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TREX1 three prime repair exonuclease 1 [ Homo sapiens (human) ]

Gene ID: 11277, updated on 9-Dec-2018

Summary

Official Symbol
TREX1provided by HGNC
Official Full Name
three prime repair exonuclease 1provided by HGNC
Primary source
HGNC:HGNC:12269
See related
Ensembl:ENSG00000213689 MIM:606609
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
CRV; AGS1; DRN3; HERNS
Summary
This gene encodes a nuclear protein with 3' exonuclease activity. The encoded protein may play a role in DNA repair and serve as a proofreading function for DNA polymerase. Mutations in this gene result in Aicardi-Goutieres syndrome, chilblain lupus, Cree encephalitis, and other diseases of the immune system. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2012]
Annotation information
Note: GeneID 11277 was annotated as a single gene with two non-overlapping coding regions. GeneID 11277 now represents only the downstream coding region encoding three prime repair exonuclease 1. The upstream coding region is represented by geneID 84126. [29 May 2007]
Expression
Ubiquitous expression in spleen (RPKM 9.5), lymph node (RPKM 7.7) and 25 other tissues See more
Orthologs

Genomic context

See TREX1 in Genome Data Viewer
Location:
3p21.31
Exon count:
3
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (48465952..48467645)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (48506919..48509044)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 51 Neighboring gene ATRIP-TREX1 readthrough Neighboring gene translation machinery associated 7 homolog Neighboring gene ATR interacting protein Neighboring gene shisa family member 5 Neighboring gene 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 Neighboring gene microRNA 6823

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Aicardi Goutieres syndrome 1
MedGen: C0796126 OMIM: 225750 GeneReviews: Aicardi-Goutieres Syndrome
Compare labs
Chilblain lupus 1
MedGen: C3277619 OMIM: 610448 GeneReviews: Not available
Compare labs
Systemic lupus erythematosus
MedGen: C0024141 OMIM: 152700 GeneReviews: Not available
Compare labs
Vasculopathy, retinal, with cerebral leukodystrophy
MedGen: C1860518 OMIM: 192315 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
HIV-1 replication requires TREX1 expression in human cervicovaginal explants as shown through TREX1 knockdown PubMed
SiRNA-mediated knockdown of one of the components of the SET complex, TREX1, inhibits HIV-1 infection with significantly reduced levels of integrated HIV-1 DNA and viral production in HeLa-CD4 cells, human cervicovaginal explants or humanized mice PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Cytosolic DNA-sensing pathway, organism-specific biosystem (from KEGG)
    Cytosolic DNA-sensing pathway, organism-specific biosystemSpecific families of pattern recognition receptors are responsible for detecting foreign DNA from invading microbes or host cells and generating innate immune responses. DAI is the first identified s...
  • Cytosolic DNA-sensing pathway, conserved biosystem (from KEGG)
    Cytosolic DNA-sensing pathway, conserved biosystemSpecific families of pattern recognition receptors are responsible for detecting foreign DNA from invading microbes or host cells and generating innate immune responses. DAI is the first identified s...
  • Cytosolic sensors of pathogen-associated DNA, organism-specific biosystem (from REACTOME)
    Cytosolic sensors of pathogen-associated DNA, organism-specific biosystemPresence of pathogen-associated DNA in cytosol induces type I IFN production. Several intracellular receptors have been implicated to some degree. These include DNA-dependent activator of interferon ...
  • IRF3-mediated induction of type I IFN, organism-specific biosystem (from REACTOME)
    IRF3-mediated induction of type I IFN, organism-specific biosystemTANK-binding kinase 1 (TBK1) and interferon regulatory factor 3 (IRF3) are central regulators of type-I interferon induction during bacterial or viral infection. TBK1 was found to form complexes with...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • Regulation by TREX1, organism-specific biosystem (from REACTOME)
    Regulation by TREX1, organism-specific biosystemThree prime repair exonuclease 1 (TREX1) is a DNase type III enzyme, which targets and digests unpaired nucleotides on ssDNA and dsDNA ends through a 3'to 5' exonuclease activity (Perrino FW et al. 1...
  • Regulation of innate immune responses to cytosolic DNA, organism-specific biosystem (from REACTOME)
    Regulation of innate immune responses to cytosolic DNA, organism-specific biosystemInnate immune responses are coordinated and regulated to provide an efficient first line of defense against pathogens and at the same time to prevent host self-damage. Here we present some regulatory...
  • STING mediated induction of host immune responses, organism-specific biosystem (from REACTOME)
    STING mediated induction of host immune responses, organism-specific biosystemSTING (stimulator of IFN genes; also known as MITA/ERIS/MPYS/TMEM173) is an endoplasmic reticulum (ER) resident, which is required for effective type I IFN production in response to nucleic acids. In...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Readthrough ATRIP-TREX1

