Human Gene IFNB1 (ENST00000380232.4_6) from GENCODE V47lift37
  Description: interferon beta 1 (from RefSeq NM_002176.4)
Gencode Transcript: ENST00000380232.4_6
Gencode Gene: ENSG00000171855.7_8
Transcript (Including UTRs)
   Position: hg19 chr9:21,077,103-21,077,941 Size: 839 Total Exon Count: 1 Strand: -
Coding Region
   Position: hg19 chr9:21,077,305-21,077,868 Size: 564 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:21,077,103-21,077,941)mRNA (may differ from genome)Protein (187 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: IFNB_HUMAN
DESCRIPTION: RecName: Full=Interferon beta; Short=IFN-beta; AltName: Full=Fibroblast interferon; Flags: Precursor;
FUNCTION: Has antiviral, antibacterial and anticancer activities.
SUBUNIT: Monomer.
SUBCELLULAR LOCATION: Secreted.
PHARMACEUTICAL: Available under the names Avonex (Biogen), Betaseron (Berlex) and Rebif (Serono). Used in the treatment of multiple sclerosis (MS). Betaseron is a slightly modified form of IFNB1 with two residue substitutions.
SIMILARITY: Belongs to the alpha/beta interferon family.
WEB RESOURCE: Name=Avonex; Note=Clinical information on Avonex; URL="http://www.avonex.com/index.xml";
WEB RESOURCE: Name=Betaseron; Note=Clinical information on Betaseron; URL="http://www.betaseron.com/home";

-  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.
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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: IFNB1
Diseases sorted by gene-association score: relapsing-remitting multiple sclerosis (41), primary progressive multiple sclerosis (32), newcastle disease (28), secondary progressive multiple sclerosis (20), hepatitis c (19), oral erosive lichen (18), demyelinating disease (17), viral infectious disease (16), multiple sclerosis, disease progression, modifier of (14), kaposi sarcoma (14), parainfluenza virus type 3 (13), measles (11), spinal cord melanoma (10), marburg hemorrhagic fever (10), venezuelan equine encephalitis (10), severe acute respiratory syndrome (9), anogenital venereal wart (9), balo concentric sclerosis (9), japanese encephalitis (9), retroperitoneal neuroblastoma (9), chronic inflammatory demyelinating polyradiculoneuropathy (8), molluscum contagiosum (8), zika fever (7), influenza (6), retinal vasculitis (6), mucinoses (6), septicemic plague (6), herpes simplex (6), pedophilia (6), pseudo-torch syndrome 1 (6), microphthalmia with limb anomalies (6), listeria meningitis (5), internuclear ophthalmoplegia (5), respiratory syncytial virus infectious disease (5), pneumatosis cystoides intestinalis (4), ocular hyperemia (4), extrinsic cardiomyopathy (4), cerebral primitive neuroectodermal tumor (4), breast abscess (4), spinal cord astrocytoma (4), neuroretinitis (4), chilblain lupus (4), vaccinia (4), la crosse encephalitis (4), paraphilia disorder (4), gliosarcoma (4), malignant skin fibrous histiocytoma (3), multiple cranial nerve palsy (3), malignant glioma (3), nervous system disease (2), central nervous system disease (2)

-  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: 0.04 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 0.04 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 -20.6073-0.282 Picture PostScript Text
3' UTR -31.50202-0.156 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
IPR009079 - 4_helix_cytokine-like_core
IPR012351 - 4_helix_cytokine_core
IPR000471 - Interferon_alpha/beta/delta
IPR015588 - Interferon_beta

Pfam Domains:
PF00143 - Interferon alpha/beta domain

SCOP Domains:
47060 - S15/NS1 RNA-binding domain
47266 - 4-helical cytokines

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1AU1 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P01574
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:0005125 cytokine activity
GO:0005126 cytokine receptor binding
GO:0005132 type I interferon receptor binding
GO:0008811 chloramphenicol O-acetyltransferase activity

Biological Process:
GO:0002286 T cell activation involved in immune response
GO:0002312 B cell activation involved in immune response
GO:0002323 natural killer cell activation involved in immune response
GO:0006952 defense response
GO:0006959 humoral immune response
GO:0007166 cell surface receptor signaling pathway
GO:0007596 blood coagulation
GO:0009615 response to virus
GO:0010469 regulation of receptor activity
GO:0030101 natural killer cell activation
GO:0030183 B cell differentiation
GO:0033141 positive regulation of peptidyl-serine phosphorylation of STAT protein
GO:0035458 cellular response to interferon-beta
GO:0042100 B cell proliferation
GO:0043330 response to exogenous dsRNA
GO:0045071 negative regulation of viral genome replication
GO:0045089 positive regulation of innate immune response
GO:0045343 regulation of MHC class I biosynthetic process
GO:0045581 negative regulation of T cell differentiation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0051607 defense response to virus
GO:0060337 type I interferon signaling pathway
GO:0071360 cellular response to exogenous dsRNA
GO:2000552 negative regulation of T-helper 2 cell cytokine production
GO:2001235 positive regulation of apoptotic signaling pathway

