubMed 18408250]
    These findings indicate that the promoter polymorphism of IRF5 is a genetic factor conferring predisposition to RA, and that it contributes considerably to disease pathogenesis in patients that were SE negative.
  3. Autoimmune Diseases|Lupus Erythematosus, Systemic|Systemic lupus erythematosus
    Budarf ML et al. 2011, A targeted association study in systemic lupus erythematosus identifies multiple susceptibility alleles., Genes and immunity 12(1) : 51-8 2011. [PubMed 20962850]
           more ... click here to view the complete list

-  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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  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 -56.60121-0.468 Picture PostScript Text
3' UTR -466.691216-0.384 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
  Pfam Domains:
PF00605 - Interferon regulatory factor transcription factor
PF10401 - Interferon-regulatory factor 3

SCOP Domains:
46785 - "Winged helix" DNA-binding domain
49879 - SMAD/FHA domain

ModBase Predicted Comparative 3D Structure on Q13568-2
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  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.
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.
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.
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.
MA442637 - JP 2018138019-A/14563: Polycomb-Associated Non-Coding RNAs.
LF212014 - JP 2014500723-A/19517: Polycomb-Associated Non-Coding RNAs.
DQ995492 - Homo sapiens IRF5 mRNA, exon 1A and 5' UTR.
JD179915 - Sequence 160939 from Patent EP1572962.
MA447591 - JP 2018138019-A/19517: Polycomb-Associated Non-Coding RNAs.
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: NM_001098629, NP_001092099, Q13568-2
UCSC ID: uc003vog.3
RefSeq Accession: NM_001098629
Protein: Q13568-2, splice isoform of Q13568 CCDS: CCDS5808.1, CCDS43645.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001098629.1
exon count: 9CDS single in 3' UTR: no RNA size: 2900
ORF size: 1545CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3245.00frame shift in genome: no % Coverage: 99.38
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

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