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    ATAD3B ATPase family AAA domain containing 3B [ Homo sapiens (human) ]

    Gene ID: 83858, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ATAD3Bprovided by HGNC
    Official Full Name
    ATPase family AAA domain containing 3Bprovided by HGNC
    Primary source
    HGNC:HGNC:24007
    See related
    Ensembl:ENSG00000160072 MIM:612317; AllianceGenome:HGNC:24007
    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
    TOB3; AAA-TOB3
    Summary
    The protein encoded by this gene is localized to the mitochondrial inner membrane, where it can bind to a highly-related protein, ATAD3A. ATAD3A appears to interact with matrix nucleoid complexes, and the encoded protein negatively regulates that interaction. This gene is expressed almost exclusively in pluripotent embryonic stem cells and some cancer cells. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]
    Expression
    Ubiquitous expression in bone marrow (RPKM 7.4), testis (RPKM 6.3) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See ATAD3B in Genome Data Viewer
    Location:
    1p36.33
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (1471765..1509466)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (906136..943970)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (1407145..1433228)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr1:1370998-1371187 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20 Neighboring gene von Willebrand factor A domain containing 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1389959-1390458 Neighboring gene ATPase family AAA domain containing 3C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1397006-1397780 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 75 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1409130-1409976 Neighboring gene MPRA-validated peak11 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1443749-1444392 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1444393-1445034 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 76 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 77 Neighboring gene ATPase family AAA domain containing 3A Neighboring gene Sharpr-MPRA regulatory region 185 Neighboring gene transmembrane protein 240

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Increased AAA-TOB3 correlates with lymph node metastasis and advanced stage of lung adenocarcinoma. Liu Y, et al. Int J Biol Markers, 2017 Jul 24. PMID 28623644
    2. ATAD3B is a mitophagy receptor mediating clearance of oxidative stress-induced damaged mitochondrial DNA. Shu L, et al. EMBO J, 2021 Apr 15. PMID 33665835, Free PMC Article
    3. Integrative analysis of deep sequencing data identifies estrogen receptor early response genes and links ATAD3B to poor survival in breast cancer. Ovaska K, et al. PLoS Comput Biol, 2013. PMID 23818839, Free PMC Article
    4. ATAD 3A and ATAD 3B are distal 1p-located genes differentially expressed in human glioma cell lines and present in vitro anti-oncogenic and chemoresistant properties. Hubstenberger A, et al. Exp Cell Res, 2008 Sep 10. PMID 18639545
    5. The AAA+ protein ATAD3 has displacement loop binding properties and is involved in mitochondrial nucleoid organization. He J, et al. J Cell Biol, 2007 Jan 15. PMID 17210950, Free PMC Article

    See all (152) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Circ_ATAD3B inhibits cell proliferation of breast cancer via mediating the miR-570-3p/MX2 axis.
      Title: Circ_ATAD3B inhibits cell proliferation of breast cancer via mediating the miR-570-3p/MX2 axis.
    2. ATAD3B and SKIL polymorphisms associated with antipsychotic-induced QTc interval change in patients with schizophrenia: a genome-wide association study.
      Title: ATAD3B and SKIL polymorphisms associated with antipsychotic-induced QTc interval change in patients with schizophrenia: a genome-wide association study.
    3. ATAD3B is a mitophagy receptor mediating clearance of oxidative stress-induced damaged mitochondrial DNA.
      Title: ATAD3B is a mitophagy receptor mediating clearance of oxidative stress-induced damaged mitochondrial DNA.
    4. AAA-TOB3 was highly expressed in lung adenocarcinoma, and the up-regulation of AAA-TOB3 correlated with lymph node metastasis and advanced stage of lung adenocarcinoma.
      Title: Increased AAA-TOB3 correlates with lymph node metastasis and advanced stage of lung adenocarcinoma.
    5. ATAD3B region deletions cause cerebellar dysfunction associated with altered mitochondrial DNA and cholesterol metabolism.
      Title: ATAD3 gene cluster deletions cause cerebellar dysfunction associated with altered mitochondrial DNA and cholesterol metabolism.
    6. exploring ATAD3 mRNA expression, we confirmed the existence of an alternative splicing in rodent and of several mRNA isoforms in human
      Title: Expression analysis of ATAD3 isoforms in rodent and human cell lines and tissues.
    7. results indicated the ATAD3B gene, which does not have ERalpha binding site within 20 kb of its TSS, to be significantly associated with poor patient survival.
      Title: Integrative analysis of deep sequencing data identifies estrogen receptor early response genes and links ATAD3B to poor survival in breast cancer.
    8. ATAD3B is a negative regulator of ATAD3A and may function as an adaptor of mitochondrial homeostasis and metabolism in human pluripotent embryonic stem cells and cancer cells.
      Title: ATAD3B is a human embryonic stem cell specific mitochondrial protein, re-expressed in cancer cells, that functions as dominant negative for the ubiquitous ATAD3A.
    9. ATAD3 may therefore be implicated in an unknown but essential and growth-linked mitochondrial function existing since pluri-cellular -organization and involved in tumorigenesis.
      Title: [ATAD3, a vital membrane-bound mitochondrial ATPase involved in tumor progression].
    10. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vpu vpu HIV-1 Vpu is identified to have a physical interaction with ATPase family, AAA domain containing 3B (ATAD3B) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1273

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in mitochondrion organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in ficolin-1-rich granule membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrial inner membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in secretory granule membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    ATPase family AAA domain-containing protein 3B
    Names
    AAA-ATPase TOB3

    NCBI Reference Sequences (RefSeq)

