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IFNL4 Gene

protein-coding   GIFtS: 16
GCID: GC19M039737

Interferon, Lambda 4 (Gene/Pseudogene)

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Interferon, Lambda 4 (Gene/Pseudogene)1 2
IFN-lambda-42 3
IFNAN2
Interferon Lambda-42

External Ids:    HGNC: 444801   Entrez Gene: 1011809762   Ensembl: ENSG000002723957   OMIM: 6150905   UniProtKB: K9M1U53   

Export aliases for IFNL4 gene to outside databases

Previous GC identifer: GC19U901613


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for IFNL4 Gene:
IFNL4 (interferon, lambda 4 (gene/pseudogene)) is a protein-coding gene. GO annotations related to this gene include cytokine activity.

UniProtKB/Swiss-Prot: IFNL4_HUMAN, K9M1U5
Function: Cytokine that may trigger an antiviral response activating the JAK-STAT pathway and up-regulating
specifically some interferon-stimulated genes




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Search for regulatory transcription factor binding sites for IFNL4
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat IFNL4


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19q13.2   Ensembl cytogenetic band:  19q13.2   HGNC cytogenetic band: 19q13.2

IFNL4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
IFNL4 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M039737:  view genomic region     (about GC identifiers)

Start:
39,737,773 bp from pter      End:
39,739,219 bp from pter
Size:
1,447 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: IFNL4_HUMAN, K9M1U5 (See protein sequence)
Recommended Name: Interferon lambda-4 precursor  
Size: 179 amino acids; 19675 Da
Caution: The reference genome assembly, GRCh37, describes the non-functional copy of that gene, frameshifted at
position 22, that is more frequent in human populations
Secondary accessions: K9M1A5 K9M269 K9M2P7
Alternative splicing: 4 isoforms:  K9M1U5-1   K9M1U5-2   K9M1U5-3   K9M1U5-4   (Inactive form unable to elicit an antiviral response)

Explore the universe of human proteins at neXtProt for IFNL4: NX_K9M1U5

REFSEQ proteins: NP_001263183.2  
ENSEMBL proteins: 
 ENSP00000476098  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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ProtoNet protein and cluster: K9M1U5

UniProtKB/Swiss-Prot: IFNL4_HUMAN, K9M1U5
Similarity: Belongs to the lambda interferon family


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: IFNL4_HUMAN, K9M1U5
Function: Cytokine that may trigger an antiviral response activating the JAK-STAT pathway and up-regulating
specifically some interferon-stimulated genes
Induction: Up-regulated by polyinosinic:polycytidylic acid (polyI:C) which mimics the double-stranded hepatitis C
virus

     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005125cytokine activity IMP--
     
Find genes that share ontologies with IFNL4           About GenesLikeMe


Animal Models:
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
IFNL4_HUMAN, K9M1U5: Cytoplasm. Secreted

Gene Ontology (GO): 2 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005615extracellular space IDA--
GO:0005737cytoplasm IDA--

Find genes that share ontologies with IFNL4           About GenesLikeMe


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for IFNL4
Interactions:

    Search GeneGlobe Interaction Network for IFNL4

Gene Ontology (GO): 3 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0042502tyrosine phosphorylation of Stat2 protein IDA--
GO:0042508tyrosine phosphorylation of Stat1 protein IMP--
GO:0051607defense response to virus IMP--

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(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Tocris compounds for IFNL4

4 PharmGKB related drug/compound annotations for IFNL4 gene    About this table
Drug/compound PharmGKB Annotation
peginterferon alfa-2aCA  
peginterferon alfa-2bCA  
ribavirinCA  
telaprevirCA  



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(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for IFNL4 gene: 
NM_001276254.2  

1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000606380
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GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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See probesets specificity/sensitivity at GeneAnnot
CGAP TAG: --

IFNL4 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
    Custom PCR Arrays for IFNL4
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In Situ
Assay Products:
 

 
Search Advanced Cell Diagnostics for RNAscope RNA in situ hybridization assays for IFNL4

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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  --

ENSEMBL Gene Tree for IFNL4 (if available)
TreeFam Gene Tree for IFNL4 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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  --

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Polymorphic Variants from UniProtKB/Swiss-Prot
IFNL4_HUMAN, K9M1U5: Genetic variation in IFNL4 is associated with susceptibility to hepatitis C virus (HCV) infection
[MIM:609532]. A one-base insertion, introducing a frameshift at position 22, results in inactivation of the gene
in a majority of the population. That polymorphism is a good marker for predicting spontaneous HCV clearance and
the response to treatment of chronic hepatitis C. Noteworthily, the allele producing a functional protein able to
induce an antiviral response and to prevent HCV replication in cell cultures, is less frequent in human
populations and is associated with impaired spontaneous clearance of HCV


Selected SNPs for IFNL4 (see all 72)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 19 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs3682348151,2
F--36186199(+) GGGCCTT/GCTGCG 3 /E /A mis13Minor allele frequency- G:0.39EU WA EA 540
rs1144241601,2
F--39737686(+) TGAGAG/TCCTCG 2 -- nc-transcript-variantut311Minor allele frequency- T:0.03WA 118
rs1503081181,2
--39737711(+) TGGACC/GACAGG 2 -- nc-transcript-variantut310--------
rs116729321,2
H--39737716(+) GACAGC/GAGCTG 2 -- nc-transcript-variantut310--------
rs3693781181,2
C,F--39737760(-) CCCTCT/CGGCAG 2 -- nc-transcript-variantut313Minor allele frequency- C:0.05EU WA EA 540
rs1379027691,2
C,F--39737788(+) GGCCCT/AGAGTG 3 /S nc-transcript-variantsyn13Minor allele frequency- A:0.06EU WA EA 540
rs1494453191,2
--39737806(+) AGCCGA/GAGCTC 3 L nc-transcript-variantsyn10--------
rs129713961,2
C,F--39737866(+) CGAGGG/CGAGTC 3 /S nc-transcript-variantsyn18Minor allele frequency- C:0.39NA WA EU EA 778
rs778117411,2
C,F--39738005(+) GCTAAC/ACCTGT 2 -- int14Minor allele frequency- A:0.01WA EU EA 658
rs1439589491,2
--39738227(+) ACTCCG/TGTCTG 2 -- int10--------

HapMap Linkage Disequilibrium report for IFNL4 (39737773 - 39739219 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for IFNL4: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing IFNL4
DNA2.0 Custom Variant and Variant Library Synthesis for IFNL4

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 615090    OMIM disorders: --


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Export disorders for IFNL4 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for IFNL4 gene integrated from 10 sources:
(articles sorted by number of sources associating them with IFNL4)
    Utopia: connect your pdf to the dynamic
world of online information

  1. A variant upstream of IFNL3 (IL28B) creating a new interferon gene IFNL4 is associated with impaired clearance of hepatitis C virus. (PubMed id 23291588)1, 2, 3 Prokunina-Olsson L.... O'Brien T.R. (Nat. Genet. 2013)
  2. Association of the IFNL4-I9G Allele With Impaired Spontaneous Clearance of Hepatitis C Virus. (PubMed id 23956438)1 Aka P.V....O'Brien T.R. (J. Infect. Dis. 2014)
  3. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)2 Grimwood J.... Lucas S.M. (Nature 2004)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 101180976 HGNC: 44480 Ensembl:ENSG00000272395 euGenes: HUgn101180976 ECgene: IFNL4
H-InvDB: IFNL4

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for IFNL4 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for IFNL4 gene:
Search GeneIP for patents involving IFNL4

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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