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LILRA1 Gene

protein-coding   GIFtS: 53
GCID: GC19P055105

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

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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
Leukocyte Immunoglobulin-Like Receptor, Subfamily A (With TM Domain),
Member 11 2
     CD85 Antigen-Like Family Member I2 3
LIR62 3 5     CD85I2
Leukocyte Immunoglobulin-Like Receptor 62 3     Leukocyte Immunoglobulin-Like Receptor Subfamily A Member 12
LIR-62 3     CD85i Antigen3

External Ids:    HGNC: 66021   Entrez Gene: 110242   Ensembl: ENSG000001049747   OMIM: 6048105   UniProtKB: O750193   

Export aliases for LILRA1 gene to outside databases

Previous GC identifers: GC19P055968 GC19M055529 GC19P059781 GC19P059796 GC19P051428


(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 LILRA1 Gene:
This gene encodes an activating member of the leukocyte immunoglobulin-like receptor (LIR) family, which is found
in a gene cluster at chromosomal region 19q13.4. The encoded protein is predominantly expressed in B cells,
interacts with major histocompatibility complex class I ligands, and contributes to the regulation of immune
responses. Alternative splicing results in multiple transcript variants encoding different isoforms. (provided by
RefSeq, May 2013)

GeneCards Summary for LILRA1 Gene:
LILRA1 (leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1) is a protein-coding gene. Diseases associated with LILRA1 include microscopic polyangiitis, and hepatitis c virus. GO annotations related to this gene include antigen binding and transmembrane signaling receptor activity. An important paralog of this gene is LILRB4.

UniProtKB/Swiss-Prot: LIRA1_HUMAN, O75019
Function: May act as receptor for class I MHC antigens




(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:
   Regulatory transcription factor binding sites in the LILRA1 gene promoter:
         AML1a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidLILRA1 promoter sequence
   Search Chromatin IP Primers for LILRA1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat LILRA1


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

LILRA1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LILRA1 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P055105:  view genomic region     (about GC identifiers)

Start:
55,105,047 bp from pter      End:
55,113,555 bp from pter
Size:
8,509 bases      Orientation:
plus strand

2 alternative locations:
Chr19+,NW_003571060 498,532-505,959      Chr19+,NW_003571054 500,038-507,465     

(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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: LIRA1_HUMAN, O75019 (See protein sequence)
Recommended Name: Leukocyte immunoglobulin-like receptor subfamily A member 1 precursor  
Size: 489 amino acids; 53275 Da
Secondary accessions: O75018 Q3MJA6
Alternative splicing: 2 isoforms:  O75019-1   O75019-2   

Explore the universe of human proteins at neXtProt for LILRA1: NX_O75019

Explore proteomics data for LILRA1 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn140, Asn281, Asn302, Asn341, Asn431, Asn448

  • See LILRA1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_001265247.1  NP_001265248.1  NP_006854.1  

    ENSEMBL proteins: 
     ENSP00000251372   ENSP00000413715  
    Reactome Protein details: O75019

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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:
    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 O75019

    ProtoNet protein and cluster: O75019

    1 Blocks protein domain: IPB003599 Immunoglobulin subtype

    UniProtKB/Swiss-Prot: LIRA1_HUMAN, O75019
    Similarity: Contains 4 Ig-like C2-type (immunoglobulin-like) domains


    LILRA1 for domains           About GeneDecksing


    (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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: LIRA1_HUMAN, O75019
    Function: May act as receptor for class I MHC antigens

         Genatlas biochemistry entry for LILRA1:
    leukocyte immunoglobulin-like receptor,subfamily A,member 1,predominantly expressed on monocytes and B
    cells,related to the Fc alpha receptor and natural killed inhibitory receptor superfamily,with two (and others ?)
    alternatively spliced isoforms

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003823antigen binding TAS9548455
    GO:0004888transmembrane signaling receptor activity TAS9548455
    GO:0005515protein binding ----
         
    LILRA1 for ontologies           About GeneDecksing


    Phenotypes:
         3 GenomeRNAi human phenotypes for LILRA1:
     Decreased cell number, increas  Decreased viability of wild-ty  Increased gamma-H2AX phosphory 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for LILRA1
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    miRTarBase miRNAs that target LILRA1:
    hsa-mir-335-5p (MIRT018055)

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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
    LIRA1_HUMAN, O75019: Membrane; Single-pass type I membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane4
    extracellular1
    lysosome1
    mitochondrion1
    peroxisome1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane TAS--
    GO:0016021integral component of membrane IEA--