Readthrough gene: ATRIP-TREX1, Included gene: ATRIP

Homology

Clone Names

  • DKFZp434J0310

Gene Ontology Provided by GOA

Function Evidence Code Pubs
3'-5' exonuclease activity IDA
Inferred from Direct Assay
more info
PubMed 
3'-5' exonuclease activity TAS
Traceable Author Statement
more info
PubMed 
3'-5'-exodeoxyribonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
3'-5'-exodeoxyribonuclease activity ISS
Inferred from Sequence or Structural Similarity
more info
 
DNA binding, bending IEA
Inferred from Electronic Annotation
more info
 
MutLalpha complex binding IDA
Inferred from Direct Assay
more info
PubMed 
MutSalpha complex binding IDA
Inferred from Direct Assay
more info
PubMed 
WW domain binding IEA
Inferred from Electronic Annotation
more info
 
adenyl deoxyribonucleotide binding IEA
Inferred from Electronic Annotation
more info
 
double-stranded DNA binding IEA
Inferred from Electronic Annotation
more info
 
exodeoxyribonuclease III activity IEA
Inferred from Electronic Annotation
more info
 
magnesium ion binding IEA
Inferred from Electronic Annotation
more info
 
metal ion binding NAS
Non-traceable Author Statement
more info
PubMed 
metal ion binding TAS
Traceable Author Statement
more info
PubMed 
protein homodimerization activity NAS
Non-traceable Author Statement
more info
PubMed 
protein homodimerization activity TAS
Traceable Author Statement
more info
PubMed 
single-stranded DNA binding TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
CD86 biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
DNA catabolic process IEA
Inferred from Electronic Annotation
more info
 
DNA duplex unwinding IEA
Inferred from Electronic Annotation
more info
 
DNA metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
DNA modification IEA
Inferred from Electronic Annotation
more info
 
DNA recombination NAS
Non-traceable Author Statement
more info
PubMed 
DNA repair TAS
Traceable Author Statement
more info
PubMed 
DNA replication NAS
Non-traceable Author Statement
more info
PubMed 
DNA synthesis involved in UV-damage excision repair IEA
Inferred from Electronic Annotation
more info
 
T cell antigen processing and presentation IEA
Inferred from Electronic Annotation
more info
 
activation of immune response IEA
Inferred from Electronic Annotation
more info
 
apoptotic cell clearance IEA
Inferred from Electronic Annotation
more info
 
atrial cardiac muscle tissue development IEA
Inferred from Electronic Annotation
more info
 
blood vessel development IEA
Inferred from Electronic Annotation
more info
 
cellular response to gamma radiation IEA
Inferred from Electronic Annotation
more info
 
cellular response to hydroxyurea IEA
Inferred from Electronic Annotation
more info
 
cellular response to interferon-beta IEA
Inferred from Electronic Annotation
more info
 
cellular response to reactive oxygen species IEA
Inferred from Electronic Annotation
more info
 
defense response to virus IEA
Inferred from Electronic Annotation
more info
 
detection of DNA damage stimulus involved in DNA damage checkpoint IEA
Inferred from Electronic Annotation
more info
 
detection of stimulus involved in cell cycle checkpoint IEA
Inferred from Electronic Annotation
more info
 
determination of adult lifespan IEA
Inferred from Electronic Annotation
more info
 
establishment of protein localization IEA
Inferred from Electronic Annotation
more info
 
generation of precursor metabolites and energy IEA
Inferred from Electronic Annotation
more info
 
