Human Gene IRF8 (uc002fji.3) Description and Page Index
  Description: Homo sapiens interferon regulatory factor 8 (IRF8), mRNA.
RefSeq Summary (NM_002163): Interferon consensus sequence-binding protein (ICSBP) is a transcription factor of the interferon (IFN) regulatory factor (IRF) family. Proteins of this family are composed of a conserved DNA-binding domain in the N-terminal region and a divergent C-terminal region that serves as the regulatory domain. The IRF family proteins bind to the IFN-stimulated response element (ISRE) and regulate expression of genes stimulated by type I IFNs, namely IFN-alpha and IFN-beta. IRF family proteins also control expression of IFN-alpha and IFN-beta-regulated genes that are induced by viral infection. [provided by RefSeq, Jul 2008]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1163657.397423.1, SRR1163657.7028.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000268638.10/ ENSP00000268638.4 RefSeq Select criteria :: based on conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr16:85,936,318-85,943,486 Size: 7,169 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg19 chr16:85,936,622-85,942,802 Size: 6,181 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:85,936,318-85,943,486)mRNA (may differ from genome)Protein (126 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblExonPrimerGeneCardsGeneNetwork
HGNCLynxMGIPubMedStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: H3BVC2_HUMAN
DESCRIPTION: SubName: Full=Interferon regulatory factor 8;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): IRF8
CDC HuGE Published Literature: IRF8
Positive Disease Associations: Alkaline Phosphatase , Arthritis, Rheumatoid , Body Mass Index , Cholesterol, HDL , Chronic lymphocytic leukemia , Colitis, Ulcerative , Coronary Artery Disease , Fibrinogen , Iron , Leukemia, Lymphocytic, Chronic, B-Cell , Leukemia, Lymphoid , Liver Cirrhosis, Biliary , multiple sclerosis , Parkinson Disease , Platelet Count , Scleroderma, Systemic , Triglycerides , Tunica Media , Uric Acid
Related Studies:
  1. Alkaline Phosphatase
    Emelia J Benjamin et al. BMC medical genetics 2007, Genome-wide association with select biomarker traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903293]
    The Framingham GWAS represents a resource to describe potentially novel genetic influences on systemic biomarker variability. The newly described associations will need to be replicated in other studies.
  2. Arthritis, Rheumatoid
    Yukinori Okada et al. Nature genetics 2012, Meta-analysis identifies nine new loci associated with rheumatoid arthritis in the Japanese population., Nature genetics. [PubMed 22446963]
  3. Body Mass Index
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: IRF8
Diseases sorted by gene-association score: immunodeficiency 32a, mycobacteriosis, autosomal dominant* (1650), immunodeficiency 32b, monocyte and dendritic cell deficiency, autosomal recessive* (1300), leukemia, chronic myeloid, somatic (11), oral candidiasis (6), bone marrow cancer (2), leukemia, acute myeloid (0)
* = 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: 64.21 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 228.84 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 -116.90304-0.385 Picture PostScript Text
3' UTR -226.62684-0.331 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
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00605 - Interferon regulatory factor transcription factor

SCOP Domains:
46785 - "Winged helix" DNA-binding domain

ModBase Predicted Comparative 3D Structure on H3BVC2
FrontTopSide
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0044212 transcription regulatory region DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AK313524 - Homo sapiens cDNA, FLJ94082, highly similar to Homo sapiens interferon consensus sequence binding protein 1(ICSBP1), mRNA.
LP895330 - Sequence 194 from Patent EP3253886.
FW340063 - Screening.
BC126247 - Homo sapiens interferon regulatory factor 8, mRNA (cDNA clone MGC:161525 IMAGE:8991963), complete cds.
M91196 - Homo sapiens DNA-binding protein mRNA, complete cds.
AX721097 - Sequence 57 from Patent WO0220754.
AB463791 - Synthetic construct DNA, clone: pF1KB7715, Homo sapiens IRF8 gene for interferon regulatory factor 8, without stop codon, in Flexi system.
KJ891420 - Synthetic construct Homo sapiens clone ccsbBroadEn_00814 IRF8 gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: AX721097, H3BVC2, H3BVC2_HUMAN
UCSC ID: uc002fji.3
RefSeq Accession: NM_002163
Protein: H3BVC2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AX721097.1
exon count: 2CDS single in 3' UTR: no RNA size: 1438
ORF size: 381CDS single in intron: no Alignment % ID: 99.05
txCdsPredict score: 729.00frame shift in genome: no % Coverage: 94.85
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: 1010# 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.