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    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_001317238.2 → NP_001304167.1  ATPase family AAA domain-containing protein 3B isoform AAA-TOB3s precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (AAA-TOB3s) has a shorter and distinct N-terminus compared to isoform AAA-TOB3l.
      Source sequence(s)
      AL157945, AL645728, BC009938
      UniProtKB/TrEMBL
      Q96T67
      Related
      ENST00000472194.6
      Conserved Domains (2) summary
      pfam00004
      Location:302 → 429
      AAA; ATPase family associated with various cellular activities (AAA)
      pfam12037
      Location:49 → 240
      DUF3523; Domain of unknown function (DUF3523)

    2. NM_031921.6 → NP_114127.3  ATPase family AAA domain-containing protein 3B isoform AAA-TOB3l

      See identical proteins and their annotated locations for NP_114127.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (AAA-TOB3l).
      Source sequence(s)
      AK290586, AL645728, BC009938
      Consensus CDS
      CCDS30.1
      UniProtKB/Swiss-Prot
      A8K3H1, Q5T9A4, Q6ZRB5, Q9BUK4, Q9ULE7
      UniProtKB/TrEMBL
      Q96T67
      Related
      ENSP00000500094.1, ENST00000673477.1
      Conserved Domains (5) summary
      TIGR01242
      Location:198 → 556
      26Sp45; 26S proteasome subunit P45 family
      pfam00004
      Location:348 → 475
      AAA; ATPase family associated with various cellular activities (AAA)
      pfam12037
      Location:42 → 286
      DUF3523; Domain of unknown function (DUF3523)
      cd16269
      Location:151 → 162
      GBP_C; coiled coil [structural motif]
      cl20817
      Location:94 → 179
      GBP_C; Guanylate-binding protein, C-terminal domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      1471765..1509466
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005244806.4 → XP_005244863.1  ATPase family AAA domain-containing protein 3B isoform X1

      UniProtKB/TrEMBL
      Q96T67
      Conserved Domains (3) summary
      TIGR01242
      Location:198 → 564
      26Sp45; 26S proteasome subunit P45 family
      pfam00004
      Location:348 → 475
      AAA; ATPase family associated with various cellular activities (AAA)
      pfam12037
      Location:42 → 286
      DUF3523; Domain of unknown function (DUF3523)

    2. XM_011542244.2 → XP_011540546.1  ATPase family AAA domain-containing protein 3B isoform X6

      UniProtKB/TrEMBL
      Q96T67
      Conserved Domains (5) summary
      TIGR01242
      Location:246 → 604
      26Sp45; 26S proteasome subunit P45 family
      pfam00004
      Location:396 → 523
      AAA; ATPase family associated with various cellular activities (AAA)
      pfam12037
      Location:42 → 334
      DUF3523; Domain of unknown function (DUF3523)
      cd16269
      Location:199 → 210
      GBP_C; coiled coil [structural motif]
      cl20817
      Location:142 → 227
      GBP_C; Guanylate-binding protein, C-terminal domain

    3. XM_047431596.1 → XP_047287552.1  ATPase family AAA domain-containing protein 3B isoform X4

    4. XM_047431583.1 → XP_047287539.1  ATPase family AAA domain-containing protein 3B isoform X2

    5. XM_047431588.1 → XP_047287544.1  ATPase family AAA domain-containing protein 3B isoform X2

    6. XM_011542241.4 → XP_011540543.1  ATPase family AAA domain-containing protein 3B isoform X2

      See identical proteins and their annotated locations for XP_011540543.1

      Conserved Domains (4) summary
      pfam00004
      Location:348 → 450
      AAA; ATPase family associated with various cellular activities (AAA)
      pfam12037
      Location:42 → 286
      DUF3523; Domain of unknown function (DUF3523)
      cd16269
      Location:151 → 162
      GBP_C; coiled coil [structural motif]
      cl20817
      Location:94 → 179
      GBP_C; Guanylate-binding protein, C-terminal domain

    7. XM_047431599.1 → XP_047287555.1  ATPase family AAA domain-containing protein 3B isoform X5

    8. XM_047431593.1 → XP_047287549.1  ATPase family AAA domain-containing protein 3B isoform X3

      UniProtKB/TrEMBL
      Q9H834

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      906136..943970
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338998.1 → XP_054194973.1  ATPase family AAA domain-containing protein 3B isoform X1

      UniProtKB/TrEMBL
      Q96T67

    2. XM_054339005.1 → XP_054194980.1  ATPase family AAA domain-containing protein 3B isoform X6

      UniProtKB/TrEMBL
      Q96T67

    3. XM_054339003.1 → XP_054194978.1  ATPase family AAA domain-containing protein 3B isoform X4

    4. XM_054338999.1 → XP_054194974.1  ATPase family AAA domain-containing protein 3B isoform X2

    5. XM_054339001.1 → XP_054194976.1  ATPase family AAA domain-containing protein 3B isoform X2

    6. XM_054339000.1 → XP_054194975.1  ATPase family AAA domain-containing protein 3B isoform X2

    7. XM_054339004.1 → XP_054194979.1  ATPase family AAA domain-containing protein 3B isoform X5

    8. XM_054338997.1 → XP_054194972.1  ATPase family AAA domain-containing protein 3B isoform X7

      UniProtKB/TrEMBL
      Q96T67

    9. XM_054339002.1 → XP_054194977.1  ATPase family AAA domain-containing protein 3B isoform X3

      UniProtKB/TrEMBL
      Q9H834
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5T9A4.1 GenPept UniProtKB/Swiss-Prot:Q5T9A4

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