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CALCOCO2 Gene

protein-coding   GIFtS: 58
GCID: GC17P046908

Calcium Binding And Coiled-Coil Domain 2

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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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Aliases
Calcium Binding And Coiled-Coil Domain 21 2     Nuclear Dot Protein 522 3
Antigen Nuclear Dot 52 KDa Protein2 3     NDP522 3
Nuclear Domain 10 Protein 522 3     Calcium-Binding And Coiled-Coil Domain-Containing Protein 22
Nuclear Domain 10 Protein NDP522 3     

External Ids:    HGNC: 299121   Entrez Gene: 102412   Ensembl: ENSG000001364367   OMIM: 6045875   UniProtKB: Q131373   

Export aliases for CALCOCO2 gene to outside databases

Previous GC identifers: GC17P044264 GC17P042276


(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 CALCOCO2 Gene:
This gene encodes a coiled-coil domain-containing protein. The encoded protein functions as a receptor for
ubiquitin-coated bacteria and plays an important role in innate immunity by mediating macroautophagy.
Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. (provided
by RefSeq, May 2012)

GeneCards Summary for CALCOCO2 Gene:
CALCOCO2 (calcium binding and coiled-coil domain 2) is a protein-coding gene. GO annotations related to this gene include protein homodimerization activity. An important paralog of this gene is TAX1BP1.

UniProtKB/Swiss-Prot: CACO2_HUMAN, Q13137
Function: May play a role in ruffle formation and actin cytoskeleton organization. Seems to negatively regulate
constitutive secretion

Gene Wiki entry for CALCOCO2 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_000017.10  NC_018928.2  NT_010783.16  
Regulatory elements:
   Regulatory transcription factor binding sites in the CALCOCO2 gene promoter:
         HFH-3   USF1   Sp1   GATA-3   USF2   USF-1:USF-2   GATA-2   GATA-1   FOXI1   USF-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCALCOCO2 promoter sequence
   Search Chromatin IP Primers for CALCOCO2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CALCOCO2


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

Entrez Gene cytogenetic band: 17q21.32   Ensembl cytogenetic band:  17q21.32   HGNC cytogenetic band: 17q21.32

CALCOCO2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CALCOCO2 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P046908:  view genomic region     (about GC identifiers)

Start:
46,908,350 bp from pter      End:
46,943,884 bp from pter
Size:
35,535 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., 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: CACO2_HUMAN, Q13137 (See protein sequence)
Recommended Name: Calcium-binding and coiled-coil domain-containing protein 2  
Size: 446 amino acids; 52254 Da
Subunit: Part of a complex consisting of CALCOCO2, TAX1BP1 and MYO6. Interacts with GEMIN4
Miscellaneous: According to PubMed:7540613, HSV-1 infection removes CALCOCO2 from the nucleus, however, it remains
faintly in areas shown to be domains, containing splicing components. Treatment with IFNB1/IFN-beta and
IFNG/IFN-gamma show an increase in number and size of CALCOCO2-specific dots and partial redistribution to the
cytoplasm. According to PubMed:9230084, IFNG/IFN-gamma increases gene expression only slightly and IFNB does not
increase expression
4 PDB 3D structures from and Proteopedia for CALCOCO2:
3VVV (3D)        3VVW (3D)        4GXL (3D)        4HAN (3D)    
Secondary accessions: B2RBT0 B4DDC4 B4DDT4 B4DP36 B4E0C0 E7ENK0 E7ETP5 E9PBE5 Q53FQ5 Q53HB5
Q6IBN9 Q9BTF7
Alternative splicing: 5 isoforms:  Q13137-1   Q13137-2   Q13137-3   Q13137-4   Q13137-5   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for CALCOCO2: NX_Q13137

Explore proteomics data for CALCOCO2 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys299, Lys312, Lys339, Lys395
  • Modification sites at PhosphoSitePlus

  • See CALCOCO2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (5 alternative transcripts): 
    NP_001248319.1  NP_001248320.1  NP_001248322.1  NP_001248324.1  NP_005822.1  

    ENSEMBL proteins: 
     ENSP00000258947   ENSP00000424352   ENSP00000398523   ENSP00000461083   ENSP00000425692  
     ENSP00000425090   ENSP00000406974   ENSP00000423437   ENSP00000461184   ENSP00000422697  
     ENSP00000424169   ENSP00000424889   ENSP00000424083   ENSP00000429963  

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    Cloud-Clone Corp. Proteins for CALCOCO2

     
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    antibodies-online proteins for CALCOCO2 (8 products) 

     
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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR012852 CoCoA

