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    TREX2 three prime repair exonuclease 2 [ Homo sapiens (human) ]

    Gene ID: 11219, updated on 9-Dec-2024

    Summary

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    Official Symbol
    TREX2provided by HGNC
    Official Full Name
    three prime repair exonuclease 2provided by HGNC
    Primary source
    HGNC:HGNC:12270
    See related
    Ensembl:ENSG00000183479 MIM:300370; AllianceGenome:HGNC:12270
    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
    Summary
    This gene encodes a nuclear protein with 3' to 5' exonuclease activity. The encoded protein participates in double-stranded DNA break repair, and may interact with DNA polymerase delta. [provided by RefSeq, Nov 2012]
    Expression
    Biased expression in skin (RPKM 5.9), spleen (RPKM 0.7) and 5 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TREX2 in Genome Data Viewer
    Location:
    Xq28
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (153444473..153446056, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (151718056..151719639, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (152709931..152711514, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373379 Neighboring gene PNMA family member 6E Neighboring gene RNA, 7SL, cytoplasmic 667, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21061 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21062 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:152677238-152677448 Neighboring gene ZFP92 zinc finger protein Neighboring gene HAUS augmin like complex subunit 7 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:152726424-152726582 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30033 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30034 Neighboring gene Sharpr-MPRA regulatory region 9358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:152741433-152741972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:152742168-152742668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:152742669-152743169 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:152753877-152754691 Neighboring gene extracellular matrix protein X-linked, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:152756808-152757380 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30035 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30036 Neighboring gene biglycan

    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. The Human TREX-2 Complex Interacts with Subunits of the ORC Complex. Kurshakova MM, et al. Dokl Biochem Biophys, 2023 Dec. PMID 38066323, Free PMC Article
    2. DNA binding induces active site conformational change in the human TREX2 3'-exonuclease. de Silva U, et al. Nucleic Acids Res, 2009 Apr. PMID 19321497, Free PMC Article
    3. Multifaceted role of TREX2 in the skin defense against UV-induced skin carcinogenesis. Manils J, et al. Oncotarget, 2015 Sep 8. PMID 26090614, Free PMC Article
    4. Cooperative DNA binding and communication across the dimer interface in the TREX2 3' --> 5'-exonuclease. Perrino FW, et al. J Biol Chem, 2008 Aug 1. PMID 18534978, Free PMC Article
    5. Cisplatin depletes TREX2 and causes Robertsonian translocations as seen in TREX2 knockout cells. Chen MJ, et al. Cancer Res, 2007 Oct 1. PMID 17909011

    See all (46) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The Human TREX-2 Complex Interacts with Subunits of the ORC Complex.
      Title: The Human TREX-2 Complex Interacts with Subunits of the ORC Complex.
    2. TREX2 Exonuclease Causes Spontaneous Mutations and Stress-Induced Replication Fork Defects in Cells Expressing RAD51(K133A).
      Title: TREX2 Exonuclease Causes Spontaneous Mutations and Stress-Induced Replication Fork Defects in Cells Expressing RAD51(K133A).
    3. Nucleoporin TPR is an integral component of the TREX-2 mRNA export pathway.
      Title: Nucleoporin TPR is an integral component of the TREX-2 mRNA export pathway.
    4. Significant methylation loss at an intragenic site of TREX2 was a frequent trait in a cohort of patients with laryngeal cancer. Methylation loss correlated with increased expression of TREX2 in laryngeal tumors and improved overall survival. These data highlight a regulatory role of TREX2 DNA methylation for gene expression which might affect incidence and survival of laryngeal cancer.
      Title: DNA methylation at an enhancer of the three prime repair exonuclease 2 gene (TREX2) is linked to gene expression and survival in laryngeal cancer.
    5. the scaffold subunit of TREX-2, GANP, positively regulates DNA repair through homologous recombination (HR). In contrast, DUBm adaptor subunits ENY2 and ATXNL3 are required to limit unscheduled HR.
      Title: Transcription and mRNA export machineries SAGA and TREX-2 maintain monoubiquitinated H2B balance required for DNA repair.
    6. Altogether, data provide new insights in the molecular mechanisms of TREX2 activity and establish cell autonomous and non-cell autonomous functions of TREX2 in the UVB-induced skin response.
      Title: Multifaceted role of TREX2 in the skin defense against UV-induced skin carcinogenesis.
    7. human TREX-2 complex prevents genome instability, as determined by the accumulation of gamma-H2AX and 53BP1 foci and single-cell electrophoresis in cells depleted of the TREX-2 subunits PCID2, GANP and DSS1
      Title: BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2.
    8. TREX-2 is an NPC-associated complex in mammalian cells.
      Title: The human TREX-2 complex is stably associated with the nuclear pore basket.
    9. Trex2 does not enable DSB repair and prompt a new model that posits Trex2 suppresses the formation of broken chromosomes.
      Title: Trex2 enables spontaneous sister chromatid exchanges without facilitating DNA double-strand break repair.
    10. a model for DNA binding and 3' hydrolysis for the TREX2 dimer.
      Title: DNA binding induces active site conformational change in the human TREX2 3'-exonuclease.
    Submit: New GeneRIF Correction See all GeneRIFs (16)

    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

    Potential readthrough

    Included gene: HAUS7

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 3'-5'-DNA exonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 3'-5'-DNA exonuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA binding EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables double-stranded DNA 3'-5' DNA exonuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables magnesium ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables molecular adaptor activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in DNA metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in DNA repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    three prime repair exonuclease 2
    Names
    3'-5' exonuclease TREX2 long form
    NP_542432.2

    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.

    Genomic

    1. NG_029986.1 RefSeqGene

      Range
      5432..7015
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_080701.4 → NP_542432.2  three prime repair exonuclease 2

      See identical proteins and their annotated locations for NP_542432.2

      Status: REVIEWED

      Source sequence(s)
      U82695
      Consensus CDS
      CCDS35437.1
      UniProtKB/Swiss-Prot
      Q45F08, Q9BQ50, Q9UN77
      UniProtKB/TrEMBL
      Q06S70
      Related
      ENSP00000359251.2, ENST00000370231.3
      Conserved Domains (1) summary
      cd06136
      Location:10 → 204
      TREX1_2; DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      153444473..153446056 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      151718056..151719639 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_080699.2: Suppressed sequence

      Description
      NM_080699.2: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.

    2. NM_080700.2: Suppressed sequence

      Description
      NM_080700.2: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BQ50.2 GenPept UniProtKB/Swiss-Prot:Q9BQ50

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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