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space


-  Descriptions from all associated GenBank mRNAs
  E00017 - DNA coding for human interferon beta.
M28622 - Human interferon beta-1 (IFN-beta-1) mRNA, complete cds.
E00098 - DNA coding of interferon(HLyc IFN-betaI).
E00171 - cDNA encoding human interferon-beta-1.
V00546 - Messenger RNA for human fibroblast interferon.
M25460 - Human interferon-beta mRNA, complete cds.
V00547 - Human messenger RNA for fibroblast (beta) interferon.
BC096151 - Homo sapiens interferon, beta 1, fibroblast, mRNA (cDNA clone MGC:116799 IMAGE:40002941), complete cds.
BC096153 - Homo sapiens interferon, beta 1, fibroblast, mRNA (cDNA clone MGC:116801 IMAGE:40002945), complete cds.
BC069314 - Homo sapiens interferon, beta 1, fibroblast, mRNA (cDNA clone MGC:96956 IMAGE:7262165), complete cds.
BC096152 - Homo sapiens interferon, beta 1, fibroblast, mRNA (cDNA clone MGC:116800 IMAGE:40002943), complete cds.
BC096150 - Homo sapiens interferon, beta 1, fibroblast, mRNA (cDNA clone MGC:116798 IMAGE:40002940), complete cds.
JD374495 - Sequence 355519 from Patent EP1572962.
E00029 - DNA coding of interferon beta.
E00198 - cDNA encoding mutain of human IFN-beta.
AB451491 - Homo sapiens IFNB1 mRNA for interferon beta precursor, partial cds, clone: FLJ08204DABN.
AB451323 - Homo sapiens IFNB1 mRNA for interferon beta precursor, complete cds, clone: FLJ08204AAAN.
KJ891438 - Synthetic construct Homo sapiens clone ccsbBroadEn_00832 IFNB1 gene, encodes complete protein.
AB451452 - Homo sapiens IFNB1 mRNA for interferon beta precursor, partial cds, clone: FLJ08204AAAF.
AB587428 - Synthetic construct DNA, clone: pF1KB6826, Homo sapiens IFNB1 gene for interferon, beta 1, fibroblast, without stop codon, in Flexi system.
A00119 - H.sapiens mRNA for fibroblast interferon (partial).
M17373 - Human interferon-beta (IFN-beta) mRNA, 5' UTR.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_il1rPathway - Signal transduction through IL1R
h_inflamPathway - Cytokines and Inflammatory Response
h_cytokinePathway - Cytokine Network
h_ranklPathway - Bone Remodelling
h_ifnaPathway - IFN alpha signaling pathway
h_dcPathway - Dendritic cells in regulating TH1 and TH2 Development

Reactome (by CSHL, EBI, and GO)

Protein P01574 (Reactome details) participates in the following event(s):

R-HSA-909720 IFN alpha/beta binds to IFNAR2
R-HSA-909732 Phosphorylation of STAT2
R-HSA-909719 Recruitment of STAT2 to p-IFNAR1
R-HSA-909726 Phosphorylation of STAT1
R-HSA-909722 Release of p-STAT2:p-STAT1 dimer
R-HSA-997309 Dephosphorylation of STAT1 by SHP2
R-HSA-909724 Recruitment of IFNAR1
R-HSA-909730 Phosphorylation of INFAR1 by TYK2
R-HSA-997311 Dephosphorylation of TYK2 by PTP1B
R-HSA-909729 Activation of JAK kinases
R-HSA-912680 Inhibition of JAK kinase activity by SOCS1/3
R-HSA-997314 Dephosphorylation of JAK1 by SHP1
R-HSA-909718 Formation of p-STAT1 homodimer
R-HSA-918233 TRAF3-dependent IRF activation pathway
R-HSA-909733 Interferon alpha/beta signaling
R-HSA-933541 TRAF6 mediated IRF7 activation
R-HSA-983231 Factors involved in megakaryocyte development and platelet production
R-HSA-168928 DDX58/IFIH1-mediated induction of interferon-alpha/beta
R-HSA-912694 Regulation of IFNA signaling
R-HSA-913531 Interferon Signaling
R-HSA-109582 Hemostasis
R-HSA-168249 Innate Immune System
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000380232.1, ENST00000380232.2, ENST00000380232.3, IFB, IFNB, IFNB1 , IFNB_HUMAN, NM_002176, P01574, Q5VWC9, uc318plu.1, uc318plu.2
UCSC ID: ENST00000380232.4_6
RefSeq Accession: NM_002176.4
Protein: P01574 (aka IFNB_HUMAN)

-  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.