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ATAD3B Gene

protein-coding   GIFtS: 50
GCID: GC01P001397

ATPase Family, AAA Domain Containing 3B

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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
ATPase Family, AAA Domain Containing 3B1 2
TOB32 3 5
AAA-TOB32 3
KIAA12733 5
AAA-ATPase TOB32
ATPase Family AAA Domain-Containing Protein 3B2

External Ids:    HGNC: 240071   Entrez Gene: 838582   Ensembl: ENSG000001600727   OMIM: 6123175   UniProtKB: Q5T9A43   

Export aliases for ATAD3B gene to outside databases

Previous GC identifers: GC01P001359 GC01P001493 GC01P000680


(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 ATAD3B Gene:
ATAD3A (MIM 612316) and ATAD3B are mitochondrial membrane proteins that contribute to the stabilization of large
mitochondrial DNA (mtDNA)-protein complexes called nucleoids (He et al., 2007 (PubMed 17210950)).(supplied by
OMIM, Sep 2008)

GeneCards Summary for ATAD3B Gene:
ATAD3B (ATPase family, AAA domain containing 3B) is a protein-coding gene. GO annotations related to this gene include nucleoside-triphosphatase activity. An important paralog of this gene is ATAD3C.

UniProtKB/Swiss-Prot: ATD3B_HUMAN, Q5T9A4
Function: May play a role in a mitochondrial network organization typical for stem cells, characterized by reduced
mitochondrial metabolism, low mtDNA copies and fragmentated mitochondrial network. may act by suppressing ATAD3A
function, interfering with ATAD3A interaction with matrix nucleoid complexes




(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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Regulatory elements:
   Regulatory transcription factor binding sites in the ATAD3B gene promoter:
         POU2F2 (Oct-2.1)   Oct-B1   oct-B3   oct-B2   Lmo2   POU2F2   POU2F2C   POU2F1   POU2F1a   POU2F2B   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidATAD3B promoter sequence
   Search Chromatin IP Primers for ATAD3B

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ATAD3B


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

Entrez Gene cytogenetic band: 1p36.33   Ensembl cytogenetic band:  1p36.33   HGNC cytogenetic band: 1p36.33

ATAD3B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ATAD3B gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P001397:  view genomic region     (about GC identifiers)

Start:
1,407,143 bp from pter      End:
1,433,228 bp from pter
Size:
26,086 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: ATD3B_HUMAN, Q5T9A4 (See protein sequence)
Recommended Name: ATPase family AAA domain-containing protein 3B  
Size: 648 amino acids; 72573 Da
Subunit: Forms heterooligomers with ATAD3A. Interacts with components of the mitochondrial ribosome, including
MRPL11 and MRPS18B, and with other proteins involved in mitochondrial RNA metabolism, possibly via interaction
with ATAD3A. Interacts with GADD45GIP1
Developmental stage: Expressed in proliferating embryonic stem cells and down-regulated during differentiation
Sequence caution: Sequence=BAA86587.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: A8K3H1 Q6ZRB5 Q9BUK4 Q9ULE7
Alternative splicing: 3 isoforms:  Q5T9A4-1   Q5T9A4-2   Q5T9A4-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for ATAD3B: NX_Q5T9A4

Explore proteomics data for ATAD3B at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys394
  • Modification sites at PhosphoSitePlus

  • See ATAD3B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_114127.3  
    ENSEMBL proteins: 
     ENSP00000311766   ENSP00000368015  

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    antibodies-online proteins for ATAD3B (3 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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    HGNC Gene Families:
    AATP: ATPases / AAA-type

    4 InterPro protein domains:
     IPR003959 ATPase_AAA_core
     IPR027417 P-loop_NTPase
     IPR003593 AAA+_ATPase
     IPR021911 DUF3523

    Graphical View of Domain Structure for InterPro Entry Q5T9A4

    ProtoNet protein and cluster: Q5T9A4

    UniProtKB/Swiss-Prot: ATD3B_HUMAN, Q5T9A4
    Similarity: Belongs to the AAA ATPase family


    Find genes that share domains with ATAD3B           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: ATD3B_HUMAN, Q5T9A4
    Function: May play a role in a mitochondrial network organization typical for stem cells, characterized by reduced
    mitochondrial metabolism, low mtDNA copies and fragmentated mitochondrial network. may act by suppressing ATAD3A
    function, interfering with ATAD3A interaction with matrix nucleoid complexes
    Induction: Up-regulated by MYC

