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LILRA4 Gene

protein-coding   GIFtS: 55
GCID: GC19M054844

Leukocyte Immunoglobulin-Like Receptor, Subfamily A (With...

  See LILRA4-related disease
at  

(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
Leukocyte Immunoglobulin-Like Receptor, Subfamily A (With TM Domain),
Member 41 2
     CD85g2
Immunoglobulin-Like Transcript 72 3     Leukocyte Immunoglobulin-Like Receptor Subfamily A Member 42
ILT-72 3     Leukocyte Immunoglobulin-Like Receptor, Subfamily A (Without TM Domain),
Member 42
ILT72 3     CD85g Antigen3
CD85 Antigen-Like Family Member G2 3     

External Ids:    HGNC: 155031   Entrez Gene: 235472   Ensembl: ENSG000002399617   OMIM: 6075175   UniProtKB: P599013   

Export aliases for LILRA4 gene to outside databases

Previous GC identifers: GC19M059540 GC19M051166


(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 LILRA4 Gene:
This gene encodes an immunoglobulin-like cell surface protein preferentially expressed in plasmacytoid dendritic
cells (PDCs). This gene is highly expressed in PDCs, and is found to be rapidly down-regulated by interleukin 3
(IL3). This gene is one of the 19 highly related genes that form a leukocyte receptor gene cluster (LRC) at
chromosomal region 19q13.4. (provided by RefSeq, Jul 2008)

GeneCards Summary for LILRA4 Gene:
LILRA4 (leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4) is a protein-coding gene. Diseases associated with LILRA4 include blastic plasmacytoid dendritic cell. An important paralog of this gene is LILRB4.

UniProtKB/Swiss-Prot: LIRA4_HUMAN, P59901
Function: May act as receptor for class I MHC antigens. Ligand binding leads to the activation of eosinophils and
to the release of RNASE2, IL4 and leukotriene C4

Gene Wiki entry for LILRA4 Gene


(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_000019.9  NC_018930.2  NT_011109.17  NT_187693.1  
Regulatory elements:
   Regulatory transcription factor binding sites in the LILRA4 gene promoter:
         ER-alpha   AML1a   SREBP-1c   SREBP-1b   AREB6   SREBP-1a   POU2F1   POU2F1a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidLILRA4 promoter sequence
   Search Chromatin IP Primers for LILRA4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat LILRA4


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

Entrez Gene cytogenetic band: 19q13.4   Ensembl cytogenetic band:  19q13.42   HGNC cytogenetic band: 19q13.4

LILRA4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LILRA4 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M054844:  view genomic region     (about GC identifiers)

Start:
54,844,456 bp from pter      End:
54,850,421 bp from pter
Size:
5,966 bases      Orientation:
minus strand

2 alternative locations:
Chr19-,NW_003571061 314,919-320,650      Chr19-,NW_003571055 314,765-320,496     

(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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: LIRA4_HUMAN, P59901 (See protein sequence)
Recommended Name: Leukocyte immunoglobulin-like receptor subfamily A member 4 precursor  
Size: 499 amino acids; 55165 Da
Subunit: Interacts with BST2
Secondary accessions: Q32MC4
Alternative splicing: 2 isoforms:  P59901-1   P59901-2   

Explore the universe of human proteins at neXtProt for LILRA4: NX_P59901

Explore proteomics data for LILRA4 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn138, Asn239, Asn279, Asn300
  • Modification sites at PhosphoSitePlus

  • See LILRA4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_036408.3  
    ENSEMBL proteins: 
     ENSP00000291759   ENSP00000471722  

    LILRA4 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for LILRA4

     
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    Search eBioscience for ELISAs for LILRA4 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    CD: CD molecules
    LILR: Leukocyte immunoglobulin-like receptors
    IGD: Immunoglobulin superfamily / Immunoglobulin-like domain containing

    4 InterPro protein domains:
     IPR016332 A1B_glyco/leuk_Ig-like_rcpt
     IPR007110 Ig-like_dom
     IPR003599 Ig_sub
     IPR013783 Ig-like_fold

    Graphical View of Domain Structure for InterPro Entry P59901

    ProtoNet protein and cluster: P59901

    1 Blocks protein domain: IPB003599 Immunoglobulin subtype

    UniProtKB/Swiss-Prot: LIRA4_HUMAN, P59901
    Similarity: Contains 4 Ig-like C2-type (immunoglobulin-like) domains


    Find genes that share domains with LILRA4           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, 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: LIRA4_HUMAN, P59901
    Function: May act as receptor for class I MHC antigens. Ligand binding leads to the activation of eosinophils and
    to the release of RNASE2, IL4 and leukotriene C4

