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    CALCOCO2 calcium binding and coiled-coil domain 2 [ Homo sapiens (human) ]

    Gene ID: 10241, updated on 12-Feb-2024

    Summary

    Official Symbol
    CALCOCO2provided by HGNC
    Official Full Name
    calcium binding and coiled-coil domain 2provided by HGNC
    Primary source
    HGNC:HGNC:29912
    See related
    Ensembl:ENSG00000136436 MIM:604587; AllianceGenome:HGNC:29912
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NDP52
    Summary
    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]
    Expression
    Ubiquitous expression in fat (RPKM 39.0), testis (RPKM 32.6) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See CALCOCO2 in Genome Data Viewer
    Location:
    17q21.32
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (48831035..48865245)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (49694621..49728978)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (46908397..46942607)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 125, pseudogene Neighboring gene tubulin tyrosine ligase like 6 Neighboring gene uncharacterized LOC105371813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8659 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:46908401-46909282 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12340 Neighboring gene uncharacterized LOC105371814 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12341 Neighboring gene small nucleolar RNA SNORA68 Neighboring gene SUMO2 pseudogene 17

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC17318

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of autophagosome maturation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of autophagosome maturation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to type II interferon IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in viral process TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in xenophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in xenophagy IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in PML body IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in PML body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in autophagosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in autophagosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in autophagosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasmic vesicle IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in membrane HDA PubMed 
    located_in nucleus TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    calcium-binding and coiled-coil domain-containing protein 2
    Names
    antigen nuclear dot 52 kDa protein
    nuclear domain 10 protein 52
    nuclear domain 10 protein NDP52
    nuclear dot protein 52

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001261390.2NP_001248319.1  calcium-binding and coiled-coil domain-containing protein 2 isoform 1

      See identical proteins and their annotated locations for NP_001248319.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC068531, AK298177, AL042638
      Consensus CDS
      CCDS58559.1
      UniProtKB/Swiss-Prot
      Q13137
      Related
      ENSP00000398523.2, ENST00000448105.6
      Conserved Domains (3) summary
      pfam06273
      Location:150211
      eIF-4B; Plant specific eukaryotic initiation factor 4B
      cl19219
      Location:189269
      DUF342; Protein of unknown function (DUF342)
      cl24005
      Location:253334
      DUF2570; Protein of unknown function (DUF2570)
    2. NM_001261391.2NP_001248320.1  calcium-binding and coiled-coil domain-containing protein 2 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon and includes an alternate exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC068531, AK293329
      Consensus CDS
      CCDS58558.1
      UniProtKB/Swiss-Prot
      Q13137
      Related
      ENSP00000424352.1, ENST00000509507.5
      Conserved Domains (3) summary
      pfam06273
      Location:147208
      eIF-4B; Plant specific eukaryotic initiation factor 4B
      cl23720
      Location:164259
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
      cl24005
      Location:250331
      DUF2570; Protein of unknown function (DUF2570)
    3. NM_001261393.2NP_001248322.1  calcium-binding and coiled-coil domain-containing protein 2 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two exons in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
      Source sequence(s)
      AC068531, AK303313
      Consensus CDS
      CCDS58560.1
      UniProtKB/Swiss-Prot
      Q13137
      Related
      ENSP00000406974.2, ENST00000416445.6
      Conserved Domains (3) summary
      pfam04871
      Location:139211
      Uso1_p115_C; Uso1 / p115 like vesicle tethering protein, C terminal region
      pfam07888
      Location:22301
      CALCOCO1; Calcium binding and coiled-coil domain (CALCOCO1) like
      cl24005
      Location:187268
      DUF2570; Protein of unknown function (DUF2570)
    4. NM_001261395.2NP_001248324.1  calcium-binding and coiled-coil domain-containing protein 2 isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks two consecutive internal exons and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (5) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC068531, AK293137, BE315542
      Consensus CDS
      CCDS58561.1
      UniProtKB/Swiss-Prot
      Q13137
      Related
      ENSP00000423437.1, ENST00000508679.5
      Conserved Domains (3) summary
      pfam06273
      Location:54115
      eIF-4B; Plant specific eukaryotic initiation factor 4B
      cl19219
      Location:93173
      DUF342; Protein of unknown function (DUF342)
      cl24005
      Location:157238
      DUF2570; Protein of unknown function (DUF2570)
    5. NM_005831.5NP_005822.1  calcium-binding and coiled-coil domain-containing protein 2 isoform 3

      See identical proteins and their annotated locations for NP_005822.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an exon in the 5' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AC068531, U22897
      Consensus CDS
      CCDS11538.1
      UniProtKB/Swiss-Prot
      B2RBT0, B4DDC4, B4DDT4, B4DP36, B4E0C0, E7ENK0, E7ETP5, E9PBE5, Q13137, Q53FQ5, Q53HB5, Q6IBN9, Q9BTF7
      Related
      ENSP00000258947.3, ENST00000258947.8
      Conserved Domains (1) summary
      cl25732
      Location:22316
      SMC_N; RecF/RecN/SMC N terminal domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      48831035..48865245
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047435100.1XP_047291056.1  calcium-binding and coiled-coil domain-containing protein 2 isoform X1

    2. XM_047435099.1XP_047291055.1  calcium-binding and coiled-coil domain-containing protein 2 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      49694621..49728978
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314673.1XP_054170648.1  calcium-binding and coiled-coil domain-containing protein 2 isoform X1

    2. XM_054314672.1XP_054170647.1  calcium-binding and coiled-coil domain-containing protein 2 isoform X1