Human Gene IRF1 (ENST00000245414.9_9) from GENCODE V47lift37
  Description: interferon regulatory factor 1, transcript variant 1 (from RefSeq NM_002198.3)
Gencode Transcript: ENST00000245414.9_9
Gencode Gene: ENSG00000125347.15_21
Transcript (Including UTRs)
   Position: hg19 chr5:131,817,301-131,826,465 Size: 9,165 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg19 chr5:131,819,643-131,825,170 Size: 5,528 Coding Exon Count: 9 

Page IndexSequence and LinksPrimersMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:131,817,301-131,826,465)mRNA (may differ from genome)Protein (325 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
BioGrid 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


-  MalaCards Disease Associations
  MalaCards Gene Search: IRF1
Diseases sorted by gene-association score: gastric cancer, somatic* (694), lung cancer* (306), stomach cancer* (151), fanconi anemia, complementation group c (13), celiac disease (9), panencephalitis, subacute sclerosing (9), venezuelan equine encephalitis (9), myelodysplastic syndrome (9), respiratory syncytial virus infectious disease (6), viral infectious disease (2), malaria (2), leukemia, acute promyelocytic, somatic (2), fanconi anemia, complementation group a (1)
* = 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: 58.05 RPKM in Whole Blood
Total median expression: 443.27 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 -83.10234-0.355 Picture PostScript Text
3' UTR -887.602342-0.379 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
IPR017431 - Interferon_reg_fac-1/2
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 Q6FHN8
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0043565 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
GO:0006915 apoptotic process
GO:0008285 negative regulation of cell proliferation
GO:0010468 regulation of gene expression
GO:0032481 positive regulation of type I interferon production
GO:0034124 regulation of MyD88-dependent toll-like receptor signaling pathway
GO:0043374 CD8-positive, alpha-beta T cell differentiation
GO:0045084 positive regulation of interleukin-12 biosynthetic process
GO:0045590 negative regulation of regulatory T cell differentiation
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0050776 regulation of immune response
GO:0051607 defense response to virus
GO:0060333 interferon-gamma-mediated signaling pathway
GO:2000564 regulation of CD8-positive, alpha-beta T cell proliferation