    LILRA1 for ontologies           About GeneDecksing


    (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 LILRA1 About                                                                                                See pathways by source

    SuperPathContained pathways About
    1Class I MHC mediated antigen processing and presentation
    Adaptive Immune System0.41
    2Osteoclast differentiation
    Osteoclast differentiation
    3Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
    Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Reactome Pathway for LILRA1
        Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell


    1 Kegg Pathway  (Kegg details for LILRA1):
        Osteoclast differentiation


    LILRA1 for pathways           About GeneDecksing

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for LILRA1
    Interactions:

        Search GeneGlobe Interaction Network for LILRA1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 7)

    Selected Interacting proteins for LILRA1 (ENSP000002513724) via UniProtKB, MINT, STRING, and/or I2D (see all 7)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    FCGR2AENSP000002714504STRING: ENSP00000271450
    FCGR3AENSP000003569464STRING: ENSP00000356946
    FCGR3BENSP000002948004STRING: ENSP00000294800
    SYKENSP000003648984STRING: ENSP00000364898
    PTPN11ENSP000003409444STRING: ENSP00000340944
    About this table

    Gene Ontology (GO): 4 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0002376immune system process IEA--
    GO:0006952defense response TAS9548455
    GO:0007166cell surface receptor signaling pathway TAS9548455
    GO:0050776regulation of immune response TAS--

    LILRA1 for ontologies           About GeneDecksing



    (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 LILRA1 (LIRA1)



    (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,
    Conferences by KenesGroup, 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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for LILRA1 gene (3 alternative transcripts): 
    NM_001278318.1  NM_001278319.1  NM_006863.3  

    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000495417 ENST00000473156 ENST00000251372(uc002qgh.1) ENST00000477255(uc010yfh.2)
    ENST00000453777

    miRNA
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    Search for qRT-PCR Assays for microRNAs that regulate LILRA1
    SwitchGear 3'UTR luciferase reporter plasmidLILRA1 3' UTR sequence
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    Primer
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    Pre-validated RT2 qPCR Primer Assay in human, mouse / rat LILRA1
      QuantiTect SYBR Green Assays in human, mouse, rat LILRA1
      QuantiFast Probe-based Assays in human, mouse, rat LILRA1

    1 AceView cDNA sequence:

    NM_006863 

    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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    LILRA1 expression in normal human tissues (normalized intensities)      LILRA1 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTAACTCACT
    LILRA1 Expression
    About this image


    LILRA1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Blood (Hematopoietic System)
             Monocytes Peripheral Blood
    LILRA1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    LILRA1 Protein Expression

    UniProtKB/Swiss-Prot: LIRA1_HUMAN, O75019
    Tissue specificity: Detected in monocytes and B-cells

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    In Situ
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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 LILRA1 gene from Selected species (see all 4)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    dog
    (Canis familiaris)
    Mammalia --
    Uncharacterized protein
    33(a)
    many ↔ many
    1(102996666-103000872)
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    20(a)
    1 → many
    GL343329.1(823590-844642)


    ENSEMBL Gene Tree for LILRA1 (if available)
    TreeFam Gene Tree for LILRA1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for LILRA1 gene
    LILRB42  KIR2DL42  LILRB12  KIR2DS42  LILRA62  LILRA52  IGSF12  KIR3DL12  
    OSCAR2  NCR12  LILRA42  ENSG000002177922  TARM12  KIR3DX12  LILRA32  LILRB52  
    KIR3DL32  KIR3DS12  KIR2DL12  LILRB22  A1BG2  KIR3DL22  LILRA22  KIR2DL32  
    FCAR2  GP62  LILRB32  
    Selected SIMAP similar genes for LILRA1 using alignment to 1 protein entry:     LIRA1_HUMAN(see all similar genes):
    LILRA3    LILRB2    MIR cl-10    LILRA2    LILRB1    LILRA4
    LILRB3    LILRA6    LILRB5    KIR2DL3    LILRA5    KIR2DS4
    KIR2DS2    KIR2DL1    KIR2DS1    KIR3DL3    KIR2DS3    KIR3DP1

