Human Gene LILRA1 (uc002qgh.2) Description and Page Index
  Description: Homo sapiens leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1 (LILRA1), transcript variant 1, mRNA.
RefSeq Summary (NM_006863): 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].
Transcript (Including UTRs)
   Position: hg19 chr19:55,105,041-55,113,687 Size: 8,647 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr19:55,105,710-55,112,282 Size: 6,573 Coding Exon Count: 9 

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 (chr19:55,105,041-55,113,687)mRNA (may differ from genome)Protein (489 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: LIRA1_HUMAN
DESCRIPTION: RecName: Full=Leukocyte immunoglobulin-like receptor subfamily A member 1; AltName: Full=CD85 antigen-like family member I; AltName: Full=Leukocyte immunoglobulin-like receptor 6; Short=LIR-6; AltName: CD_antigen=CD85i; Flags: Precursor;
FUNCTION: May act as receptor for class I MHC antigens.
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein.
TISSUE SPECIFICITY: Detected in monocytes and B-cells.
SIMILARITY: Contains 4 Ig-like C2-type (immunoglobulin-like) domains.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LILRA1
CDC HuGE Published Literature: LILRA1
Positive Disease Associations: Kidney Diseases
Related Studies:
  1. Kidney Diseases
    Shih-Jen Hwang et al. BMC medical genetics 2007, A genome-wide association for kidney function and endocrine-related traits in the NHLBI's Framingham Heart Study., BMC medical genetics. [PubMed 17903292]
    Kidney function traits and TSH are associated with SNPs on the Affymetrix GeneChip Human Mapping 100K SNP set. These data will serve as a valuable resource for replication as more SNPs associated with kidney function and endocrine traits are identified.

-  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: 16.22 RPKM in Whole Blood
Total median expression: 40.99 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 -94.70254-0.373 Picture PostScript Text
3' UTR -394.771405-0.281 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
IPR016332 - A1B_glyco/leuk_Ig-like_rcpt
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR003599 - Ig_sub

Pfam Domains:
PF00047 - Immunoglobulin domain
PF13895 - Immunoglobulin domain

SCOP Domains:
48726 - Immunoglobulin

ModBase Predicted Comparative 3D Structure on O75019
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 Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003823 antigen binding
GO:0004888 transmembrane signaling receptor activity

Biological Process:
GO:0002250 adaptive immune response
GO:0002376 immune system process
GO:0006952 defense response
GO:0007166 cell surface receptor signaling pathway
GO:0050776 regulation of immune response