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166nucleotide binding ----
    GO:0005524ATP binding IEA--
    GO:0017111nucleoside-triphosphatase activity IEA--
         
    Find genes that share ontologies with ATAD3B           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for ATAD3B

    miRNA
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    miRTarBase miRNAs that target ATAD3B:
    hsa-let-7b-5p (MIRT001652)

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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
    ATD3B_HUMAN, Q5T9A4: Mitochondrion inner membrane; Peripheral membrane protein. Note=Has been found to co-purify
    with nucleoids (PubMed:22453275). Since it does not face the mitochondrial matrix, the association with nucleoids
    could be mediated by ATAD3A
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    mitochondrion5
    cytosol2
    nucleus2
    extracellular1
    golgi apparatus1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005743mitochondrial inner membrane IEA--

    Find genes that share ontologies with ATAD3B           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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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for ATAD3B
    Interactions:

        Search GeneGlobe Interaction Network for ATAD3B

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

    Selected Interacting proteins for ATAD3B (Q5T9A42, 3 ENSP000003117664) via UniProtKB, MINT, STRING, and/or I2D (see all 437)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ICT1Q141972, 3, ENSP000003015854MINT-8079030 I2D: score=1 STRING: ENSP00000301585
    SLC25A3Q003252, ENSP000002283184MINT-8079030 MINT-6488791 STRING: ENSP00000228318
    PHB2Q996232, ENSP000003823624MINT-8079030 MINT-6488791 STRING: ENSP00000382362
    SARS2Q9NP812, ENSP000002214314MINT-8079030 MINT-8415512 STRING: ENSP00000221431
    AGO3Q9H9G73, ENSP000003622874I2D: score=2 STRING: ENSP00000362287
    About this table

    (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 ATAD3B (ATD3B)



    (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 ATAD3B gene: 
    NM_031921.4  

    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000308647(uc001afv.3 uc021oeq.1) ENST00000472194(uc001afw.2 uc001afx.3)
    ENST00000378736 ENST00000485748 ENST00000474481 ENST00000378741
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      QuantiTect SYBR Green Assays in human, mouse, rat ATAD3B
      QuantiFast Probe-based Assays in human, mouse, rat ATAD3B

    Selected AceView cDNA sequences (see all 466):

    CR609514 BQ129356 BU155205 BU552768 CA431591 BM561826 BC002542 BQ053152 
    C20767 CK823587 BQ925983 BU507084 BC018701 CF127746 BQ223719 BQ943893 
    BU159690 BG760426 BG695858 BQ688832 BQ069149 BE251451 BF312210 NM_031921 

    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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    ATAD3B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCCAGGGGCC
    ATAD3B Expression
    About this image


    ATAD3B 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
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Ovary (Reproductive System)
             Oviduct
     
     Pancreas (Endocrine System)
             Islets of Langerhans
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
    ATAD3B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ATAD3B Protein Expression

    UniProtKB/Swiss-Prot: ATD3B_HUMAN, Q5T9A4
    Tissue specificity: Tends to be down-regulated in differentiated cells and re-expressed in pluripotent stem cells
    or cancer cells (at protein level)

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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 eukaryotes.

    Orthologs for ATAD3B gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves --
    Uncharacterized protein
    77(a)
    1 → many
    21(2156093-2174774)
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    75(a)
    1 → many
    AAWZ02037771(1424-14229)
    zebrafish
    (Danio rerio)
    Actinopterygii atad3b6
    ATPase family, AAA domain containing 3B
    81(a)
    1 → many
    22(47436-49330) ENSDARG00000086848
    fruit fly
    (Drosophila melanogaster)
    Insecta bor6
    belphegor
    58(a)
    1 → many
    3R(12087077-12089837)
    worm
    (Caenorhabditis elegans)
    Secernentea atad-36
    Protein ATAD-3 (atad-3) mRNA, complete cds
    54(a)
    1 → many
    II(10248991-10251171) WBGene00010015
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT2G183301 AT2G18330 47.47(n)
    40.12(a)
      816348  NM_127390.3  NP_565435.1 
    rice
    (Oryza sativa)
    Liliopsida Os02g07065001 Os02g0706500 47.45(n)
    38.88(a)
      4330465  NM_001054406.1  NP_001047871.1 
            Species with no ortholog for ATAD3B

