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KLRF1 Gene

protein-coding   GIFtS: 49
GCID: GC12P009980

Killer Cell Lectin-Like Receptor Subfamily F, Member 1

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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
Killer Cell Lectin-Like Receptor Subfamily F, Member 11 2     NKp802
Activating Coreceptor NKp802 3     Killer Cell Lectin-Like Receptor F12
Lectin-Like Receptor F12 3     Killer Cell Lectin-Like Receptor Subfamily F Member 12
CLEC5C2 3     ML3
C-Type Lectin Domain Family 5 Member C2 3     

External Ids:    HGNC: 133421   Entrez Gene: 513482   Ensembl: ENSG000001500457   OMIM: 6050295   UniProtKB: Q9NZS23   

Export aliases for KLRF1 gene to outside databases

Previous GC identifers: GC12P009662 GC12P010102 GC12P009880 GC12P009871


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for KLRF1 Gene:
KLRF1, an activating homodimeric C-type lectin-like receptor (CTLR), is expressed on nearly all natural killer
(NK) cells and stimulates their cytoxicity and cytokine release (Kuttruff et al., 2009 (PubMed
18922855)).(supplied by OMIM, Oct 2009)

GeneCards Summary for KLRF1 Gene:
KLRF1 (killer cell lectin-like receptor subfamily F, member 1) is a protein-coding gene. GO annotations related to this gene include carbohydrate binding and MHC class I receptor activity. An important paralog of this gene is CLECL1.

UniProtKB/Swiss-Prot: KLRF1_HUMAN, Q9NZS2
Function: Involved in the natural killer (NK)-mediated cytolysis of PHA-induced lymphoblasts




(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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RefSeq DNA sequence at NCBI GenBank:
NC_000012.11  NC_018923.2  NT_009714.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the KLRF1 gene promoter:
         IRF-2   IRF-1   RORalpha2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidKLRF1 promoter sequence
   Search Chromatin IP Primers for KLRF1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat KLRF1


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

Entrez Gene cytogenetic band: 12p13.31   Ensembl cytogenetic band:  12p13.31   HGNC cytogenetic band: 12p13.31

KLRF1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
KLRF1 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P009980:  view genomic region     (about GC identifiers)

Start:
9,980,077 bp from pter      End:
9,997,606 bp from pter
Size:
17,530 bases      Orientation:
plus 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: KLRF1_HUMAN, Q9NZS2 (See protein sequence)
Recommended Name: Killer cell lectin-like receptor subfamily F member 1  
Size: 232 amino acids; 26666 Da
Subunit: Homodimer
Secondary accessions: Q4KMT5 Q96PR2 Q96PR3 Q9NZS1
Alternative splicing: 4 isoforms:  Q9NZS2-1   Q9NZS2-2   Q9NZS2-3   Q9NZS2-4   (May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay)

Explore the universe of human proteins at neXtProt for KLRF1: NX_Q9NZS2

Explore proteomics data for KLRF1 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn77, Asn91, Asn96, Asn177
  • Modification sites at PhosphoSitePlus

  • See KLRF1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_057607.1  
    ENSEMBL proteins: 
     ENSP00000346919   ENSP00000322487   ENSP00000279544   ENSP00000279545   ENSP00000445022  
     ENSP00000443054   ENSP00000442884  

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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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    HGNC Gene Families:
    KLR: Killer cell lectin-like receptors
    CLEC: C-type lectin domain containing

    3 InterPro protein domains:
     IPR016187 C-type_lectin_fold
     IPR016186 C-type_lectin-like
     IPR001304 C-type_lectin

    Graphical View of Domain Structure for InterPro Entry Q9NZS2

    ProtoNet protein and cluster: Q9NZS2

    UniProtKB/Swiss-Prot: KLRF1_HUMAN, Q9NZS2
    Similarity: Contains 1 C-type lectin domain


    Find genes that share domains with KLRF1           About GenesLikeMe


    (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: KLRF1_HUMAN, Q9NZS2
    Function: Involved in the natural killer (NK)-mediated cytolysis of PHA-induced lymphoblasts

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004888transmembrane signaling receptor activity TAS10671213
    GO:0030246carbohydrate binding IEA--
    GO:0032393MHC class I receptor activity TAS10671213
         