    Graphical View of Domain Structure for InterPro Entry Q13137

    ProtoNet protein and cluster: Q13137

    1 Blocks protein domain: IPB012852 Coiled-coil transcriptional coactivator-like


    Find genes that share domains with CALCOCO2           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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CACO2_HUMAN, Q13137
    Function: May play a role in ruffle formation and actin cytoskeleton organization. Seems to negatively regulate
    constitutive secretion

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI12869526
    GO:0042803protein homodimerization activity IPI9230084
         
    Find genes that share ontologies with CALCOCO2           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for CALCOCO2:
     Decreased influenza A virus in  Increased gamma-H2AX phosphory 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for CALCOCO2

    miRNA
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    miRTarBase miRNAs that target CALCOCO2:
    hsa-let-7b-5p (MIRT001647), hsa-mir-93-5p (MIRT028168), hsa-mir-142-3p (MIRT021616), hsa-mir-361-5p (MIRT044091), hsa-let-7d-5p (MIRT032106)

    Block miRNA regulation of human, mouse, rat CALCOCO2 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate CALCOCO2 (see all 10):
    hsa-miR-539 hsa-miR-3117-3p hsa-miR-134 hsa-miR-1258 hsa-miR-4275 hsa-miR-661 hsa-miR-34b hsa-miR-3118
    SwitchGear 3'UTR luciferase reporter plasmidCALCOCO2 3' UTR sequence
    Inhib. RNA
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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
    CACO2_HUMAN, Q13137: Cytoplasm, perinuclear region. Golgi apparatus. Cytoplasm, cytoskeleton. Note=According to
    PubMed:7540613, localizes to nuclear dots. According to PubMed:9230084 and PubMed:12869526, it is not a nuclear
    dot-associated protein but localizes predominantly in the cytoplasm with a coarse-grained distribution
    preferentially close to the nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytoskeleton5
    golgi apparatus5
    nucleus4
    cytosol2
    lysosome2
    vacuole2
    extracellular1
    plasma membrane1

    Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus TAS7540613
    GO:0005737cytoplasm IDA--
    GO:0005794Golgi apparatus IEA--
    GO:0005856cytoskeleton IEA--
    GO:0043231intracellular membrane-bounded organelle IDA--

    Find genes that share ontologies with CALCOCO2           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 CALCOCO2 About    
    See pathways by source

    SuperPathContained pathways About
    1NF-kappaB Signaling
    NF-kappaB Signaling
    2Apoptosis and Autophagy
    Apoptosis and Autophagy


    Find genes that share SuperPaths with CALCOCO2           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    2 Cell Signaling Technology (CST) Pathways for CALCOCO2
        Apoptosis and Autophagy
    NF-kappaB Signaling


        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for CALCOCO2
    Interactions:

        Search GeneGlobe Interaction Network for CALCOCO2

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

    Selected Interacting proteins for CALCOCO2 (Q131371, 2, 3 ENSP000002589474) via UniProtKB, MINT, STRING, and/or I2D (see all 130)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    APEX2Q9UBZ42, 3, ENSP000003641264MINT-68260 I2D: score=5 STRING: ENSP00000364126
    C20orf195Q9BVV22, 3, ENSP000003591154MINT-67765 I2D: score=5 STRING: ENSP00000359115
    CPNE7Q9UBL62, 3, ENSP000002687204MINT-66571 I2D: score=5 STRING: ENSP00000268720
    FXR2P511162, 3, ENSP000002501134MINT-67257 I2D: score=5 STRING: ENSP00000250113
    GABARAPL1Q9H0R82, 3, ENSP000002664584MINT-68290 I2D: score=5 STRING: ENSP00000266458
    About this table

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016032viral process TAS7540613
    GO:0034341response to interferon-gamma IDA9230084

    Find genes that share ontologies with CALCOCO2           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 CALCOCO2 (CACO2)



    (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 CALCOCO2 gene (5 alternative transcripts): 
    NM_001261390.1  NM_001261391.1  NM_001261393.1  NM_001261395.1  NM_005831.4  

    Unigene Cluster for CALCOCO2:

