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LILRB2 leukocyte immunoglobulin like receptor B2 [ Homo sapiens (human) ]

Gene ID: 10288, updated on 24-Feb-2019

Summary

Official Symbol
LILRB2provided by HGNC
Official Full Name
leukocyte immunoglobulin like receptor B2provided by HGNC
Primary source
HGNC:HGNC:6606
See related
Ensembl:ENSG00000131042 MIM:604815
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
ILT4; LIR2; CD85D; ILT-4; LIR-2; MIR10; MIR-10
Summary
This gene is a member of the leukocyte immunoglobulin-like receptor (LIR) family, which is found in a gene cluster at chromosomal region 19q13.4. The encoded protein belongs to the subfamily B class of LIR receptors which contain two or four extracellular immunoglobulin domains, a transmembrane domain, and two to four cytoplasmic immunoreceptor tyrosine-based inhibitory motifs (ITIMs). The receptor is expressed on immune cells where it binds to MHC class I molecules on antigen-presenting cells and transduces a negative signal that inhibits stimulation of an immune response. It is thought to control inflammatory responses and cytotoxicity to help focus the immune response and limit autoreactivity. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Biased expression in appendix (RPKM 54.6), bone marrow (RPKM 26.2) and 5 other tissues See more
Orthologs

Genomic context

See LILRB2 in Genome Data Viewer
Location:
19q13.42
Exon count:
15
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 19 NC_000019.10 (54273821..54281178, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (54777675..54785033, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 1307, pseudogene Neighboring gene YME1 like 1 ATPase pseudogene Neighboring gene microRNA 4752 Neighboring gene leukocyte immunoglobulin like receptor A5

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Adaptive Immune System, organism-specific biosystem (from REACTOME)
    Adaptive Immune System, organism-specific biosystemAdaptive immunity refers to antigen-specific immune response efficiently involved in clearing the pathogens. The adaptive immune system is comprised of B and T lymphocytes that express receptors with...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, organism-specific biosystem (from REACTOME)
    Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, organism-specific biosystemA number of receptors and cell adhesion molecules play a key role in modifying the response of cells of lymphoid origin (such as B-, T- and NK cells) to self and tumor antigens, as well as to pathoge...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • Neutrophil degranulation, organism-specific biosystem (from REACTOME)
    Neutrophil degranulation, organism-specific biosystemNeutrophils are the most abundant leukocytes (white blood cells), indispensable in defending the body against invading microorganisms. In response to infection, neutrophils leave the circulation and ...
  • Osteoclast differentiation, organism-specific biosystem (from KEGG)
    Osteoclast differentiation, organism-specific biosystemThe osteoclasts, multinucleared cells originating from the hematopoietic monocyte-macrophage lineage, are responsible for bone resorption. Osteoclastogenesis is mainly regulated by signaling pathways...
  • Osteoclast differentiation, conserved biosystem (from KEGG)
    Osteoclast differentiation, conserved biosystemThe osteoclasts, multinucleared cells originating from the hematopoietic monocyte-macrophage lineage, are responsible for bone resorption. Osteoclastogenesis is mainly regulated by signaling pathways...
  • Spinal Cord Injury, organism-specific biosystem (from WikiPathways)
    Spinal Cord Injury, organism-specific biosystemThis pathway provides an overview of cell types, therapeutic targets, drugs, new proposed targets and pathways implicated in spinal cord injury. Spinal cord injury is a complex multistep process that...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
MHC class I protein binding IDA
Inferred from Direct Assay
more info
PubMed 
MHC class I protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
MHC class Ib protein binding IDA
Inferred from Direct Assay
more info
PubMed 
MHC class Ib protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
MHC class Ib protein complex binding IDA
Inferred from Direct Assay
more info
PubMed 
amyloid-beta binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
amyloid-beta binding TAS
Traceable Author Statement
more info
PubMed 
cell adhesion molecule binding IPI
Inferred from Physical Interaction
more info
PubMed 
inhibitory MHC class I receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
inhibitory MHC class I receptor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
protein phosphatase 1 binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
Fc receptor mediated inhibitory signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
adaptive immune response IEA
Inferred from Electronic Annotation
more info
 
cell surface receptor signaling pathway TAS
Traceable Author Statement
more info
PubMed 
cell-cell signaling TAS
Traceable Author Statement
more info
PubMed 
cellular defense response TAS
Traceable Author Statement
more info
PubMed 
cellular response to lipopolysaccharide IMP
Inferred from Mutant Phenotype
more info
PubMed 
heterotypic cell-cell adhesion IDA
Inferred from Direct Assay
more info
PubMed 
immune response TAS
Traceable Author Statement
more info
PubMed 
immune response-inhibiting cell surface receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
immune response-inhibiting cell surface receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
learning or memory ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
negative regulation of T cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of T cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of antigen processing and presentation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of calcium ion transport IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of postsynaptic density organization IC
Inferred by Curator
more info
 
negative regulation of protein metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
neutrophil degranulation TAS
Traceable Author Statement
more info
 
positive regulation of T cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of T cell tolerance induction IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of interleukin-6 production NAS
Non-traceable Author Statement
more info
PubMed 
positive regulation of long-term synaptic depression ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
positive regulation of protein dephosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
positive regulation of regulatory T cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of tolerance induction IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of dendritic cell differentiation IC
Inferred by Curator
more info
PubMed 
regulation of immune response TAS
Traceable Author Statement
more info
 