    ENSEMBL Gene Tree for ATAD3B (if available)
    TreeFam Gene Tree for ATAD3B (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ATAD3B gene
    ATAD3C2  ATAD3A2  
    3 SIMAP similar genes for ATAD3B using alignment to 2 protein entries:     ATD3B_HUMAN (see all proteins):
    ATAD3A    DKFZp761L1023    ATAD3C

    Find genes that share paralogs with ATAD3B           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 ATAD3B (see all 890)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1396132271,2
    --1406266(+) CTGCAC/GGTATA 1 -- us2k10--------
    rs1838775351,2
    C--1406453(+) ACGCCC/TTTTGT 1 -- us2k10--------
    rs1880652681,2
    --1406517(+) TCGTCA/GACTCT 1 -- us2k10--------
    rs773400741,2
    C--1406518(+) TGCTGA/GCTCCT 1 -- us2k10--------
    rs12407341,2
    C--1406524(+) ctcttC/Gggact 1 -- us2k15Minor allele frequency- G:0.31WA CSA EA 242
    rs1445316741,2
    --1406607(+) TGGACA/GCACAT 1 -- us2k10--------
    rs1478167061,2
    C--1406707(+) CATACC/TGACAT 1 -- us2k10--------
    rs1413362611,2
    --1406716(+) ATACCA/GGTTCT 1 -- us2k10--------
    rs1450891331,2
    C--1406761(+) TTATTA/CAGGCT 1 -- us2k10--------
    rs1449423491,2
    --1406799(+) AGTCAC/TTCCAT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for ATAD3B (1407143 - 1433228 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for ATAD3B (see all 27):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2747585CNV Deletion23290073
    esv2747696CNV Deletion23290073
    esv2661503CNV Deletion23128226
    esv2662001CNV Deletion23128226
    esv2747363CNV Deletion23290073
    esv2747474CNV Deletion23290073
    esv1254392CNV Insertion17803354
    esv25832CNV Loss19812545
    nsv871421CNV Loss21882294
    nsv871954CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing ATAD3B
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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: 612317    OMIM disorders: --


    Find genes that share disorders with ATAD3B           About GenesLikeMe

    Genetic Association Database (GAD): ATAD3B
    Human Genome Epidemiology (HuGE) Navigator: ATAD3B (4 documents)

    Export disorders for ATAD3B 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 ATAD3B gene, integrated from 10 sources (see all 40):
    (articles sorted by number of sources associating them with ATAD3B)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Prediction of the coding sequences of unidentified human genes. XV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 10574462)1, 2, 3 Nagase T.... Ohara O. (DNA Res. 1999)
    2. ATAD3B is a human embryonic stem cell specific mitochondrial protein, re-expressed in cancer cells, that functions as dominant negative for the ubiquitous ATAD3A. (PubMed id 22664726)1, 2 Merle N....Baudier J. (Mitochondrion 2012)
    3. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PubMed id 20877624)1, 4 Hendrickson S.L....O'Brien S.J. (PLoS ONE 2010)
    4. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (Nature 2006)
    5. Molecular characterization of the tumor-associated antigen AAA- TOB3. (PubMed id 16909202)1, 2 Schaffrik M.... Gires O. (Cell. Mol. Life Sci. 2006)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    7. 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)
    8. Expression analysis of ATAD3 isoforms in rodent and human cell lines and tissues. (PubMed id 24239551)1 Li S....Rousseau D. (Gene 2014)
    9. The protein interaction landscape of the human CMGC kinase group. (PubMed id 23602568)1 Varjosalo M....Gstaiger M. (Cell Rep 2013)
    10. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)

    (in PubMed, OMIM, and NCBI Bookshelf)
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      Query String
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    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: 83858 HGNC: 24007 AceView: ATAD3AandATAD3BandFLJ37183 Ensembl:ENSG00000160072 euGenes: HUgn83858
    ECgene: ATAD3B H-InvDB: ATAD3B

    (According to HUGE)
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    HUGE: KIAA1273

    (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 ATAD3B 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 ATAD3B gene:
    Search GeneIP for patents involving ATAD3B

    GeneCards and IP:
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