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    ATP23 ATP23 metallopeptidase and ATP synthase assembly factor homolog [ Homo sapiens (human) ]

    Gene ID: 91419, updated on 27-Aug-2024

    Summary

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    Official Symbol
    ATP23provided by HGNC
    Official Full Name
    ATP23 metallopeptidase and ATP synthase assembly factor homologprovided by HGNC
    Primary source
    HGNC:HGNC:29452
    See related
    Ensembl:ENSG00000166896 MIM:619760; AllianceGenome:HGNC:29452
    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
    KUB3; XRCC6BP1
    Summary
    The protein encoded by this gene is amplified in glioblastomas and interacts with the DNA binding subunit of DNA-dependent protein kinase. This kinase is involved in double-strand break repair (DSB), and higher expression of the encoded protein increases the efficiency of DSB. In addition, comparison to orthologous proteins strongly suggests that this protein is a metalloprotease important in the biosynthesis of mitochondrial ATPase. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]
    Expression
    Broad expression in testis (RPKM 13.5), bone marrow (RPKM 4.5) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    12q14.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (57941567..57959148)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (57909929..57927510)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (58335350..58352931)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC283387 Neighboring gene uncharacterized LOC101927608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6564 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6565 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6566 Neighboring gene Sharpr-MPRA regulatory region 14765 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:58329372-58329872 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:58329873-58330373 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:58335219-58336028 Neighboring gene GIHCG inhibitor of miR-200b/200a/429 expression Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_29909 Neighboring gene zinc finger protein 100 pseudogene Neighboring gene RN7SK pseudogene 65

    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 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. Glioma-amplified sequence KUB3 influences double-strand break repair after ionizing radiation. Fischer U, et al. Int J Oncol, 2013 Jul. PMID 23670597, Free PMC Article
    2. KUB3 amplification and overexpression in human gliomas. Fischer U, et al. Glia, 2001 Oct. PMID 11571779
    3. The metalloprotease encoded by ATP23 has a dual function in processing and assembly of subunit 6 of mitochondrial ATPase. Zeng X, et al. Mol Biol Cell, 2007 Feb. PMID 17135290, Free PMC Article
    4. Isolation of Ku70-binding proteins (KUBs). Yang CR, et al. Nucleic Acids Res, 1999 May 15. PMID 10219089, Free PMC Article
    5. MICALL2 as a substrate of ubiquitinase TRIM21 regulates tumorigenesis of colorectal cancer. Wen P, et al. Cell Commun Signal, 2022 Oct 28. PMID 36307841, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC134817, MGC134818

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-dependent protein kinase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metalloendopeptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in double-strand break repair via nonhomologous end joining TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in mitochondrial protein processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitochondrial proton-transporting ATP synthase complex assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of DNA-dependent protein kinase-DNA ligase 4 complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cell junction IDA
    Inferred from Direct Assay
    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 mitochondrion IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    mitochondrial inner membrane protease ATP23 homolog
    Names
    Ku70-binding protein 3
    XRCC6-binding protein 1
    NP_001307337.1
    NP_001307338.1
    NP_001307339.1
    NP_150592.1
    XP_011537278.1
    XP_016875695.1
    XP_054185539.1
    XP_054185540.1
    XP_054229779.1
    XP_054229780.1

    NCBI Reference Sequences (RefSeq)

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    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_001320408.2 → NP_001307337.1  mitochondrial inner membrane protease ATP23 homolog isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice junction in the 5' end compared to variant 1. The resulting isoform (b) has a shorter and distinct N-terminus compared to isoform a.
      Source sequence(s)
      AC084033, BC012776, BM544500, BU601924
      UniProtKB/Swiss-Prot
      Q9Y6H3
      Conserved Domains (1) summary
      pfam09768
      Location:3 → 168
      Peptidase_M76; Peptidase M76 family

    2. NM_001320409.2 → NP_001307338.1  mitochondrial inner membrane protease ATP23 homolog isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate exon in the 5' end compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a. Variants 3 and 4 both encode the same isoform (c).
      Source sequence(s)
      AC084033, BC012776, BU601924, DA711361
      UniProtKB/Swiss-Prot
      Q9Y6H3
      Conserved Domains (1) summary
      pfam09768
      Location:1 → 102
      Peptidase_M76; Peptidase M76 family

    3. NM_001320410.2 → NP_001307339.1  mitochondrial inner membrane protease ATP23 homolog isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an alternate exon compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a. Variants 3 and 4 both encode the same isoform (c).
      Source sequence(s)
      AC084033, BC012776, BM557436, BU601924
      UniProtKB/Swiss-Prot
      Q9Y6H3
      Conserved Domains (1) summary
      pfam09768
      Location:1 → 102
      Peptidase_M76; Peptidase M76 family

    4. NM_033276.4 → NP_150592.1  mitochondrial inner membrane protease ATP23 homolog isoform a

      See identical proteins and their annotated locations for NP_150592.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AC084033, BC012776, BU601924
      Consensus CDS
      CCDS41802.1
      UniProtKB/Swiss-Prot
      Q1RLM4, Q96E81, Q9Y6H3
      Related
      ENSP00000300145.3, ENST00000300145.4
      Conserved Domains (1) summary
      pfam09768
      Location:50 → 220
      Peptidase_M76; Peptidase M76 family

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      57941567..57959148
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017020206.2 → XP_016875695.1  mitochondrial inner membrane protease ATP23 homolog isoform X2

      Related
      ENST00000647763.1
      Conserved Domains (1) summary
      pfam09768
      Location:1 → 148
      Peptidase_M76; Peptidase M76 family

    2. XM_011538976.3 → XP_011537278.1  mitochondrial inner membrane protease ATP23 homolog isoform X1

      See identical proteins and their annotated locations for XP_011537278.1

      Conserved Domains (1) summary
      pfam09768
      Location:29 → 166
      Peptidase_M76; Peptidase M76 family

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NW_003315939.2 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      142767..160348 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329565.1 → XP_054185540.1  mitochondrial inner membrane protease ATP23 homolog isoform X2

    2. XM_054329564.1 → XP_054185539.1  mitochondrial inner membrane protease ATP23 homolog isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      57909929..57927510
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054373805.1 → XP_054229780.1  mitochondrial inner membrane protease ATP23 homolog isoform X2

    2. XM_054373804.1 → XP_054229779.1  mitochondrial inner membrane protease ATP23 homolog isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y6H3.3 GenPept UniProtKB/Swiss-Prot:Q9Y6H3

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