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI19564354
         
    Find genes that share ontologies with LILRA4           About GenesLikeMe


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for LILRA4
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    hsa-mir-26b-5p (MIRT028869)

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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
    LIRA4_HUMAN, P59901: Membrane; Single-pass type I membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane3
    extracellular2
    lysosome1
    mitochondrion1
    peroxisome1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with LILRA4           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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    SuperPaths for LILRA4 About    
    See pathways by source

    SuperPathContained pathways About
    1Osteoclast differentiation
    Osteoclast differentiation


    Find genes that share SuperPaths with LILRA4           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways




    1 Kegg Pathway  (Kegg details for LILRA4):
        Osteoclast differentiation

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for LILRA4
    Interactions:

        Search GeneGlobe Interaction Network for LILRA4

    STRING Interaction Network Preview (showing 5 interactants - click image to see 6)

    Selected Interacting proteins for LILRA4 (P599013 ENSP000002917594) via UniProtKB, MINT, STRING, and/or I2D (see all 7)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    BST2Q105893I2D: score=1 
    FCGR2AENSP000002714504STRING: ENSP00000271450
    FCGR3AENSP000003569464STRING: ENSP00000356946
    FCGR3BENSP000002948004STRING: ENSP00000294800
    SYKENSP000003648984STRING: ENSP00000364898
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0002376immune system process IEA--

    Find genes that share ontologies with LILRA4           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 Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for LILRA4 (LIRA4)

    1 Novoseek inferred chemical compound relationship for LILRA4 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    tyrosine 16.3 2 12384430 (1), 16735691 (1)



    Find genes that share compounds with LILRA4           About GenesLikeMe



    (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 LILRA4 gene: 
    NM_012276.3  

    Unigene Cluster for LILRA4:

    Leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4
    Hs.406708  [show with all ESTs]
    Unigene Representative Sequence: BM285391
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000291759(uc002qfi.3 uc002qfj.3) ENST00000595581 ENST00000421056

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      QuantiFast Probe-based Assays in human, mouse, rat LILRA4

    Additional mRNA sequence: 

    AF041261.1 AF283989.1 BC038829.1 BC109198.1 BC109199.1 

    5 DOTS entries:

    DT.95263522  DT.95263521  DT.99934982  DT.121487405  DT.95091468 

    3 AceView cDNA sequences:

    BG059554 NM_012276 AF283989 

    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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    LILRA4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    LILRA4 Expression
    About this image


    LILRA4 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Blood (Hematopoietic System)
             Plasmacytoid Dendritic cells Peripheral Blood
    LILRA4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    LILRA4 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.406708

    UniProtKB/Swiss-Prot: LIRA4_HUMAN, P59901
    Tissue specificity: Detected in eosinophils, neutrophils and monocytes

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    In Situ
    Assay Products:
     

     
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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 LILRA4 gene from Selected species (see all 5)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    20(a)
    1 → many
    GL343329.1(823590-844642)
            Species with no ortholog for LILRA4

    ENSEMBL Gene Tree for LILRA4 (if available)
    TreeFam Gene Tree for LILRA4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for LILRA4 gene
    LILRB42  KIR2DL42  LILRB12  KIR2DS42  LILRA62  LILRA52  IGSF12  KIR3DL12  
    OSCAR2  NCR12  ENSG000002177922  TARM12  KIR3DX12  LILRA32  LILRB52  KIR3DL32  
    LILRA12  KIR3DS12  KIR2DL12  LILRB22  A1BG2  KIR3DL22  LILRA22  KIR2DL32  
    FCAR2  GP62  LILRB32  
    Selected SIMAP similar genes for LILRA4 using alignment to 1 protein entry:     LIRA4_HUMAN(see all similar genes):
    LILRA6    LILRB3    LILRA1    LILRA2    LILRA5    LILRA3
    LILRB1    LILRB5    LILRB2    MIR cl-10    LILRB4    KIR-K36
    KIR412    KIR-K39    KIR-K64    KIR-K9    KIR-K3    KIR-K65

