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COA3 Gene

protein-coding   GIFtS: 33
GCID: GC17M040950

Cytochrome C Oxidase Assembly Factor 3

(Previous name: coiled-coil domain containing 56)
(Previous symbol: CCDC56)
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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
Cytochrome C Oxidase Assembly Factor 31 2     MITRAC122 3
CCDC561 2 3 5     Coiled-Coil Domain Containing 561
Coiled-Coil Domain-Containing Protein 562 3     Cytochrome C Oxidase Assembly Factor 3 Homolog, Mitochondrial2
Mitochondrial Translation Regulation Assembly Intermediate Of Cytochrome C
Oxidase Protein Of 12 KDa2 3
     Cytochrome C Oxidase Assembly Protein 3 Homolog, Mitochondrial2

External Ids:    HGNC: 249901   Entrez Gene: 289582   Ensembl: ENSG000001839787   OMIM: 6147755   UniProtKB: Q9Y2R03   

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(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 COA3 Gene:
This gene encodes a member of the cytochrome c oxidase assembly factor family. Studies of a related gene in fly
suggest that the encoded protein is localized to mitochondria and is essential for cytochrome c oxidase function.
(provided by RefSeq, Nov 2012)

GeneCards Summary for COA3 Gene:
COA3 (cytochrome c oxidase assembly factor 3) is a protein-coding gene.

UniProtKB/Swiss-Prot: COA3_HUMAN, Q9Y2R0
Function: Component of some MITRAC complex, a cytochrome c oxidase (COX) assembly intermediate complex that
regulates COX assembly. MITRAC complexes regulate both translation of mitochondrial encoded components and
assembly of nuclear-encoded components imported in mitochondrion. Required for efficient translation of MT-CO1
and mitochondrial respiratory chain complex IV assembly




(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:
   Search for regulatory transcription factor binding sites for COA3
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat COA3


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

Entrez Gene cytogenetic band: 17q21   Ensembl cytogenetic band:  17q21.31   HGNC cytogenetic band: 17q21.31

COA3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
COA3 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M040950:  view genomic region     (about GC identifiers)

Start:
40,947,165 bp from pter      End:
40,950,722 bp from pter
Size:
3,558 bases      Orientation:
minus 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: COA3_HUMAN, Q9Y2R0 (See protein sequence)
Recommended Name: Cytochrome c oxidase assembly factor 3 homolog, mitochondrial  
Size: 106 amino acids; 11731 Da
Subunit: Component of some MITRAC complex
Secondary accessions: A8K498

Explore the universe of human proteins at neXtProt for COA3: NX_Q9Y2R0

Explore proteomics data for COA3 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys48
  • Modification sites at PhosphoSitePlus

  • See COA3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001035521.1  
    ENSEMBL proteins: 
     ENSP00000467546   ENSP00000354762  

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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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    HGNC Gene Families:
    MITOAF: Mitochondrial respiratory chain complex assembly factors

    1 InterPro protein domain:
     IPR018628 Coiled-coil_56

    Graphical View of Domain Structure for InterPro Entry Q9Y2R0

    ProtoNet protein and cluster: Q9Y2R0

    UniProtKB/Swiss-Prot: COA3_HUMAN, Q9Y2R0
    Similarity: Belongs to the COA3 family


    Find genes that share domains with COA3           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: COA3_HUMAN, Q9Y2R0
    Function: Component of some MITRAC complex, a cytochrome c oxidase (COX) assembly intermediate complex that
    regulates COX assembly. MITRAC complexes regulate both translation of mitochondrial encoded components and
    assembly of nuclear-encoded components imported in mitochondrion. Required for efficient translation of MT-CO1
    and mitochondrial respiratory chain complex IV assembly

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI--
         
    Find genes that share ontologies with COA3           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for COA3:
     Increased gamma-H2AX phosphory 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for COA3

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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
    COA3_HUMAN, Q9Y2R0: Mitochondrion inner membrane; Single-pass membrane protein

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005739mitochondrion IDA--
    GO:0031305integral component of mitochondrial inner membrane IDA--

    Find genes that share ontologies with COA3           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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    Interactions:

        Search GeneGlobe Interaction Network for COA3

    2 Interacting proteins for COA3 (Q9Y2R01) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MT-CO1P003951EBI-6570446,EBI-2117234
    SURF1Q155261EBI-6570446,EBI-3915286
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0033617mitochondrial respiratory chain complex IV assembly IMP--
    GO:0070131positive regulation of mitochondrial translation IMP--