    Find genes that share ontologies with KLRF1           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for KLRF1

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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
    KLRF1_HUMAN, Q9NZS2: Membrane; Single-pass type II membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane4
    cytosol2
    extracellular1
    mitochondrion1
    nucleus1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005887integral component of plasma membrane TAS10671213
    GO:0016020membrane TAS10671213

    Find genes that share ontologies with KLRF1           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 KLRF1
    Interactions:

        Search GeneGlobe Interaction Network for KLRF1

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007166cell surface receptor signaling pathway TAS10671213

    Find genes that share ontologies with KLRF1           About GenesLikeMe



    (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 KLRF1



    (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 KLRF1 gene: 
    NM_016523.1  

    Unigene Cluster for KLRF1:

    Killer cell lectin-like receptor subfamily F, member 1
    Hs.183125  [show with all ESTs]
    Unigene Representative Sequence: AJ305370
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000354855(uc009zha.3) ENST00000324214(uc009zgw.3) ENST00000279544(uc021qux.1 uc009zgx.3 uc001qwm.3 uc009zgz.3)
    ENST00000279545(uc009zgy.3) ENST00000545196 ENST00000537723 ENST00000535631

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    Additional mRNA sequence: 

    AF175206.1 AF175207.1 AF267244.1 AF267245.1 AJ305370.1 BC096734.1 BC098166.1 BC098257.1 
    BC098354.1 

    4 DOTS entries:

    DT.435636  DT.92417532  DT.95263208  DT.92417533 

    12 AceView cDNA sequences:

    AF267245 AA173389 AF267244 NM_016523 AA426628 BG220404 AJ305370 AF175206 
    AF175207 AA424848 BX098311 T60164 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for KLRF1 (see all 8)    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c
    SP1:                                -                           
    SP2:                    -           -                           
    SP3:                          -                                 
    SP4:                          -     -                           
    SP5:                    -     -     -                           


    ECgene alternative splicing isoforms for KLRF1

    (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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    KLRF1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGATCATATC
    KLRF1 Expression
    About this image


    KLRF1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Blood (Hematopoietic System)
             Natural Killer Cells Peripheral Blood
    KLRF1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    KLRF1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.183125

    UniProtKB/Swiss-Prot: KLRF1_HUMAN, Q9NZS2
    Tissue specificity: Strongly expressed in peripheral blood leukocytes and spleen, with weaker expression in lymph
    node and adult liver, and no expression detected in bone marrow, thymus, and fetal liver. Not expressed in brain,
    heart, placenta, lung, kidney, skeletal muscle, and pancreas. Within peripheral blood leukocyte and immunocyte
    cell lines, expression was predominant in NK cells but was also detected in monocytes

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    (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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    This gene was present in the common ancestor of chordates.

    Orthologs for KLRF1 gene from Selected species (see all 5)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    dog
    (Canis familiaris)
    Mammalia KLRF11 killer cell lectin-like receptor subfamily F, member more 85.22(n)
    78.7(a)
      611429  XM_849098.2  XP_854191.2 
    chicken
    (Gallus gallus)
    Aves BLEC26
    Gallus gallus NK receptor-like (B-NK), mRNA.
    24(a)
    1 → many
    16(108301-110805)
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    (see all 3)
    Uncharacterized protein
    (see all 3)
    28(a)
    27(a)
    (see all 3)
    many ↔ many
    many ↔ many
    (see all 3)
    2(193036120-193041758)
    2(193063886-193078041)


    ENSEMBL Gene Tree for KLRF1 (if available)
    TreeFam Gene Tree for KLRF1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for KLRF1 gene
    CLECL12  KLRF22  KLRB12  
    8 SIMAP similar genes for KLRF1 using alignment to 5 protein entries:     KLRF1_HUMAN (see all proteins):
    CLEC10A    KLRC1    KLRD1    KLRC2    ASGR1    NCAN
    KLRG1    CLEC2B

    Find genes that share paralogs with KLRF1           About GenesLikeMe



    (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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    Selected SNPs for KLRF1 (see all 418)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1145551701,2
    C,F--9851391(+) GATGGA/GTAAAA 1 -- us2k11Minor allele frequency- G:0.03WA 118
    rs1927928121,2
    --9851421(+) AAAATA/GTAAAA 1 -- us2k10--------
    rs1434683271,2
    --9851461(+) TCCTGC/GACACA 1 -- us2k10--------
    rs1156997871,2
    F--9851482(+) AATATT/GTCATG 1 -- us2k11Minor allele frequency- G:0.03WA 118
    rs2003566571,2
    --9851542(+) CAAAC-/AAAA  
            
