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CD1D Gene

protein-coding   GIFtS: 66
GCID: GC01P158149

CD1d Molecule

(Previous names: CD1D antigen, d polypeptide, CD1d antigen)
  See CD1D-related diseases
at  

(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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Aliases
CD1d Molecule1 2     Antigen-Presenting Glycoprotein CD1d2
CD1D Antigen, D Polypeptide1 2     Differentiation Antigen CD1-Alpha-32
CD1d Antigen1 3     HMC Class I Antigen-Like Glycoprotein CD1D2
R3G12 3     T-Cell Surface Glycoprotein CD1d2
CD1A2     Thymocyte Antigen CD1D2
R32     

External Ids:    HGNC: 16371   Entrez Gene: 9122   Ensembl: ENSG000001584737   OMIM: 1884105   UniProtKB: P158133   

Export aliases for CD1D gene to outside databases

Previous GC identifers: GC01P155941 GC01P153882 GC01P154927 GC01P155366 GC01P154962 GC01P156416 GC01P129508


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for CD1D Gene:
This gene encodes a divergent member of the CD1 family of transmembrane glycoproteins, which are structurally
related to the major histocompatibility complex (MHC) proteins and form heterodimers with beta-2-microglobulin.
The CD1 proteins mediate the presentation of primarily lipid and glycolipid antigens of self or microbial origin
to T cells. The human genome contains five CD1 family genes organized in a cluster on chromosome 1. The CD1
family members are thought to differ in their cellular localization and specificity for particular lipid ligands.
The protein encoded by this gene localizes to late endosomes and lysosomes via a tyrosine-based motif in the
cytoplasmic tail. (provided by RefSeq, Jul 2008)

GeneCards Summary for CD1D Gene:
CD1D (CD1d molecule) is a protein-coding gene. Diseases associated with CD1D include mycobacterium malmoense, and relapsing polychondritis. GO annotations related to this gene include receptor activity and cell adhesion molecule binding. An important paralog of this gene is CD1A.

UniProtKB/Swiss-Prot: CD1D_HUMAN, P15813
Function: Antigen-presenting protein that binds self and non-self glycolipids and presents them to T-cell
receptors on natural killer T-cells

Gene Wiki entry for CD1D Gene


(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_000001.10  NT_004487.20  NC_018912.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the CD1D gene promoter:
         AML1a   FOXD3   E47   AREB6   PPAR-gamma1   POU2F1   POU2F1a   HOXA5   STAT3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCD1D promoter sequence
   Search Chromatin IP Primers for CD1D

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CD1D


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

Entrez Gene cytogenetic band: 1q23.1   Ensembl cytogenetic band:  1q23.1   HGNC cytogenetic band: 1q23.1

CD1D Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CD1D gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P158149:  view genomic region     (about GC identifiers)

Start:
158,149,737 bp from pter      End:
158,156,217 bp from pter
Size:
6,481 bases      Orientation:
plus strand

(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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: CD1D_HUMAN, P15813 (See protein sequence)
Recommended Name: Antigen-presenting glycoprotein CD1d precursor  
Size: 335 amino acids; 37717 Da
Subunit: Heterodimer with B2M (beta-2-microglobulin). Interacts with MHC II
Miscellaneous: During protein synthesis and maturation, CD1 family members bind endogenous lipids that are
replaced by lipid or glycolipid antigens when the proteins are internalized and pass through endosomes, before
trafficking back to the cell surface (By similarity)
Selected PDB 3D structures from and Proteopedia for CD1D (see all 12):
1ZT4 (3D)        2PO6 (3D)        3HUJ (3D)        3SDX (3D)        3TZV (3D)        3U0P (3D)    
Secondary accessions: D3DVD5 Q5W0J3 Q9UMM3 Q9Y5M4

Explore the universe of human proteins at neXtProt for CD1D: NX_P15813

Explore proteomics data for CD1D at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn38, Asn60, Asn126, Asn181
  • Modification sites at PhosphoSitePlus

  • See CD1D Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001757.1  
    ENSEMBL proteins: 
     ENSP00000357153  