Cellular Component:
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AF041034 - Homo sapiens immunoglobulin-like transcript 1-like protein mRNA, partial cds.
BC047007 - Homo sapiens leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1, mRNA (cDNA clone IMAGE:4431264), containing frame-shift errors.
AK290919 - Homo sapiens cDNA FLJ76163 complete cds, highly similar to Homo sapiens leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1 (LILRA1), mRNA.
AK311226 - Homo sapiens cDNA, FLJ18268.
AF025530 - Homo sapiens leucocyte immunoglobulin-like receptor-6a (LIR-6) mRNA, complete cds.
BC063009 - Homo sapiens leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1, mRNA (cDNA clone IMAGE:5215529), partial cds.
BC032238 - Homo sapiens leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1, mRNA (cDNA clone IMAGE:5177304), containing frame-shift errors.
AF025529 - Homo sapiens leucocyte immunoglobulin-like receptor-6b (LIR-6) mRNA, complete cds.
JD138348 - Sequence 119372 from Patent EP1572962.
JD419636 - Sequence 400660 from Patent EP1572962.
JD261266 - Sequence 242290 from Patent EP1572962.
AK310122 - Homo sapiens cDNA, FLJ17164.
JD227135 - Sequence 208159 from Patent EP1572962.
BC093708 - Homo sapiens leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1, mRNA (cDNA clone MGC:120743 IMAGE:7939553), complete cds.
BC101514 - Homo sapiens leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1, mRNA (cDNA clone MGC:126563 IMAGE:8069020), complete cds.
EU915602 - Homo sapiens leukocyte immunoglobulin-like receptor subfamily A member 1 soluble isoform (LILRA1) mRNA, complete cds, alternatively spliced.
KJ893205 - Synthetic construct Homo sapiens clone ccsbBroadEn_02599 LILRA1 gene, encodes complete protein.
JD369942 - Sequence 350966 from Patent EP1572962.
JD187244 - Sequence 168268 from Patent EP1572962.
JD269333 - Sequence 250357 from Patent EP1572962.
JD566450 - Sequence 547474 from Patent EP1572962.
JD091371 - Sequence 72395 from Patent EP1572962.
MA877523 - JP 2018536436-A/9359: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877524 - JP 2018536436-A/9360: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877525 - JP 2018536436-A/9361: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877526 - JP 2018536436-A/9362: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877527 - JP 2018536436-A/9363: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877528 - JP 2018536436-A/9364: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877529 - JP 2018536436-A/9365: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877530 - JP 2018536436-A/9366: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877531 - JP 2018536436-A/9367: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877532 - JP 2018536436-A/9368: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877574 - JP 2018536436-A/9410: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877575 - JP 2018536436-A/9411: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877576 - JP 2018536436-A/9412: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877589 - JP 2018536436-A/9425: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877590 - JP 2018536436-A/9426: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877600 - JP 2018536436-A/9436: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877601 - JP 2018536436-A/9437: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877604 - JP 2018536436-A/9440: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877605 - JP 2018536436-A/9441: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877606 - JP 2018536436-A/9442: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877607 - JP 2018536436-A/9443: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877608 - JP 2018536436-A/9444: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877613 - JP 2018536436-A/9449: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877614 - JP 2018536436-A/9450: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877669 - JP 2018536436-A/9505: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877670 - JP 2018536436-A/9506: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877671 - JP 2018536436-A/9507: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877674 - JP 2018536436-A/9510: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877675 - JP 2018536436-A/9511: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877676 - JP 2018536436-A/9512: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877721 - JP 2018536436-A/9557: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877727 - JP 2018536436-A/9563: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877734 - JP 2018536436-A/9570: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877735 - JP 2018536436-A/9571: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877736 - JP 2018536436-A/9572: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877737 - JP 2018536436-A/9573: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877738 - JP 2018536436-A/9574: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877739 - JP 2018536436-A/9575: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877740 - JP 2018536436-A/9576: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877743 - JP 2018536436-A/9579: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877744 - JP 2018536436-A/9580: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877745 - JP 2018536436-A/9581: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877746 - JP 2018536436-A/9582: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
MA877793 - JP 2018536436-A/9629: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY599935 - KR 1020180133840-A/10095: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY599936 - KR 1020180133840-A/10096: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY599937 - KR 1020180133840-A/10097: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY599938 - KR 1020180133840-A/10098: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY599939 - KR 1020180133840-A/10099: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY599940 - KR 1020180133840-A/10100: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY599941 - KR 1020180133840-A/10101: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY599942 - KR 1020180133840-A/10102: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY599943 - KR 1020180133840-A/10103: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY599944 - KR 1020180133840-A/10104: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY599986 - KR 1020180133840-A/10146: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY599987 - KR 1020180133840-A/10147: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY599988 - KR 1020180133840-A/10148: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600001 - KR 1020180133840-A/10161: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600002 - KR 1020180133840-A/10162: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600012 - KR 1020180133840-A/10172: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600013 - KR 1020180133840-A/10173: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600016 - KR 1020180133840-A/10176: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600017 - KR 1020180133840-A/10177: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600018 - KR 1020180133840-A/10178: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600019 - KR 1020180133840-A/10179: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600020 - KR 1020180133840-A/10180: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600025 - KR 1020180133840-A/10185: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600026 - KR 1020180133840-A/10186: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600081 - KR 1020180133840-A/10241: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600082 - KR 1020180133840-A/10242: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600083 - KR 1020180133840-A/10243: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600086 - KR 1020180133840-A/10246: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600087 - KR 1020180133840-A/10247: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600088 - KR 1020180133840-A/10248: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600133 - KR 1020180133840-A/10293: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600139 - KR 1020180133840-A/10299: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600146 - KR 1020180133840-A/10306: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600147 - KR 1020180133840-A/10307: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600148 - KR 1020180133840-A/10308: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600149 - KR 1020180133840-A/10309: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600150 - KR 1020180133840-A/10310: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600151 - KR 1020180133840-A/10311: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600152 - KR 1020180133840-A/10312: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600155 - KR 1020180133840-A/10315: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600156 - KR 1020180133840-A/10316: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600157 - KR 1020180133840-A/10317: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600158 - KR 1020180133840-A/10318: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.
LY600205 - KR 1020180133840-A/10365: COMPOSITIONS AND METHODS FOR IMMUNOONCOLOGY.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O75019 (Reactome details) participates in the following event(s):

R-HSA-199043 LILRs interact with MHC Class I
R-HSA-198933 Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
R-HSA-1280218 Adaptive Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: LIR6, LIRA1_HUMAN, NM_006863, NP_006854, O75018, O75019, Q3MJA6, uc002qgh.1
UCSC ID: uc002qgh.2
RefSeq Accession: NM_006863
Protein: O75019 (aka LIRA1_HUMAN or LIA1_HUMAN)
CCDS: CCDS12901.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006863.2
exon count: 10CDS single in 3' UTR: no RNA size: 3129
ORF size: 1470CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3197.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # 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.