    LILRA1 for paralogs           About GeneDecksing



    (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 LILRA1 (see all 486)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1507040101,2
    C--55103060(+) GGCTCC/TGAGCT 1 -- us2k10--------
    rs621333941,2
    C,F--55103061(+) GCTCCG/AAGCTG 1 -- us2k16Minor allele frequency- A:0.20NA CSA WA 245
    rs1837930281,2
    --55103099(+) CAGATA/TGAAGG 1 -- us2k10--------
    rs284189591,2
    C,F--55103111(+) CCATTC/TTCCAA 1 -- us2k15Minor allele frequency- T:0.04CSA WA NA EA 362
    rs1399485421,2
    --55103173(+) ACTGGC/TTTCAA 1 -- us2k10--------
    rs1497732541,2
    --55103189(+) GGATCC/GCATGA 1 -- us2k10--------
    rs1456956351,2
    --55103194(+) CCATGA/C/GCCACC 1 -- us2k10--------
    rs1152083561,2
    C,F--55103335(+) GGACCG/AGAGCA 1 -- us2k11Minor allele frequency- A:0.02WA 118
    rs284684261,2
    C,F--55103359(+) TGGGCG/ACCACG 1 -- us2k18Minor allele frequency- A:0.30WA NA CSA EA 366
    rs1396337931,2
    --55103364(+) GCCACA/GCTCCA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for LILRA1 (55105047 - 55113555 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for LILRA1 (see all 13):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2667609CNV Deletion23128226
    dgv17e196CNV Deletion17116639
    esv2718872CNV Deletion23290073
    dgv16e196CNV Duplication17116639
    nsv470158CNV Loss18288195
    dgv435n27CNV Loss19166990
    esv7755CNV Loss19470904
    nsv522872CNV Loss19592680
    dgv4005n71CNV Loss21882294
    nsv428372CNV Gain+Loss18775914

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing LILRA1
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 604810    OMIM disorders: --

    10 diseases for LILRA1:    About MalaCards
    microscopic polyangiitis    hepatitis c virus    alcohol dependence    hepatitis c
    hepatitis b    hepatitis    systemic lupus erythematosus    lupus erythematosus
    rheumatoid arthritis    arthritis


    LILRA1 for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:
    The International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD) 9 - 13 March 2014
    Genetic Association Database (GAD): LILRA1
    Human Genome Epidemiology (HuGE) Navigator: LILRA1 (4 documents)

    Export disorders for LILRA1 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 LILRA1 gene, integrated from 10 sources (see all 22):
    (articles sorted by number of sources associating them with LILRA1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A family of human lymphoid and myeloid Ig-like receptors, some of which bind to MHC class I molecules. (PubMed id 9548455)1, 2, 3 Borges L.... Cosman D. (J. Immunol. 1997)
    2. 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)
    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. Genomic organization of the human leukocyte immunoglobulin-like receptors within the leukocyte receptor complex on chromosome 19q13.4. (PubMed id 10941837)1, 9 Liu W.R.... Arm J.P. (Immunogenetics 2000)
    5. Polymorphisms in ABLIM1 are associated with personality traits and alcohol dependence. (PubMed id 21547531)1 Wang K.S....Liu Y. (J. Mol. Neurosci. 2012)
    6. Expression of activating and inhibitory leukocyte immunoglobulin-like receptors in rheumatoid synovium: correlations to disease activity. (PubMed id 21388353)1 Tedla N....McNeil H.P. (Tissue Antigens 2011)
    7. HLA class I allelic sequence and conformation regulate leukocyte Ig-like receptor binding. (PubMed id 21270408)1 Jones D.C....Allen R.L. (J. Immunol. 2011)
    8. LILRA3 binds both classical and non-classical HLA class I molecules but with reduced affinities compared to LILRB1/LILRB2: structural evidence. (PubMed id 21559424)1 Ryu M....Gao G.F. (PLoS ONE 2011)
    9. New genetic associations detected in a host response study to hepatitis B vaccine. (PubMed id 20237496)1 Davila S....Seielstad M. (Genes Immun. 2010)
    10. Soluble LILRA3, a potential natural antiinflammatory protein, is increased in patients with rheumatoid arthritis and is tightly regulated by interleukin 10, tumor necrosis factor-alpha, and interferon-gamma. (PubMed id 20595277)1 An H....Tedla N. (J. Rheumatol. 2010)

    (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: 11024 HGNC: 6602 AceView: LILRA1 Ensembl:ENSG00000104974 euGenes: HUgn11024
    ECgene: LILRA1 Kegg: 11024 H-InvDB: LILRA1

    (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 LILRA1 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 LILRA1 gene:
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    GeneCards and IP:
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