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    Search eBioscience for ELISAs for CD1D 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    CD: CD molecules
    C1SET: Immunoglobulin superfamily / C1-set domain containing

    5 InterPro protein domains:
     IPR011162 MHC_I/II-like_Ag-recog
     IPR013783 Ig-like_fold
     IPR003597 Ig_C1-set
     IPR007110 Ig-like_dom
     IPR011161 MHC_I-like_Ag-recog

    Graphical View of Domain Structure for InterPro Entry P15813

    ProtoNet protein and cluster: P15813

    1 Blocks protein domain: IPB003597 Immunoglobulin C-type

    UniProtKB/Swiss-Prot: CD1D_HUMAN, P15813
    Similarity: Contains 1 Ig-like (immunoglobulin-like) domain


    Find genes that share domains with CD1D           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, 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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CD1D_HUMAN, P15813
    Function: Antigen-presenting protein that binds self and non-self glycolipids and presents them to T-cell
    receptors on natural killer T-cells

         Genatlas biochemistry entry for CD1D:
    cell differentiation antigen CD1D,49kDa,cell surface molecule,B2M associated,identified by monoclonal antibody
    NOR3.2 expressed on a cortical thymocyte cell line (see CD1@)

         Gene Ontology (GO): Selected molecular function terms (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004872receptor activity IC11315191
    GO:0005515protein binding ----
    GO:0030881beta-2-microglobulin binding TAS14500461
    GO:0030882lipid antigen binding IDA19124746
    GO:0030883endogenous lipid antigen binding IBA--
         
    Find genes that share ontologies with CD1D           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for CD1D:
     Decreased Hepatitis C virus re 

         11 MGI mutant phenotypes (inferred from 8 alleles(MGI details for Cd1d1):
     behavior/neurological  cardiovascular system  hematopoietic system  homeostasis/metabolism  immune system 
     liver/biliary system  mortality/aging  nervous system  renal/urinary system  respiratory system 
     skeleton 

    Find genes that share phenotypes with CD1D           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for CD1D: Cd1d1/Cd1d2Cd1d1/tm1Crw Cd1d1tm1.2Aben Cd1d1tm1Luc Cd1d1tm1Crw Cd1d1/Cd1d2Cd1d1/tm1Spb

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CD1D
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for CD1D
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for CD1D

    miRNA
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    miRTarBase miRNAs that target CD1D:
    hsa-mir-335-5p (MIRT019031)

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    6 qRT-PCR Assays for microRNAs that regulate CD1D:
    hsa-miR-22 hsa-miR-4311 hsa-miR-1271 hsa-miR-514b-5p hsa-miR-513c hsa-miR-96
    SwitchGear 3'UTR luciferase reporter plasmidCD1D 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat CD1D

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    Sino Biological Human cDNA Clone for CD1D
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CD1D


    (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
    CD1D_HUMAN, P15813: Cell membrane; Single-pass type I membrane protein. Endosome membrane. Lysosome membrane.
    Note=Subject to intracellular trafficking between the cell membrane, endosomes and lysosomes
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    endosome5
    lysosome5
    plasma membrane5
    vacuole5
    endoplasmic reticulum2
    extracellular1
    nucleus1

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IDA19124746
    GO:0005765lysosomal membrane IEA--
    GO:0005887integral component of plasma membrane TAS11315191
    GO:0009986cell surface IDA19124746
    GO:0010008endosome membrane IEA--

    Find genes that share ontologies with CD1D           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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    SuperPaths for CD1D About    
    See pathways by source

    SuperPathContained pathways About
    1TNF Signaling
    NF-kB (NFkB) Pathway0.46
    2Hematopoietic cell lineage
    Hematopoietic cell lineage
    3Amoebiasis
    Amoebiasis


    Find genes that share SuperPaths with CD1D           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Sino Biological Pathway for CD1D
        NF-kB (NFkB) Pathway


    2 Kegg Pathways  (Kegg details for CD1D):
        Hematopoietic cell lineage
    Amoebiasis

        Pathway & Disease-focused RT2 Profiler PCR Arrays including CD1D: 
              Innate & Adaptive Immune Responses in human mouse rat
              Cell Surface Markers in human mouse rat
              Antigen Presenting Cells in human mouse rat
              T-cell & B-cell Activation in human mouse rat
              Hematopoiesis in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for CD1D

