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

Gene ID: 11024, updated on 11-Apr-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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Location:
19q13.42
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (54593632..54602381)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (57687147..57695896)
105.20220307 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
  • 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. Association of LILRA2 (ILT1, LIR7) splice site polymorphism with systemic lupus erythematosus and microscopic polyangiitis. Mamegano K, et al. Genes Immun, 2008 Apr. PMID 18273033

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_2023_10

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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