Human Gene LILRB2 (uc002qfb.3) Description and Page Index
  Description: Homo sapiens leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2 (LILRB2), transcript variant 1, mRNA.
RefSeq Summary (NM_005874): 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].
Transcript (Including UTRs)
   Position: hg19 chr19:54,777,675-54,785,033 Size: 7,359 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg19 chr19:54,778,537-54,784,351 Size: 5,815 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:54,777,675-54,785,033)mRNA (may differ from genome)Protein (598 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: LIRB2_HUMAN
DESCRIPTION: RecName: Full=Leukocyte immunoglobulin-like receptor subfamily B member 2; Short=LIR-2; Short=Leukocyte immunoglobulin-like receptor 2; AltName: Full=CD85 antigen-like family member D; AltName: Full=Immunoglobulin-like transcript 4; Short=ILT-4; AltName: Full=Monocyte/macrophage immunoglobulin-like receptor 10; Short=MIR-10; AltName: CD_antigen=CD85d; Flags: Precursor;
FUNCTION: Receptor for class I MHC antigens. Recognizes a broad spectrum of HLA-A, HLA-B, HLA-C and HLA-G alleles. Involved in the down-regulation of the immune response and the development of tolerance. Competes with CD8A for binding to class I MHC antigens. Inhibits FCGR1A-mediated phosphorylation of cellular proteins and mobilization of intracellular calcium ions.
SUBUNIT: Binds PTPN6 when phosphorylated. Binds FCGR1A.
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein.
TISSUE SPECIFICITY: Expressed on monocytes and B-cells, and at lower levels on dendritic cells. Detected at low levels in natural killer (NK) cells.
DOMAIN: Contains 3 copies of a cytoplasmic motif that is referred to as the immunoreceptor tyrosine-based inhibitor motif (ITIM). This motif is involved in modulation of cellular responses. The phosphorylated ITIM motif can bind the SH2 domain of several SH2- containing phosphatases.
PTM: Phosphorylated on tyrosine residues. Dephosphorylated by PTPN6.
SIMILARITY: Contains 4 Ig-like C2-type (immunoglobulin-like) domains.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LILRB2
CDC HuGE Published Literature: LILRB2
Positive Disease Associations: Cholesterol, HDL
Related Studies:
  1. Cholesterol, HDL
    Tanya M Teslovich et al. Nature 2010, Biological, clinical and population relevance of 95 loci for blood lipids., Nature. [PubMed 20686565]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 77.69 RPKM in Whole Blood
Total median expression: 206.26 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -105.70266-0.397 Picture PostScript Text
3' UTR -189.46862-0.220 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR003599 - Ig_sub

Pfam Domains:
PF13895 - Immunoglobulin domain

SCOP Domains:
48726 - Immunoglobulin

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2DYP
- X-ray MuPIT

2GW5
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q8N423
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001540 beta-amyloid binding
GO:0005515 protein binding
GO:0008157 protein phosphatase 1 binding
GO:0023029 MHC class Ib protein binding
GO:0032396 inhibitory MHC class I receptor activity
GO:0042288 MHC class I protein binding
GO:0042803 protein homodimerization activity
GO:0044877 macromolecular complex binding
GO:0050839 cell adhesion molecule binding

Biological Process:
GO:0002250 adaptive immune response
GO:0002376 immune system process
GO:0002578 negative regulation of antigen processing and presentation
GO:0002645 positive regulation of tolerance induction
GO:0002666 positive regulation of T cell tolerance induction
GO:0002767 immune response-inhibiting cell surface receptor signaling pathway
GO:0002774 Fc receptor mediated inhibitory signaling pathway
GO:0006955 immune response
GO:0006968 cellular defense response
GO:0007165 signal transduction
GO:0007166 cell surface receptor signaling pathway
GO:0007267 cell-cell signaling
GO:0007611 learning or memory
GO:0032755 positive regulation of interleukin-6 production
GO:0034113 heterotypic cell-cell adhesion
GO:0035307 positive regulation of protein dephosphorylation
GO:0042102 positive regulation of T cell proliferation
GO:0042130 negative regulation of T cell proliferation
GO:0043312 neutrophil degranulation
GO:0045591 positive regulation of regulatory T cell differentiation
GO:0050776 regulation of immune response
GO:0051248 negative regulation of protein metabolic process
GO:0051926 negative regulation of calcium ion transport
GO:0071222 cellular response to lipopolysaccharide
GO:1900271 regulation of long-term synaptic potentiation
GO:1900454 positive regulation of long term synaptic depression
GO:2001198 regulation of dendritic cell differentiation