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for CD1D (P158133 ENSP000003571534) via UniProtKB, MINT, STRING, and/or I2D (see all 27)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    B2MP617693, ENSP000003408584I2D: score=5 STRING: ENSP00000340858
    CALRP277973, ENSP000003208664I2D: score=3 STRING: ENSP00000320866
    PTPRCP085753, ENSP000003563464I2D: score=3 STRING: ENSP00000356346
    CD74P042333, ENSP000000095304I2D: score=2 STRING: ENSP00000009530
    P4HTMQ9NXG63, ENSP000003414224I2D: score=1 STRING: ENSP00000341422
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 10):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016032viral process IEA--
    GO:0016045detection of bacterium TAS14500461
    GO:0019048modulation by virus of host morphology or physiology ----
    GO:0034113heterotypic cell-cell adhesion TAS19124746
    GO:0042102positive regulation of T cell proliferation IDA19124746

    Find genes that share ontologies with CD1D           About GenesLikeMe



    (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 CD1D

    Selected HMDB Compounds for CD1D (see all 519)    About this table
    CompoundSynonyms CAS #PubMed Ids
    3-Dehydrosphinganine1-Hydroxy-2-amino-3-oxo-octadecane (see all 9)16105-69-4--
    3-O-Sulfogalactosylceramide (d18:1/12:0)Sulfatide (d18:1/12:0) (see all 13)852100-88-0--
    3-O-Sulfogalactosylceramide (d18:1/14:0)Sulfatide (d18:1/14:0) (see all 13)----
    3-O-Sulfogalactosylceramide (d18:1/16:0)Sulfatide (d18:1/16:0) (see all 13)862509-48-6--
    3-O-Sulfogalactosylceramide (d18:1/18:0)Sulfatide (d18:1/18:0) (see all 13)244215-65-4--
    3-O-Sulfogalactosylceramide (d18:1/18:1(9Z))Sulfatide (d18:1/18:1(9Z)) (see all 13)----
    3-O-Sulfogalactosylceramide (d18:1/20:0)Sulfatide (d18:1/20:0) (see all 13)265096-81-9--
    3-O-Sulfogalactosylceramide (d18:1/22:0)Sulfatide (d18:1/22:0) (see all 13)265096-83-1--
    3-O-Sulfogalactosylceramide (d18:1/24:0)Sulfatide (d18:1/24:0) (see all 16)151122-71-3--
    3-O-Sulfogalactosylceramide (d18:1/24:1(15Z))Sulfatide (d18:1/24:1(15Z)) (see all 13)151057-28-2--

    1 DrugBank Compound for CD1D    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Cis-tetracosenoyl sulfatide-- --target--10592235

    7 Novoseek inferred chemical compound relationships for CD1D gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    alpha-galactosylceramide 90 18 19651460 (1), 10692041 (1), 12360465 (1), 15147365 (1) (see all 13)
    glycolipid 80.5 23 12730881 (4), 17277112 (2), 10754338 (1), 18460919 (1) (see all 15)
    lipid 44.3 26 17372201 (6), 19124746 (2), 19863613 (2), 16982809 (2) (see all 11)
    retinoid 19 2 16982809 (1), 17392484 (1)
    ceramide 18.1 6 16456021 (2), 14551186 (1)
    retinoic acid 11 19 17392484 (6), 16982809 (3), 19651460 (2)
    vitamin a 4.47 1 17392484 (1)



    Find genes that share compounds with CD1D           About GenesLikeMe



    (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 CD1D gene: 
    NM_001766.3  

    Unigene Cluster for CD1D:

    CD1d molecule
    Hs.1799  [show with all ESTs]
    Unigene Representative Sequence: NM_001766
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000368171(uc009wsr.1 uc009wst.1 uc001frr.3 uc009wss.3)

    miRNA
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    6 qRT-PCR Assays for microRNAs that regulate CD1D:
    hsa-miR-22 hsa-miR-4311 hsa-miR-1271 hsa-miR-514b-5p hsa-miR-513c hsa-miR-96
    SwitchGear 3'UTR luciferase reporter plasmidCD1D 3' UTR sequence
    Inhib. RNA
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    GenScript: all cDNA clones in your preferred vector: CD1D (NM_001766)
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    Primer
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    OriGene qPCR primer pairs and template standards for CD1D
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat CD1D
      QuantiTect SYBR Green Assays in human, mouse, rat CD1D
      QuantiFast Probe-based Assays in human, mouse, rat CD1D

    Additional mRNA sequence: 

    AK225996.1 AK310749.1 BC027926.1 J04142.1 

    6 DOTS entries:

    DT.113444  DT.100674898  DT.113445  DT.121337575  DT.100713243  DT.100644124 

    Selected AceView cDNA sequences (see all 44):

    AU099295 AI990497 NM_001766 CR615787 T29620 AU105006 F02407 T08190 
    F01433 BC027926 AI344373 BX370654 AA450238 AA380729 BI834737 AA451684 
    AI825555 T08191 AL561022 J04142 AW949814 F06138 AW956859 AA974299 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for CD1D (see all 7)    About this scheme

    ExUns: 1a · 1b ^ 2a · 2b · 2c · 2d ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b · 5c · 5d ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b
    SP1:                                      -                                               -                                 
    SP2:        -                             -                                                                                 
    SP3:                                -     -                                                                                 
    SP4:                                      -     -                                                                           
    SP5:                                -     -     -                                                                           


    ECgene alternative splicing isoforms for CD1D

    (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)
    About This Section

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    CD1D expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CCTGATTTTA
    CD1D Expression
    About this image


    CD1D expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 7) fully expand
     
     Blood (Cardiovascular System)    fully expand to see all 7 entries
             Double Negative 2 Thymocytes Thymus
     
     Thymus (Hematopoietic System)    fully expand to see all 5 entries
             Double Negative 2 Thymocytes Thymus
     
     Endothelium (Cardiovascular System)    fully expand to see all 2 entries
             Endothelial Cells Blood Brain Barrier
     
     Brain (Nervous System)    fully expand to see all 2 entries
             Endothelial Cells Blood Brain Barrier
     
     Limb (Muscoskeletal System)
             Mesenchymal Condensate Cells Zeugopod
    CD1D Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CD1D Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.1799

    UniProtKB/Swiss-Prot: CD1D_HUMAN, P15813
    Tissue specificity: Expressed on cortical thymocytes, on certain T-cell leukemias, and in various other tissues

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              Hematopoiesis in human mouse rat

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    (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 CD1D gene from Selected species (see all 7)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Cd1d11 , 5 CD1d1 antigen1, 5 75.47(n)1
    62.58(a)1
      3 (37.91 cM)5
    124791  NM_007639.31  NP_031665.21 
     869958345 
    chicken
    (Gallus gallus)
    Aves CD1A16
    CD1.26
    Gallus gallus CD1b molecule (CD1B), mRNA.
    24(a)
    22(a)
    many ↔ many
    many ↔ many
    16(2102-4938)
    16(5769-8509)
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    26(a)
    1 → many
    2(189404875-189415760)


    ENSEMBL Gene Tree for CD1D (if available)
    TreeFam Gene Tree for CD1D (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CD1D gene
    CD1A2  CD1B2  CD1C2  CD1E2  
    4 SIMAP similar genes for CD1D using alignment to 1 protein entry:     CD1D_HUMAN:
    CD1A    CD1C    CD1E    CD1B