    Calcium binding and coiled-coil domain 2
    Hs.514920  [show with all ESTs]
    Unigene Representative Sequence: NM_001261390
    Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 28):
    ENST00000258947(uc002iof.3 uc010wlp.2 uc010wlq.2 uc010wlr.2 uc010wls.2)
    ENST00000503463 ENST00000509507 ENST00000448105 ENST00000510356 ENST00000575560
    ENST00000570513 ENST00000509415 ENST00000513119 ENST00000416445 ENST00000508679
    ENST00000372317 ENST00000576582 ENST00000511697 ENST00000505071 ENST00000507076
    ENST00000502761 ENST00000509014
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate CALCOCO2 (see all 10):
    hsa-miR-539 hsa-miR-3117-3p hsa-miR-134 hsa-miR-1258 hsa-miR-4275 hsa-miR-661 hsa-miR-34b hsa-miR-3118
    SwitchGear 3'UTR luciferase reporter plasmidCALCOCO2 3' UTR sequence
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CALCOCO2
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    Pre-validated RT2 qPCR Primer Assay in human, mouse / rat CALCOCO2
      QuantiTect SYBR Green Assays in human, mouse, rat CALCOCO2
      QuantiFast Probe-based Assays in human, mouse, rat CALCOCO2

    Additional mRNA sequence: 

    AF085965.1 AK222666.1 AK223227.1 AK293137.1 AK293329.1 AK298177.1 AK303313.1 AK304024.1 
    AK310648.1 AK314796.1 BC004130.2 BC015893.2 CR456763.1 U22897.1 

    23 DOTS entries:

    DT.117717  DT.100016048  DT.95237406  DT.96085432  DT.97771081  DT.95237405  DT.206252  DT.99957369 
    DT.99986777  DT.92443486  DT.95113656  DT.97779365  DT.120949524  DT.120949531  DT.120949540  DT.92443482 
    DT.92443488  DT.95108827  DT.100828387  DT.91841599  DT.92443480  DT.95237415  DT.95175794 

    Selected AceView cDNA sequences (see all 425):

    AW439679 BM854998 W76221 BQ672952 BI711269 AA854841 AA843821 CA414720 
    BE045697 BC015893 BF445960 BM542776 BC004130 T61167 CA415014 W37183 
    BU628882 BX398921 BP369002 CA443249 AU141952 W15405 AA856598 BQ962978 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for CALCOCO2 (see all 11)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c · 7d · 7e ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11a · 11b · 11c · 11d ^ 12a · 12b ^
    SP1:                    -           -     -     -           -                                                     -           -           -     -               
    SP2:                                                                                                              -           -           -     -               
    SP3:                    -           -     -     -           -                 -     -     -                                                                     
    SP4:                    -           -     -                 -                                                                                                   
    SP5:                                                                                                                                      -     -               

    ExUns: 13 ^ 14a · 14b ^ 15
    SP1:                        
    SP2:                        
    SP3:                        
    SP4:                        
    SP5:                        


    ECgene alternative splicing isoforms for CALCOCO2

    (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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    CALCOCO2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTAATTTCTC
    CALCOCO2 Expression
    About this image


    CALCOCO2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 21) fully expand
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
     
     Ovary (Reproductive System)
             Oviduct
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Brain (Nervous System)
             Cerebral Cortex
     
     Inner Cell Mass (Early Embryonic Tissues)
             Inner Cell Mass Cells Inner Cell Mass
    CALCOCO2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CALCOCO2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.514920

    UniProtKB/Swiss-Prot: CACO2_HUMAN, Q13137
    Tissue specificity: Expressed in all tissues tested with highest expression in skeletal muscle and lowest in brain

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    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CALCOCO2

    (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)
    About This Section

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    This gene was present in the common ancestor of chordates.

    Orthologs for CALCOCO2 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Calcoco25 calcium binding and coiled-coil domain 2   --   11 (59.40 cM) 96099326 
    chicken
    (Gallus gallus)
    Aves CALCOCO21 calcium binding and coiled-coil domain 2 62.12(n)
    52.05(a)
      419993  XM_004948566.1  XP_004948623.1 
    lizard
    (Anolis carolinensis)
    Reptilia CALCOCO26
    calcium binding and coiled-coil domain 2
    42(a)
    1 ↔ 1
    6(75917227-75939347)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia calcoco21 calcium binding and coiled-coil domain 2 52.03(n)
    38.46(a)
      448562  NM_001006827.1  NP_001006828.1 
    zebrafish
    (Danio rerio)
    Actinopterygii calcoco21 calcium binding and coiled-coil domain 2 47.95(n)
    34.22(a)
      553776  NM_001020741.1  NP_001018577.1 


    ENSEMBL Gene Tree for CALCOCO2 (if available)
    TreeFam Gene Tree for CALCOCO2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CALCOCO2 gene
    TAX1BP12  CALCOCO12  
    Selected SIMAP similar genes for CALCOCO2 using alignment to 10 protein entries:     CACO2_HUMAN (see all proteins) (see all similar genes):
    RBP7    C14orf105    DCAF17    IK    RHBG    SLC24A1
    HDGFRP2    MTO1    ARL6IP5    DUSP3    HEXDC    TNNT1
    TAF2    FRG1    ZNF429    ASPSCR1    CSPP1    TUBA1C