    Find genes that share ontologies with COA3           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
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      Browse compounds at ApexBio 

    Browse Tocris compounds for COA3



    (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 COA3 gene: 
    NM_001040431.2  

    Unigene Cluster for COA3:

    Cytochrome c oxidase assembly factor 3
    Hs.16059  [show with all ESTs]
    Unigene Representative Sequence: AK295023
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000586680 ENST00000328434(uc010wgz.1 uc002ibl.3)
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    Additional mRNA sequence: 

    AF070665.1 AK225611.1 AK290863.1 AK295023.1 BC002698.2 L38939.1 

    7 DOTS entries:

    DT.100883501  DT.100687790  DT.418667  DT.100883499  DT.100883503  DT.121006654  DT.95189650 

    Selected AceView cDNA sequences (see all 307):

    AI880118 BM695454 CR593427 BE395966 BQ771958 BU682744 CA941024 BM852772 
    BQ007233 BF589445 BG746387 AI186897 W93677 AI138484 AW161486 BM833188 
    AI432957 CB156071 AA603172 AA972535 AA595485 BM820249 BQ787040 AI092282 

    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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    COA3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    COA3 Expression
    About this image

    COA3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    COA3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.16059
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    In Situ
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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 COA3 gene from Selected species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Coa31 , 5 coiled-coil domain containing 565
    cytochrome C oxidase assembly factor 31
    83.15(n)1
    81.32(a)1
      11 (64.56 cM)5
    524691  NM_026618.21  NP_080894.11 
     1012779685 
    lizard
    (Anolis carolinensis)
    Reptilia COA36
    cytochrome c oxidase assembly factor 3
    72(a)
    1 ↔ 1
    6(62262325-62264366)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia ccdc561 coiled-coil domain containing 56 64.63(n)
    64.63(a)
      100135386  NM_001172297.1  NP_001165768.1 
    zebrafish
    (Danio rerio)
    Actinopterygii coa31 cytochrome C oxidase assembly factor 3 61.11(n)
    59.52(a)
      100141351  NM_001114916.2  NP_001108388.2 


    ENSEMBL Gene Tree for COA3 (if available)
    TreeFam Gene Tree for COA3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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      --

    (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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    Site Specific Mutation Identification with PCR Assays
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    (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: 614775    OMIM disorders: --


    Find genes that share disorders with COA3           About GenesLikeMe


    Export disorders for COA3 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 COA3 gene, integrated from 10 sources (see all 16):
    (articles sorted by number of sources associating them with COA3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Coiled coil domain-containing protein 56 (CCDC56) is a novel mitochondrial protein essential for cytochrome c oxidase function. (PubMed id 22610097)1, 3 Peralta S....Garesse R. (J. Biol. Chem. 2012)
    2. MITRAC links mitochondrial protein translocation to respiratory-chain assembly and translational regulation. (PubMed id 23260140)1, 2 Mick D.U.... Rehling P. (Cell 2012)
    3. Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase. (PubMed id 22356826)1, 3 Szklarczyk R.... Huynen M.A. (Genome Biol. 2012)
    4. 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)
    5. Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells. (PubMed id 11042152)1, 2 Zhang Q.-H.... Chen Z. (Genome Res. 2000)
    6. hCOA3 stabilizes cytochrome c oxidase 1 (COX1) and promotes cytochrome c oxidase assembly in human mitochondria. (PubMed id 23362268)1 Clemente P....Garesse R. (J. Biol. Chem. 2013)
    7. N-terminal acetylome analyses and functional insights of the N- terminal acetyltransferase NatB. (PubMed id 22814378)2 Van Damme P....Aldabe R. (Proc. Natl. Acad. Sci. U.S.A. 2012)
    8. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    9. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    10. Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach. (PubMed id 19413330)2 Gauci S....Mohammed S. (Anal. Chem. 2009)

    (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: 28958 HGNC: 24990 AceView: HSPC009 Ensembl:ENSG00000183978 euGenes: HUgn28958
    ECgene: COA3 H-InvDB: COA3

    (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 COA3 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 COA3 gene:
    Search GeneIP for patents involving COA3

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



    (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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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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