regulation of long-term synaptic potentiation ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
signal transduction IDA
Inferred from Direct Assay
more info
PubMed 
signal transduction IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
cell surface IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
ficolin-1-rich granule membrane TAS
Traceable Author Statement
more info
 
integral component of plasma membrane IC
Inferred by Curator
more info
PubMed 
membrane TAS
Traceable Author Statement
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
tertiary granule membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
leukocyte immunoglobulin-like receptor subfamily B member 2
Names
CD85 antigen-like family member D
Ig-like transcript 4
leucocyte Ig-like receptor B2
leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2
monocyte/macrophage immunoglobulin-like receptor 10
myeloid inhibitory receptor 10

NCBI Reference Sequences (RefSeq)

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_001080978.3NP_001074447.2  leukocyte immunoglobulin-like receptor subfamily B member 2 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001074447.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1. Both variants 2 and 3 encode the same isoform.
    Source sequence(s)
    AF004231, AK226015, DC429053
    Consensus CDS
    CCDS42612.1
    UniProtKB/TrEMBL
    A2IXV5
    Related
    ENSP00000319960.5, ENST00000314446.9
    Conserved Domains (2) summary
    smart00410
    Location:231296
    IG_like; Immunoglobulin like
    cl11960
    Location:27118
    Ig; Immunoglobulin domain
  2. NM_001278403.2NP_001265332.2  leukocyte immunoglobulin-like receptor subfamily B member 2 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001265332.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1. Both variants 2 and 3 encode the same isoform.
    Source sequence(s)
    AF004231
    Consensus CDS
    CCDS42612.1
    UniProtKB/TrEMBL
    A2IXV5
    Related
    ENSP00000375628.1, ENST00000391748.5
    Conserved Domains (2) summary
    smart00410
    Location:231296
    IG_like; Immunoglobulin like
    cl11960
    Location:27118
    Ig; Immunoglobulin domain
  3. NM_001278404.2NP_001265333.2  leukocyte immunoglobulin-like receptor subfamily B member 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks a portion of the 5' coding region, and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AF004231, AK226015, AK297041, DC429053
    Consensus CDS
    CCDS62791.1
    UniProtKB/TrEMBL
    A2IXV5
    Related
    ENSP00000410117.1, ENST00000434421.5
    Conserved Domains (2) summary
    smart00410
    Location:115180
    IG_like; Immunoglobulin like
    cl11960
    Location:7102
    Ig; Immunoglobulin domain
  4. NM_001278405.2NP_001265334.2  leukocyte immunoglobulin-like receptor subfamily B member 2 isoform 4 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) has a shorter 5' UTR, and lacks an internal exon which results in a frameshift and an early stop codon, compared to variant 1. The encoded isoform (4) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AF004231, AF011566
    Consensus CDS
    CCDS62792.1
    UniProtKB/TrEMBL
    A2IXV5
    Related
    ENSP00000375626.1, ENST00000391746.5
    Conserved Domains (2) summary
    smart00410
    Location:231296
    IG_like; Immunoglobulin like
    cl11960
    Location:27118
    Ig; Immunoglobulin domain
  5. NM_001278406.2NP_001265335.2  leukocyte immunoglobulin-like receptor subfamily B member 2 isoform 5 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) 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 resulting protein (isoform 5) has a shorter and distinct C-terminus, compared to isoform 1. Isoform 5 lacks the transmembrane domain found in isoform 1 and is suspected to be soluble (PMID: 19658091).
    Source sequence(s)
    AF004231, EU915606
    UniProtKB/TrEMBL
    A2IXV5
    Conserved Domains (2) summary
    smart00410
    Location:231296
    IG_like; Immunoglobulin like
    cl11960
    Location:27118
    Ig; Immunoglobulin domain
  6. NM_005874.4NP_005865.3  leukocyte immunoglobulin-like receptor subfamily B member 2 isoform 1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AF004231, AK226015, AK297041, DC429053
    Consensus CDS
    CCDS12886.1
    UniProtKB/TrEMBL
    A2IXV5
    Related
    ENSP00000375629.4, ENST00000391749.4
    Conserved Domains (2) summary
    smart00410
    Location:231296
    IG_like; Immunoglobulin like
    cl11960
    Location:27118
    Ig; Immunoglobulin domain

RNA

  1. NR_103521.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) uses an alternate 5' exon structure and two alternate splice sites at internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF004231, AK310263, DC429031

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p12 Primary Assembly

    Range
    54273821..54281178 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_1

Genomic

  1. NW_003571054.1 Reference GRCh38.p12 ALT_REF_LOCI_1

    Range
    248562..255917 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_7

Genomic

  1. NW_003571060.1 Reference GRCh38.p12 ALT_REF_LOCI_7

    Range
    248805..253362 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_8

Genomic

  1. NW_003571061.2 Reference GRCh38.p12 ALT_REF_LOCI_8

    Range
    248817..256172 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_9

Genomic

  1. NT_187693.1 Reference GRCh38.p12 ALT_REF_LOCI_9

    Range
    248789..256147 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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