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

Gene ID: 10241, updated on 24-Nov-2020

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
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

Genomic context

See CALCOCO2 in Genome Data Viewer
Location:
17q21.32
Exon count:
15
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (48831035..48865245)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (46908350..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 uncharacterized LOC105371814 Neighboring gene SUMO2 pseudogene 17 Neighboring gene ATP synthase membrane subunit c locus 1

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

Homology

Clone Names

  • MGC17318

Gene Ontology Provided by GOA

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

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
    Q13137
    Related
    ENSP00000258947.3, ENST00000258947.7
    Conserved Domains (1) summary
    cl25732
    Location:22316
    SMC_N; RecF/RecN/SMC N terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20201120

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

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