    AAAAT
    1 -- us2k10--------
    rs1412437751,2
    C--9851546(+) CAAAA-/AAAC  
            
    TAATT
    1 -- us2k10--------
    rs1161707621,2
    F--9851589(+) TATCAA/GCAGAG 1 -- us2k11Minor allele frequency- G:0.03WA 118
    rs732409331,2
    C,F--9851689(+) CCAATC/TAACAA 1 -- us2k13Minor allele frequency- T:0.11WA CSA 122
    rs1479811941,2
    --9851706(+) AATAAA/GCAACC 1 -- us2k10--------
    rs1426938941,2
    --9851752(+) TTTTCA/GTGTTT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for KLRF1 (9980077 - 9997606 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for KLRF1: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing KLRF1
    DNA2.0 Custom Variant and Variant Library Synthesis for KLRF1

    (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: 605029    OMIM disorders: --


    Find genes that share disorders with KLRF1           About GenesLikeMe

    Human Genome Epidemiology (HuGE) Navigator: KLRF1 (1 document)

    Export disorders for KLRF1 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 KLRF1 gene, integrated from 10 sources (see all 11):
    (articles sorted by number of sources associating them with KLRF1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Human KLRF1, a novel member of the killer cell lectin-like receptor gene family: molecular characterization, genomic structure, physical mapping to the NK gene complex and expression analysis. (PubMed id 10671213)1, 2, 3, 9 Roda-Navarro P....Fernandez-Ruiz E. (Eur. J. Immunol. 2000)
    2. Molecular characterization of two novel alternative spliced variants of the KLRF1 gene and subcellular distribution of KLRF1 isoforms. (PubMed id 11513955)1, 2, 9 Roda-Navarro P.... Fernandez-Ruiz E. (Biochim. Biophys. Acta 2001)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    4. Identification of NKp80, a novel triggering molecule expressed by human natural killer cells. (PubMed id 11265639)1, 2 Vitale M.... Moretta A. (Eur. J. Immunol. 2001)
    5. Attenuated natural killer (NK) cell activation through C-type lectin-like receptor NKp80 is due to an anomalous hemi-immunoreceptor tyrosine-based activation motif (HemITAM) with impaired Syk kinase recruitment capacity. (PubMed id 23609447)1 RA1ckrich T. and Steinle A. (J. Biol. Chem. 2013)
    6. Genetically coupled receptor-ligand pair NKp80-AICL enables autonomous control of human NK cell responses. (PubMed id 23929856)1 Klimosch S.N....Steinle A. (Blood 2013)
    7. Cutting edge: NKp80 uses an atypical hemi-ITAM to trigger NK cytotoxicity. (PubMed id 21149606)1 Dennehy K.M....Steinle A. (J. Immunol. 2011)
    8. New genetic associations detected in a host response study to hepatitis B vaccine. (PubMed id 20237496)1 Davila S....Seielstad M. (Genes Immun. 2010)
    9. NKp80 defines and stimulates a reactive subset of CD8 T cells. (PubMed id 18922855)1 Kuttruff S....Steinle A. (Blood 2009)
    10. The finished DNA sequence of human chromosome 12. (PubMed id 16541075)2 Scherer S.E.... Gibbs R.A. (Nature 2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 51348 HGNC: 13342 AceView: KLRF1 Ensembl:ENSG00000150045 euGenes: HUgn51348
    ECgene: KLRF1 H-InvDB: KLRF1

    (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 KLRF1 Pharmacogenomics, SNPs, Pathways
    Functional Glycomics Gateway - Glycan Bindinghttp://www.functionalglycomics.org/glycomics/GBPServlet?&operationType=view&cbpId=cbp_hum_Ctlect_241

    (Patent information from GeneIP,
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    IP news from LifeMap Sciences, Inc.)
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    Patent Information for KLRF1 gene:
    Search GeneIP for patents involving KLRF1

    GeneCards and IP:
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