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AK298770 - Homo sapiens cDNA FLJ52019 complete cds, moderately similar to Interferon regulatory factor 1.
JD366623 - Sequence 347647 from Patent EP1572962.
JD366624 - Sequence 347648 from Patent EP1572962.
JD534855 - Sequence 515879 from Patent EP1572962.
JD292587 - Sequence 273611 from Patent EP1572962.
JD155924 - Sequence 136948 from Patent EP1572962.
JD106014 - Sequence 87038 from Patent EP1572962.
JD517826 - Sequence 498850 from Patent EP1572962.
JD447184 - Sequence 428208 from Patent EP1572962.
JD364479 - Sequence 345503 from Patent EP1572962.
JD139766 - Sequence 120790 from Patent EP1572962.
JD451468 - Sequence 432492 from Patent EP1572962.
JD522711 - Sequence 503735 from Patent EP1572962.
JD351535 - Sequence 332559 from Patent EP1572962.
JD515192 - Sequence 496216 from Patent EP1572962.
JD148346 - Sequence 129370 from Patent EP1572962.
JD249916 - Sequence 230940 from Patent EP1572962.
JD249915 - Sequence 230939 from Patent EP1572962.
JD127746 - Sequence 108770 from Patent EP1572962.
JD179696 - Sequence 160720 from Patent EP1572962.
JD561347 - Sequence 542371 from Patent EP1572962.
JD561346 - Sequence 542370 from Patent EP1572962.
JD101922 - Sequence 82946 from Patent EP1572962.
JD185863 - Sequence 166887 from Patent EP1572962.
JD481354 - Sequence 462378 from Patent EP1572962.
JD481355 - Sequence 462379 from Patent EP1572962.
JD101923 - Sequence 82947 from Patent EP1572962.
JD101924 - Sequence 82948 from Patent EP1572962.
JD185864 - Sequence 166888 from Patent EP1572962.
AB209624 - Homo sapiens mRNA for interferon regulatory factor 1 variant protein.
BC009483 - Homo sapiens interferon regulatory factor 1, mRNA (cDNA clone MGC:15355 IMAGE:3623414), complete cds.
X14454 - Human mRNA for interferon regulatory factor 1.
JD336144 - Sequence 317168 from Patent EP1572962.
JD389412 - Sequence 370436 from Patent EP1572962.
JD262011 - Sequence 243035 from Patent EP1572962.
JD448857 - Sequence 429881 from Patent EP1572962.
JD042097 - Sequence 23121 from Patent EP1572962.
JD417534 - Sequence 398558 from Patent EP1572962.
JD414140 - Sequence 395164 from Patent EP1572962.
JD131712 - Sequence 112736 from Patent EP1572962.
JD131654 - Sequence 112678 from Patent EP1572962.
JD087717 - Sequence 68741 from Patent EP1572962.
JD071526 - Sequence 52550 from Patent EP1572962.
JD117745 - Sequence 98769 from Patent EP1572962.
JD215475 - Sequence 196499 from Patent EP1572962.
JD515513 - Sequence 496537 from Patent EP1572962.
JD223451 - Sequence 204475 from Patent EP1572962.
JD109306 - Sequence 90330 from Patent EP1572962.
JD515372 - Sequence 496396 from Patent EP1572962.
JD123471 - Sequence 104495 from Patent EP1572962.
JD371014 - Sequence 352038 from Patent EP1572962.
KJ200632 - Homo sapiens interferon regulatory factor 1 isoform +I9 (IRF-1) mRNA, complete cds, alternatively spliced.
KJ200633 - Homo sapiens interferon regulatory factor 1 isoform delta4 (IRF-1) mRNA, complete cds, alternatively spliced.
KJ200634 - Homo sapiens interferon regulatory factor 1 isoform delta7 (IRF-1) mRNA, complete cds, alternatively spliced.
KJ200635 - Homo sapiens nonfunctional interferon regulatory factor 1 isoform d1-8 +I8 (IRF-1) mRNA, complete sequence, alternatively spliced.
KU561832 - Homo sapiens interferon regulatory factor 1 isoform d9,10+ (IRF1) mRNA, partial cds, alternatively spliced.
JD221787 - Sequence 202811 from Patent EP1572962.
JD274004 - Sequence 255028 from Patent EP1572962.
BT019755 - Homo sapiens interferon regulatory factor 1 mRNA, complete cds.
BT019756 - Homo sapiens interferon regulatory factor 1 mRNA, complete cds.
AK314025 - Homo sapiens cDNA, FLJ94683, Homo sapiens interferon regulatory factor 1 (IRF1), mRNA.
DQ893269 - Synthetic construct clone IMAGE:100005899; FLH195792.01X; RZPDo839G04152D interferon regulatory factor 1 (IRF1) gene, encodes complete protein.
DQ896599 - Synthetic construct Homo sapiens clone IMAGE:100011059; FLH195788.01L; RZPDo839G04151D interferon regulatory factor 1 (IRF1) gene, encodes complete protein.
CR541713 - Homo sapiens full open reading frame cDNA clone RZPDo834B0329D for gene IRF1, interferon regulatory factor 1; complete cds, without stopcodon.
AB528367 - Synthetic construct DNA, clone: pF1KB7986, Homo sapiens IRF1 gene for interferon regulatory factor 1, without stop codon, in Flexi system.
LN607829 - Homo sapiens partial mRNA for interferon regulatory factor 1 (IRF1 gene).
LN626686 - Homo sapiens partial mRNA for Interferon regulatory factor 1 (IRF1 gene).
KC209827 - Homo sapiens interferon regulatory factor 1 isoform d78 (IRF1) mRNA, complete cds, alternatively spliced.
KC209828 - Homo sapiens interferon regulatory factor 1 isoform I4 (IRF1) mRNA, complete cds, alternatively spliced.
AB103081 - Homo sapiens IRF1 mRNA for interferon regulatory factor 1 nirs variant 1, complete cds.
AF082503 - Homo sapiens interferon regulatory factor 1 (IRF-1) gene, exon 1 and exon 4 splice junction.
JD523563 - Sequence 504587 from Patent EP1572962.
JD461793 - Sequence 442817 from Patent EP1572962.
JD208308 - Sequence 189332 from Patent EP1572962.
JD284542 - Sequence 265566 from Patent EP1572962.
JD428933 - Sequence 409957 from Patent EP1572962.
JD394684 - Sequence 375708 from Patent EP1572962.
JD191230 - Sequence 172254 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  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: ENST00000245414.1, ENST00000245414.2, ENST00000245414.3, ENST00000245414.4, ENST00000245414.5, ENST00000245414.6, ENST00000245414.7, ENST00000245414.8, hCG_24115 , IRF1 , NM_002198, Q6FHN8, Q6FHN8_HUMAN, uc317eqo.1, uc317eqo.2
UCSC ID: ENST00000245414.9_9
RefSeq Accession: NM_002198.3
Protein: Q6FHN8

-  Gene Model Information
  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.