    Find genes that share paralogs with CD1D           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 CD1D (see all 206)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs8590021,2
    C,F--158147792(-) GTGGAG/AGGCGG 1 -- us2k13Minor allele frequency- A:0.19WA NA EA 358
    rs1409053511,2
    --158147908(+) AGTGGA/TTCTCC 1 -- us2k10--------
    rs8590031,2
    C,F,O,H--158148054(-) AAGTTT/CAACAG 1 -- us2k112Minor allele frequency- C:0.22NS EA NA WA 920
    rs1501608601,2
    --158148129(+) GAGTTA/CTTTAG 1 -- us2k10--------
    rs8590041,2
    C,F,H--158148184(-) GAGGAT/CACATC 1 -- us2k117Minor allele frequency- C:0.01NS EA NA WA CSA 798
    rs789540641,2
    C,F--158148412(+) AATTAA/GCACAT 1 -- us2k11Minor allele frequency- G:0.05WA 118
    rs8590051,2
    C,F,O,H--158148599(-) AAATAT/GTTTAT 1 -- us2k1 tfbs313Minor allele frequency- G:0.21MN NS EA NA WA 1106
    rs1886236611,2
    --158148629(+) AAAACA/GTTTCA 1 -- us2k10--------
    rs1927639501,2
    --158148691(+) AAAAAA/GTGTCT 1 -- us2k10--------
    rs1849827741,2
    --158148727(+) TATCCA/GTATAA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for CD1D (158149737 - 158156217 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for CD1D:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv393n71CNV Gain21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing CD1D
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 188410    OMIM disorders: --

    2 diseases for CD1D:    
    About MalaCards
    mycobacterium malmoense    relapsing polychondritis

    1 disease from the University of Copenhagen DISEASES database for CD1D:
    Hypersensitivity reaction type II disease

    Find genes that share disorders with CD1D           About GenesLikeMe

    7 Novoseek inferred disease relationships for CD1D gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    autoimmunity 40.5 1 15100293 (1)
    autoimmune diseases 37.5 5 14719188 (1), 19415116 (1), 20477630 (1), 15654963 (1) (see all 5)
    rheumatoid arthritis 6.37 2 14719188 (1), 16178791 (1)
    multiple sclerosis 4.53 2 10884613 (1), 16178791 (1)
    inflammation 1.59 4 19651460 (2), 11927549 (1)
    shock 0 3 12952923 (2), 12952910 (1)
    tumors 0 9 17071498 (3), 15100293 (1), 16403914 (1), 10450506 (1) (see all 6)

    Genetic Association Database (GAD): CD1D
    Human Genome Epidemiology (HuGE) Navigator: CD1D (5 documents)

    Export disorders for CD1D 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 CD1D gene, integrated from 10 sources (see all 204):
    (articles sorted by number of sources associating them with CD1D)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Isolation and characterization of a cDNA and gene coding for a fourth CD1 molecule. (PubMed id 2463622)1, 2, 3 Balk S.P.... Terhorst C. (Proc. Natl. Acad. Sci. U.S.A. 1989)
    2. Regulation of intracellular trafficking of human CD1d by association with MHC class II molecules. (PubMed id 11927549)1, 2, 9 Kang S.-J. and Cresswell P. (EMBO J. 2002)
    3. Susceptibility to Guillain-BarrAc syndrome is associated to polymorphisms of CD1 genes. (PubMed id 16820217)1, 4, 9 Caporale C.M....Uncini A. (J. Neuroimmunol. 2006)
    4. CD1d-lipid-antigen recognition by the semi-invariant NKT T-cell receptor. (PubMed id 17581592)1, 2, 9 Borg N.A....Rossjohn J. (Nature 2007)
    5. Distinct endosomal trafficking requirements for presentation of autoantigens and exogenous lipids by human CD1d molecules. (PubMed id 17475845)1, 2 Chen X.... Gumperz J.E. (J. Immunol. 2007)
    6. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (Nature 2006)
    7. CD1d ligands: the good, the bad, and the ugly. (PubMed id 16818729)1, 2 Brutkiewicz R.R. (J. Immunol. 2006)
    8. The crystal structure of human CD1d with and without alpha- galactosylceramide. (PubMed id 16007090)1, 2 Koch M.... Cerundolo V. (Nat. Immunol. 2005)
    9. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    10. CD1 genotyping of patients with Mycobacterium malmoense pulmonary disease. (PubMed id 11580851)1, 4 Jones D.C....Bunce M. (Tissue Antigens 2001)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    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: 912 HGNC: 1637 AceView: CD1D Ensembl:ENSG00000158473 euGenes: HUgn912
    ECgene: CD1D Kegg: 912 H-InvDB: CD1D

    (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 CD1D Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for CD1D Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for CD1D gene:
    Search GeneIP for patents involving CD1D

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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