Human Gene IRF5 (uc010llr.1)
Description: Homo sapiens interferon regulatory factor 5 (IRF5), transcript variant 2, mRNA.
RefSeq Summary (NM_001242452): 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 chr7:128,577,769-128,587,589 Size: 9,821 Total Exon Count: 5 Strand: +
Coding Region
Position: hg19 chr7:128,582,136-128,587,568 Size: 5,433 Coding Exon Count: 4
Data last updated at UCSC: 2013-06-14
Sequence and Links to Tools and Databases
Primer design for this transcript
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: 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 ]
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.
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 ]
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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)
Common Gene Haplotype Alleles
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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
Microarray Expression Data
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mRNA Secondary Structure of 3' and 5' UTRs
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 IPR001346 - Interferon_reg_fact_DNA-bd_dom
IPR011991 - WHTH_trsnscrt_rep_DNA-bd
Pfam Domains: PF00605 - Interferon regulatory factor transcription factor
PF13885 - Keratin, high sulfur B2 protein
SCOP Domains: 46785 - "Winged helix" DNA-binding domain
ModBase Predicted Comparative 3D Structure on A9LSF3
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.
Mouse Rat Zebrafish D. melanogaster C. elegans S. cerevisiae
No ortholog No ortholog No ortholog No ortholog No ortholog No ortholog
Gene Details
Gene Sorter
Gene Ontology (GO) Annotations with Structured Vocabulary
Molecular Function: GO:0003677 DNA binding
GO:0044212 transcription regulatory region DNA binding
Biological Process: GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0019221 cytokine-mediated signaling pathway
GO:0051607 defense response to virus
Cellular Component: GO:0005634 nucleus
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.DQ995491 - Homo sapiens IRF5 mRNA, exon 1D and 5' UTR.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.
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
Other Names for This Gene
Alternate Gene Symbols: A9LSF3, A9LSF3_HUMAN, EU258897, NM_001242452, NP_001229381UCSC ID: uc010llr.1RefSeq Accession: NM_001242452
Protein: A9LSF3
Gene Model Information
category:
coding
nonsense-mediated-decay:
no
RNA accession:
EU258897.1
exon count:
5 CDS single in 3' UTR:
no
RNA size:
596
ORF size:
684 CDS single in intron:
no
Alignment % ID:
100.00
txCdsPredict score:
1523.00 frame shift in genome:
no
% Coverage:
100.00
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
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Methods, Credits, and Use Restrictions
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for details on how this gene model was made and data restrictions if any.