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    LILRA1 leukocyte immunoglobulin like receptor A1 [ Homo sapiens (human) ]

    Gene ID: 11024, updated on 28-Oct-2024

    Summary

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    Official Symbol
    LILRA1provided by HGNC
    Official Full Name
    leukocyte immunoglobulin like receptor A1provided by HGNC
    Primary source
    HGNC:HGNC:6602
    See related
    Ensembl:ENSG00000104974 MIM:604810; AllianceGenome:HGNC:6602
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LIR6; CD85I; LIR-6
    Summary
    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]
    Expression
    Biased expression in appendix (RPKM 8.6), spleen (RPKM 6.8) and 6 other tissues See more
    Orthologs
    all
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    Genomic context

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    See LILRA1 in Genome Data Viewer
    Location:
    19q13.42
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (54593632..54602381)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (57687147..57695896)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (55105097..55113846)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372461 Neighboring gene uncharacterized LOC107985347 Neighboring gene leukocyte immunoglobulin like receptor A2 Neighboring gene leukocyte immunoglobulin like receptor B1 Neighboring gene microRNA 8061

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Expression of activating and inhibitory leukocyte immunoglobulin-like receptors in rheumatoid synovium: correlations to disease activity. Tedla N, et al. Tissue Antigens, 2011 Apr. PMID 21388353
    2. Modulation of Toll-like receptor activity by leukocyte Ig-like receptors and their effects during bacterial infection. Pilsbury LE, et al. Mediators Inflamm, 2010. PMID 20634939, Free PMC Article
    3. Polymorphisms in ABLIM1 are associated with personality traits and alcohol dependence. Wang KS, et al. J Mol Neurosci, 2012 Feb. PMID 21547531
    4. 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. An H, et al. J Rheumatol, 2010 Aug 1. PMID 20595277
    5. Leukocyte receptor complex-encoded immunomodulatory receptors show differing specificity for alternative HLA-B27 structures. Allen RL, et al. J Immunol, 2001 Nov 15. PMID 11698424

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: Large-scale candidate gene analysis of spontaneous clearance of hepatitis C virus.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC126563

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables antigen binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables inhibitory MHC class I receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transmembrane signaling receptor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell surface receptor signaling pathway TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in defense response TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in immune response-regulating signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in interleukin-10-mediated signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    leukocyte immunoglobulin-like receptor subfamily A member 1
    Names
    CD85 antigen-like family member I
    leucocyte Ig-like receptor A1
    leukocyte immunoglobulin-like receptor 6
    leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001278318.2 → NP_001265247.1  leukocyte immunoglobulin-like receptor subfamily A member 1 isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2, also known as LIR6b) lacks two consecutive in-frame exons in the coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      AC245036, AF025530, DA999265
      Consensus CDS
      CCDS62802.1
      UniProtKB/Swiss-Prot
      O75019
      Related
      ENSP00000413715.1, ENST00000453777.1
      Conserved Domains (2) summary
      cd05751
      Location:27 → 119
      Ig1_LILRB1_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1) and similar proteins
      cl11960
      Location:124 → 219
      Ig; Immunoglobulin domain

    2. NM_001278319.1 → NP_001265248.1  leukocyte immunoglobulin-like receptor subfamily A member 1 isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has a shorter 5' UTR, lacks several exons and its 3'-terminal exon extends past a splice site that is used in variant 1. The encoded isoform (3) has a shorter and distinct C-terminus, compared to isoform 1. Isoform 3 lacks the transmembrane domain found in isoform 1 and is suspected to be soluble (PMID: 19658091).
      Source sequence(s)
      AF025530, BC032238, BC063009, EU915602
      UniProtKB/TrEMBL
      A0A0G2JP96
      Conserved Domains (3) summary
      cd05751
      Location:27 → 119
      Ig1_LILRB1_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1) and similar proteins
      smart00410
      Location:335 → 397
      IG_like; Immunoglobulin like
      cl11960
      Location:124 → 219
      Ig; Immunoglobulin domain

    3. NM_006863.4 → NP_006854.1  leukocyte immunoglobulin-like receptor subfamily A member 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_006854.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1, also known as LIR6a) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC245036, AF025530, BC101514, DA999265
      Consensus CDS
      CCDS12901.1
      UniProtKB/Swiss-Prot
      O75018, O75019, Q3MJA6
      UniProtKB/TrEMBL
      A0A0G2JP96
      Related
      ENSP00000251372.3, ENST00000251372.8
      Conserved Domains (2) summary
      cd05751
      Location:27 → 119
      Ig1_LILR_KIR_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILRs), Natural killer inhibitory receptors (KIRs) and similar domains
      cl11960
      Location:124 → 219
      Ig; Immunoglobulin domain

    RNA

    1. NR_103501.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an exon and uses an alternate splice site compared to variant 1. This variant is represented as non-coding because it lacks the translation start site used in variant 1 and does not include a supported in-frame ORF.
      Source sequence(s)
      AC245036, BC047007, BC101514, DA999265
      Related
      ENST00000473156.5

    2. NR_103502.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate splice site and its 3'-terminal exon extends past a splice site that is used in variant 1. This variant is represented as non-coding because it does not include a supported in-frame ORF.
      Source sequence(s)
      BC063009, DA999265
      Related
      ENST00000477255.1

    3. NR_103503.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks an exon and its 3'-terminal exon extends past a splice site that is used in variant 1. This variant is represented as non-coding because it lacks the translation start site used in variant 1 and does not include a supported in-frame ORF.
      Source sequence(s)
      BC063009, DA999265
      Related
      ENST00000495417.5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      54593632..54602381
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NW_003571054.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      500022..508771
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_7

    Genomic

    1. NW_003571060.1 Reference GRCh38.p14 ALT_REF_LOCI_7

      Range
      498516..507265
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_9

    Genomic

    1. NT_187693.1 Reference GRCh38.p14 ALT_REF_LOCI_9

      Range
      576211..584960
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      57687147..57695896
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75019.1 GenPept UniProtKB/Swiss-Prot:O75019

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