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KIR3DX1 Gene

protein-coding   GIFtS: 37
GCID: GC19P055044

Killer Cell Immunoglobulin-Like Receptor, Three Domains,...

(Previous name: leukocyte receptor cluster (LRC) member 12)
(Previous symbol: LENG12)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Killer Cell Immunoglobulin-Like Receptor, Three Domains, X11 2
LENG121 2 3
KIR3DL02 3
Leukocyte Receptor Cluster (LRC) Member 121
Leukocyte Receptor Cluster Member 123

External Ids:    HGNC: 250431   Entrez Gene: 900112   Ensembl: ENSG000001049707   UniProtKB: Q9H7L23   
ORGUL members:         

Export aliases for KIR3DX1 gene to outside databases

Previous GC identifers: GC19P059740 GC19P051367


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for KIR3DX1 Gene:
KIR3DX1 (killer cell immunoglobulin-like receptor, three domains, X1) is a protein-coding gene. An important paralog of this gene is LILRB4.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000019.9  NC_018930.2  NT_011109.17  NT_187693.1  
Regulatory elements:
   Regulatory transcription factor binding sites in the KIR3DX1 gene promoter:
         GR   RORalpha1   NRSF form 1   ARP-1   GR-alpha   NRSF form 2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for KIR3DX1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat KIR3DX1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19q13.42   Ensembl cytogenetic band:  19q13.42   HGNC cytogenetic band: 19q13.42

KIR3DX1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
KIR3DX1 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P055044:  view genomic region     (about GC identifiers)

Start:
55,043,909 bp from pter      End:
55,057,053 bp from pter
Size:
13,145 bases      Orientation:
plus strand

2 alternative locations:
Chr19+,NW_003571054 438,900-450,185      Chr19+,NW_003571060 437,417-448,703     

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: KI3X1_HUMAN, Q9H7L2 (See protein sequence)
Recommended Name: Putative killer cell immunoglobulin-like receptor-like protein KIR3DX1 precursor  
Size: 352 amino acids; 38777 Da
Caution: Could be the product of a pseudogene. According to PubMed:16911775, it could constitute the ancestral
killer immunoglobulin-like receptor gene in primates
Sequence caution: Sequence=BAB15757.1; Type=Miscellaneous discrepancy; Note=Unlikely isoform. Aberrant splice
sites and probable target of nonsense-mediated mRNA decay;
Secondary accessions: B7WNL0 Q8N0S4

Explore the universe of human proteins at neXtProt for KIR3DX1: NX_Q9H7L2

Explore proteomics data for KIR3DX1 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn78
  • Modification sites at PhosphoSitePlus

  • See KIR3DX1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


    ENSEMBL proteins: 
     ENSP00000396692   ENSP00000395115   ENSP00000401224   ENSP00000335388   ENSP00000221567  

    KIR3DX1 Human Recombinant Protein Products:

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    Browse Sino Biological Cell Lysates
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    Browse Proteins at Cloud-Clone Corp.

     
    Search eBioscience for Proteins for KIR3DX1 

     
    antibodies-online proteins for KIR3DX1 (2 products) 

     
    Search antibodies-online for peptides for KIR3DX1

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    antibodies-online kits for KIR3DX1 (2 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    IGD: Immunoglobulin superfamily / Immunoglobulin-like domain containing

    3 InterPro protein domains:
     IPR007110 Ig-like_dom
     IPR003599 Ig_sub
     IPR013783 Ig-like_fold

    Graphical View of Domain Structure for InterPro Entry Q9H7L2

    ProtoNet protein and cluster: Q9H7L2

    UniProtKB/Swiss-Prot: KI3X1_HUMAN, Q9H7L2
    Similarity: Contains 2 Ig-like C2-type (immunoglobulin-like) domains


    Find genes that share domains with KIR3DX1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
         
    Find genes that share ontologies with KIR3DX1           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for KIR3DX1

    miRNA
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    miRTarBase miRNAs that target KIR3DX1:
    hsa-mir-26b-5p (MIRT029150)

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    KI3X1_HUMAN, Q9H7L2: Secreted (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular3
    plasma membrane3
    cytosol1
    endoplasmic reticulum1
    mitochondrion1
    peroxisome1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--

    Find genes that share ontologies with KIR3DX1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for KIR3DX1
    Interactions:

        Search GeneGlobe Interaction Network for KIR3DX1

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for KIR3DX1 (ENSP000003353884) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    IKBKGENSP000003586224STRING: ENSP00000358622
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for KIR3DX1 (KI3X1)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for KIR3DX1 gene (2 alternative transcripts): 
    NM_001047605.1  NM_033206.1  

    Unigene Cluster for KIR3DX1:

    Killer cell immunoglobulin-like receptor, three domains, X1
    Hs.288520  [show with all ESTs]
    Unigene Representative Sequence: BC033195
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000446586(uc010yfc.1) ENST00000447145(uc010yfd.1) ENST00000434659(uc010yfb.1)
    ENST00000465702 ENST00000471931 ENST00000335056(uc010yfa.1 uc010erm.2)
    ENST00000221567 ENST00000482404
    miRNA
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    OriGene qSTAR qPCR primer pairs in human, mouse for KIR3DX1
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      QuantiTect SYBR Green Assays in human, mouse, rat KIR3DX1
      QuantiFast Probe-based Assays in human, mouse, rat KIR3DX1

    Additional mRNA sequence: 

    BC033195.1 BC171827.1 BC171832.1 BC171834.1 BC171838.1 BC171839.1 DQ224421.1 NR_026716.1 

    2 DOTS entries:

    DT.95133086  DT.95198652 

    5 AceView cDNA sequences:

    BC033195 BG743947 NM_033206 AK024467 BG744627 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    KIR3DX1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    KIR3DX1 Expression
    About this image