    Find genes that share paralogs with LILRA4           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 LILRA4 (see all 346)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1858448681,2
    C--54844216(+) AGAATC/GTTGAA 1 -- ds50010--------
    rs1881213721,2
    --54844283(+) GCTTTA/TTAGAA 1 -- ds50010--------
    rs64171651,2
    C,F,A,H--54844381(+) TGTATC/TTCTGG 1 -- ds500126Minor allele frequency- T:0.30NA NS EA WA CSA 2770
    rs1407411161,2
    --54844386(+) CTCTGC/GAGAAA 1 -- ds50010--------
    rs12053221,2
    C,F,O,A,H--54844437(+) ACTTAA/GATTTT 1 -- ds500132Minor allele frequency- N:0.00NS EA NA WA CSA 2983
    rs1808863631,2
    --54844453(+) CACGAA/TTCTGA 1 -- ds50010--------
    rs110843301,2
    C,F,H--54844480(+) TAATTA/GTCAAA 1 -- ds500112Minor allele frequency- G:0.18NA NS EA WA 906
    rs1458958281,2
    --54844503(+) GTTATC/GAGCTG 1 -- ds50010--------
    rs1381672021,2
    --54844515(+) AGAGAG/TAGTCC 1 -- ds50010--------
    rs1840448471,2
    --54844552(+) AGTTAA/GAAATA 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for LILRA4 (54844456 - 54850421 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for LILRA4:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv912411CNV Loss21882294
    nsv833878CNV Loss17160897
    nsv527908CNV Gain19592680
    nsv912412CNV Gain21882294
    nsv428371CNV Gain+Loss18775914
    dgv1119e1CNV Complex17122850

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing LILRA4
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    (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: 607517    OMIM disorders: --

    1 disease for LILRA4:    
    About MalaCards
    blastic plasmacytoid dendritic cell


    Find genes that share disorders with LILRA4           About GenesLikeMe

    Genetic Association Database (GAD): LILRA4
    Human Genome Epidemiology (HuGE) Navigator: LILRA4 (4 documents)

    Export disorders for LILRA4 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 LILRA4 gene, integrated from 10 sources (see all 20):
    (articles sorted by number of sources associating them with LILRA4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Regulation of TLR7/9 responses in plasmacytoid dendritic cells by BST2 and ILT7 receptor interaction. (PubMed id 19564354)1, 2, 9 Cao W....Liu Y.J. (J. Exp. Med. 2009)
    2. Nitroproteins from a human pituitary adenoma tissue discovered with a nitrotyrosine affinity column and tandem mass spectrometry. (PubMed id 16777052)1, 2, 9 Zhan X. and Desiderio D.M. (Anal. Biochem. 2006)
    3. Large-scale candidate gene analysis of spontaneous clearance of hepatitis C virus. (PubMed id 20331378)1, 4 Mosbruger T.L....Thio C.L. (J. Infect. Dis. 2010)
    4. Scan of 977 nonsynonymous SNPs in CLL4 trial patients for the identification of genetic variants influencing prognosis. (PubMed id 18006695)1, 4 Sellick G.S....Houlston R.S. (Blood 2008)
    5. Activation of human eosinophils through leukocyte immunoglobulin-like receptor 7. (PubMed id 12529506)1, 2 Tedla N.... Arm J.P. (Proc. Natl. Acad. Sci. U.S.A. 2003)
    6. Extensive gene duplications and a large inversion characterize the human leukocyte receptor cluster. (PubMed id 10941842)1, 3 Wende H.... Ziegler A. (Immunogenetics 2000)
    7. Plasmacytoid dendritic cell-specific receptor ILT7-Fc epsilonRI gamma inhibits Toll-like receptor-induced interferon production. (PubMed id 16735691)1, 9 Cao W....Liu Y.J. (J. Exp. Med. 2006)
    8. Immunoglobulin-like transcripts ILT2, ILT3 and ILT7 are expressed by human dendritic cells and down-regulated following activation. (PubMed id 15094202)1, 9 Ju X.S....Zenke M. (Gene 2004)
    9. Subtractive hybridization reveals the expression of immunoglobulin like transcript 7, Eph-B1, granzyme B, and 3 novel transcripts in human plasmacytoid dendritic cells. (PubMed id 12384430)1, 9 Rissoan M.-C.... Bates E.E.M. (Blood 2002)
    10. Ig-like transcript 7, but not bone marrow stromal cell antigen 2 (also known as HM1.24, tetherin, or CD317), modulates plasmacytoid dendritic cell function in primary human blood leukocytes. (PubMed id 23401591)1 Tavano B....Boasso A. (J. Immunol. 2013)

    (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: 23547 HGNC: 15503 AceView: ILT7 Ensembl:ENSG00000239961 euGenes: HUgn23547
    ECgene: LILRA4 Kegg: 23547 H-InvDB: LILRA4

    (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 LILRA4 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 LILRA4 gene:
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    GeneCards and IP:
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