Cellular Component:
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0070821 tertiary granule membrane
GO:0101003 ficolin-1-rich granule membrane


-  Descriptions from all associated GenBank mRNAs
  AF004231 - Homo sapiens monocyte/macrophage Ig-related receptor MIR-10 (MIR cl-10) mRNA, complete cds.
AF283987 - Homo sapiens leukocyte immunoglobulin-like receptor-2 (LILRB2) mRNA, LILRB2-v2 allele, complete cds.
AF283986 - Homo sapiens leukocyte immunoglobulin-like receptor-2 (LILRB2) mRNA, LILRB2-v1 allele, complete cds.
AK310263 - Homo sapiens cDNA, FLJ17305.
AK297071 - Homo sapiens cDNA FLJ53803 complete cds, highly similar to Leukocyte immunoglobulin-like receptorsubfamily B member 2 precursor.
BC036827 - Homo sapiens leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2, mRNA (cDNA clone MGC:46153 IMAGE:5212543), complete cds.
AF025528 - Homo sapiens leucocyte immunoglobulin-like receptor-2 (LIR-2) mRNA, complete cds.
BC025766 - Homo sapiens leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2, mRNA (cDNA clone IMAGE:5205611), with apparent retained intron.
AK226015 - Homo sapiens mRNA for Splice isoform 2 of Q8N423 variant, clone: FCC107A03.
AK297041 - Homo sapiens cDNA FLJ50797 complete cds, highly similar to Leukocyte immunoglobulin-like receptor subfamily B member 2 precursor.
AF000574 - Homo sapiens clone 1 immunoglobulin-like transcript 4 mRNA, complete cds.
AF011565 - Homo sapiens clone 26 immunoglobulin-like transcript 4 mRNA, complete cds.
AF011566 - Homo sapiens clone 17 immunoglobulin-like transcript 4 mRNA, complete cds.
JD176107 - Sequence 157131 from Patent EP1572962.
JD178177 - Sequence 159201 from Patent EP1572962.
JD437661 - Sequence 418685 from Patent EP1572962.
JD055101 - Sequence 36125 from Patent EP1572962.
JD486356 - Sequence 467380 from Patent EP1572962.
EU832815 - Synthetic construct Homo sapiens clone HAIB:100067844; DKFZo008E1133 leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2 protein (LILRB2) gene, encodes complete protein.
GQ129422 - Synthetic construct Homo sapiens clone HAIB:100068505; DKFZo004E1134 leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2 protein (LILRB2) gene, partial cds.
LC125264 - Homo sapiens LILRB2 mRNA for leukocyte immunoglobulin-like receptor subfamily B member 2, partial cds.
EU915606 - Homo sapiens leukocyte immunoglobulin-like receptor subfamily B member 2 soluble isoform (LILRB2) mRNA, complete cds, alternatively spliced.
AK298649 - Homo sapiens cDNA FLJ60053 complete cds, highly similar to Leukocyte immunoglobulin-like receptor subfamily B member 2 precursor.
DQ655938 - Homo sapiens clone UGL11c10, mRNA sequence.
JD261266 - Sequence 242290 from Patent EP1572962.
JD419636 - Sequence 400660 from Patent EP1572962.
JD138348 - Sequence 119372 from Patent EP1572962.
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-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8N423 (Reactome details) participates in the following event(s):

R-HSA-199043 LILRs interact with MHC Class I
R-HSA-6798747 Exocytosis of tertiary granule membrane proteins
R-HSA-6800426 Exocytosis of ficolin-rich granule membrane proteins
R-HSA-198933 Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
R-HSA-6798695 Neutrophil degranulation
R-HSA-1280218 Adaptive Immune System
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: ILT4, LIR2, LIRB2_HUMAN, MIR10, NM_005874, NP_005865, O75017, Q8N423, Q8NHJ7, Q8NHJ8
UCSC ID: uc002qfb.3
RefSeq Accession: NM_005874
Protein: Q8N423 (aka LIRB2_HUMAN or LIB2_HUMAN)
CCDS: CCDS12886.1, CCDS42612.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005874.3
exon count: 14CDS single in 3' UTR: no RNA size: 2940
ORF size: 1797CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2312.00frame shift in genome: no % Coverage: 99.49
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.