    KIR3DX1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    KIR3DX1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.288520

    UniProtKB/Swiss-Prot: KI3X1_HUMAN, Q9H7L2
    Tissue specificity: Expressed in NK-cells

        Custom PCR Arrays for KIR3DX1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for KIR3DX1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for KIR3DX1 gene from Selected species (see all 6)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    dog
    (Canis familiaris)
    Mammalia --
    Uncharacterized protein
    25(a)
    1 → many
    1(102576554-102577732)
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    14(a)
    1 → many
    GL343329.1(1197670-1218701)


    ENSEMBL Gene Tree for KIR3DX1 (if available)
    TreeFam Gene Tree for KIR3DX1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for KIR3DX1 gene
    LILRB42  KIR2DL42  LILRB12  KIR2DS42  LILRA62  LILRA52  IGSF12  KIR3DL12  
    OSCAR2  NCR12  LILRA42  ENSG000002177922  TARM12  LILRA32  LILRB52  KIR3DL32  
    LILRA12  KIR3DS12  KIR2DL12  A1BG2  LILRB22  KIR3DL22  LILRA22  KIR2DL32  
    FCAR2  GP62  LILRB32  
    Selected SIMAP similar genes for KIR3DX1 using alignment to 3 protein entries:     KI3X1_HUMAN (see all proteins) (see all similar genes):
    p58    KIR-G2    KIR-K39    KIR-K65    KIR-K61    KIR-K78
    KIR-K3    KIR-K36    KIR-K15    KIR-K64    KIR-K9    KIR3DL1/2V
    KIR3DS1    KIR-123FM    KIR222    KIR3DL1    KIR2DL4    KIR2DS5

    Find genes that share paralogs with KIR3DX1           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for KIR3DX1 (see all 443)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs110843471,2
    C,F,A,H--55041957(+) ATTTCG/CAATTT 1 -- us2k111Minor allele frequency- C:0.46NS EA NA WA 784
    rs1156106311,2
    C--55042001(+) CCTCAC/TCTTCA 1 -- us2k10--------
    rs1397038381,2
    C--55042002(+) CTCACC/GTTCAA 1 -- us2k10--------
    rs110843481,2
    C,F,A,H--55042060(+) GGCCAC/TGGCCC 1 -- us2k113Minor allele frequency- T:0.43NS EA NA WA CSA 761
    rs1822856451,2
    --55042061(+) GCCATA/GGCCCC 1 -- us2k10--------
    rs730619291,2
    --55042073(+) CTGCTA/GTTACT 1 -- us2k10--------
    rs110843491,2
    C,F,A,H--55042124(+) TCTTAG/TAACTT 1 -- us2k120Minor allele frequency- T:0.18NS EA NA WA CSA 2344
    rs1154022471,2
    C,F--55042132(+) CTTTAA/TTTTGT 1 -- us2k11Minor allele frequency- T:0.09WA 118
    rs1867961891,2
    --55042153(+) AATTGC/TACTGG 1 -- us2k10--------
    rs759046531,2
    C--55042165(+) TTAAAA/GCAGTT 1 -- us2k11Minor allele frequency- G:0.01EA 120

    HapMap Linkage Disequilibrium report for KIR3DX1 (55043909 - 55057053 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 9 variations for KIR3DX1:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2667609CNV Deletion23128226
    esv2718872CNV Deletion23290073
    nsv470158CNV Loss18288195
    nsv828638CNV Loss20364138
    dgv435n27CNV Loss19166990
    nsv522872CNV Loss19592680
    dgv4005n71CNV Loss21882294
    nsv518262CNV Gain19592680
    dgv1119e1CNV Complex17122850

    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing KIR3DX1
    DNA2.0 Custom Variant and Variant Library Synthesis for KIR3DX1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    Find genes that share disorders with KIR3DX1           About GenesLikeMe

    Human Genome Epidemiology (HuGE) Navigator: KIR3DX1 (1 document)

    Export disorders for KIR3DX1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for KIR3DX1 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with KIR3DX1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification of the ancestral killer immunoglobulin-like receptor gene in primates. (PubMed id 16911775)1, 2 Sambrook J.G.... Beck S. (BMC Genomics 2006)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. Human chromosome 19 and related regions in mouse: conservative and lineage-specific evolution. (PubMed id 11441184)1, 3 Dehal P....Stubbs L. (Science 2001)
    4. New genetic associations detected in a host response study to hepatitis B vaccine. (PubMed id 20237496)1 Davila S....Seielstad M. (Genes Immun. 2010)
    5. Expanding the substantial interactome of NEMO using protein microarrays. (PubMed id 20098747)1 Fenner B.J....Prehn J.H. (PLoS ONE 2010)
    6. Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. (PubMed id 21145461)1 Bennett E.J....Harper J.W. (Cell 2010)
    7. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)2 Grimwood J.... Lucas S.M. (Nature 2004)
    8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 90011 HGNC: 25043 AceView: FLJ00060 Ensembl:ENSG00000104970 euGenes: HUgn90011
    ECgene: KIR3DX1 H-InvDB: KIR3DX1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for KIR3DX1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for KIR3DX1 gene:
    Search GeneIP for patents involving KIR3DX1

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    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from genOway)
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     Browse ESI BIO Cell Lines and PureStem Progenitors for KIR3DX1
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     antibodies-online antibodies for KIR3DX1 (5 products)
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      Search antibodies-online for peptides for KIR3DX1
     antibodies-online proteins for KIR3DX1 (2 products)
           
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