    Find genes that share paralogs with CALCOCO2           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)
    About This Section

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    Selected SNPs for CALCOCO2 (see all 749)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs37604491,2
    C,F--46906400(+) CCATCT/CGTTCA 5 -- us2k17Minor allele frequency- C:0.35EA NA CSA WA 1845
    rs1867497321,2
    --46906568(+) AACCCC/TGTCTT 5 -- us2k10--------
    rs58207291,2
    C,F--46906743(+) AAAAAA/-GGAAT 5 -- us2k1 trp32Minor allele frequency- -:0.50NA 4
    rs1900024651,2
    --46906777(+) TTCCCC/TTGCCT 5 -- us2k10--------
    rs1811239641,2
    --46907099(+) GCCAGA/GGTTAT 5 -- us2k10--------
    rs352516971,2
    C--46907173(+) TTTTT-/TGAGAC 5 -- us2k11Minor allele frequency- T:0.00NA 2
    rs360227631,2
    C,F,H--46907173(+) TATTCT/CTTTTT 5 -- us2k13Minor allele frequency- C:0.03NS 554
    rs1850901701,2
    --46907281(+) GGCTCA/TAGTGA 5 -- us2k10--------
    rs1896026611,2
    --46907630(+) AGGCAC/TGAGAA 5 -- us2k10--------
    rs2001824581,2
    --46907722(+) GTCTC-/AAAAAA 5 -- us2k10--------

    HapMap Linkage Disequilibrium report for CALCOCO2 (46908350 - 46943884 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for CALCOCO2:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv482969CNV Loss15286789
    esv29639CNV Loss19812545

    Human Gene Mutation Database (HGMD): CALCOCO2
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing CALCOCO2
    DNA2.0 Custom Variant and Variant Library Synthesis for CALCOCO2

    (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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    OMIM gene information: 604587    OMIM disorders: --


    Find genes that share disorders with CALCOCO2           About GenesLikeMe

    Genetic Association Database (GAD): CALCOCO2

    Export disorders for CALCOCO2 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 CALCOCO2 gene, integrated from 10 sources (see all 41):
    (articles sorted by number of sources associating them with CALCOCO2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular characterization of NDP52, a novel protein of the nuclear domain 10, which is redistributed upon virus infection and interferon treatment. (PubMed id 7540613)1, 2, 3 Korioth F.... Frey J. (J. Cell Biol. 1995)
    2. T6BP and NDP52 are myosin VI binding partners with potential roles in cytokine signalling and cell adhesion. (PubMed id 17635994)1, 2 Morriswood B.... Buss F. (J. Cell Sci. 2007)
    3. HCC-associated protein HCAP1, a variant of GEMIN4, interacts with zinc-finger proteins. (PubMed id 12869526)1, 2 Di Y.... Gu J. (J. Biochem. 2003)
    4. Cellular localization, expression, and structure of the nuclear dot protein 52. (PubMed id 9230084)1, 2 Sternsdorf T.... Will H. (J. Cell Biol. 1997)
    5. Sterical hindrance promotes selectivity of the autophagy cargo receptor NDP52 for the danger receptor galectin-8 in antibacterial autophagy. (PubMed id 23386746)1 Li S....Randow F. (Sci Signal 2013)
    6. Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies. (PubMed id 23624108)1 Ellinghaus D....Franke A. (Gastroenterology 2013)
    7. Structural basis for recognition of autophagic receptor NDP52 by the sugar receptor galectin-8. (PubMed id 23511477)1 Kim B.W....Song H.K. (Nat Commun 2013)
    8. Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization. (PubMed id 23503661)1 Sarraf S.A....Harper J.W. (Nature 2013)
    9. Selective autophagy degrades DICER and AGO2 and regulates miRNA activity. (PubMed id 23143396)1 Gibbings D....Voinnet O. (Nat. Cell Biol. 2012)
    10. LC3C, bound selectively by a noncanonical LIR motif in NDP52, is required for antibacterial autophagy. (PubMed id 23022382)1 von Muhlinen N.... Randow F. (Mol. Cell 2012)

    (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: 10241 HGNC: 29912 AceView: NDP52 Ensembl:ENSG00000136436 euGenes: HUgn10241
    ECgene: CALCOCO2 H-InvDB: CALCOCO2

    (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)
    About This Section

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    NameDescription
    PharmGKB entry for CALCOCO2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for CALCOCO2 gene:
    Search GeneIP for patents involving CALCOCO2

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



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