heart morphogenesis IEA
Inferred from Electronic Annotation
more info
 
heart process IEA
Inferred from Electronic Annotation
more info
 
immune complex formation IEA
Inferred from Electronic Annotation
more info
 
immune response in brain or nervous system IEA
Inferred from Electronic Annotation
more info
 
immunoglobulin biosynthetic process involved in immune response IEA
Inferred from Electronic Annotation
more info
 
inflammatory response to antigenic stimulus IEA
Inferred from Electronic Annotation
more info
 
interferon-alpha production IEA
Inferred from Electronic Annotation
more info
 
kidney development IEA
Inferred from Electronic Annotation
more info
 
lymphoid progenitor cell differentiation IEA
Inferred from Electronic Annotation
more info
 
macrophage activation involved in immune response IEA
Inferred from Electronic Annotation
more info
 
mismatch repair NAS
Non-traceable Author Statement
more info
PubMed 
negative regulation of type I interferon-mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
nucleic acid phosphodiester bond hydrolysis IEA
Inferred from Electronic Annotation
more info
 
protein stabilization IEA
Inferred from Electronic Annotation
more info
 
regulation of T cell activation IEA
Inferred from Electronic Annotation
more info
 
regulation of catalytic activity IEA
Inferred from Electronic Annotation
more info
 
regulation of cellular respiration IEA
Inferred from Electronic Annotation
more info
 
regulation of fatty acid metabolic process IEA
Inferred from Electronic Annotation
more info
 
regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
regulation of glycolytic process IEA
Inferred from Electronic Annotation
more info
 
regulation of immunoglobulin production IEA
Inferred from Electronic Annotation
more info
 
regulation of inflammatory response IEA
Inferred from Electronic Annotation
more info
 
regulation of lipid biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
regulation of lysosome organization IEA
Inferred from Electronic Annotation
more info
 
regulation of protein complex stability IEA
Inferred from Electronic Annotation
more info
 
regulation of tumor necrosis factor production IEA
Inferred from Electronic Annotation
more info
 
regulation of type I interferon production TAS
Traceable Author Statement
more info
 
signal transduction involved in DNA damage checkpoint IEA
Inferred from Electronic Annotation
more info
 
transposition, RNA-mediated IEA
Inferred from Electronic Annotation
more info
 
type I interferon signaling pathway IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
nuclear envelope NAS
Non-traceable Author Statement
more info
PubMed 
nuclear replication fork IEA
Inferred from Electronic Annotation
more info
 
oligosaccharyltransferase complex IEA
Inferred from Electronic Annotation
more info
 
protein-DNA complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
three-prime repair exonuclease 1
Names
3' repair exonuclease 1
3'-5' exonuclease TREX1
DNase III
deoxyribonuclease III
NP_009179.2
NP_338599.1

NCBI Reference Sequences (RefSeq)

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_009820.2 RefSeqGene

    Range
    4691..6816
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_007248.4NP_009179.2  three-prime repair exonuclease 1 isoform c

    See identical proteins and their annotated locations for NP_009179.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate splice site in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The resulting isoform (c) has a shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AC134772, AF319566, AF319569, AJ243797, BT020053, W24304
    Consensus CDS
    CCDS59451.1
    UniProtKB/Swiss-Prot
    Q9NSU2
    UniProtKB/TrEMBL
    Q5TZT0
    Related
    ENSP00000415972.1, ENST00000444177.1
    Conserved Domains (1) summary
    cl10012
    Location:4201
    DnaQ_like_exo; DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily
  2. NM_033629.6NP_338599.1  three-prime repair exonuclease 1 isoform b

    See identical proteins and their annotated locations for NP_338599.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The resulting isoform (b) has a shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AF319569, AL137745, BT020053
    Consensus CDS
    CCDS2769.1
    UniProtKB/Swiss-Prot
    Q9NSU2
    Related
    ENSP00000486676.2, ENST00000625293.2
    Conserved Domains (1) summary
    cl10012
    Location:14211
    DnaQ_like_exo; DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    48465952..48467645
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_016381.5: Suppressed sequence

    Description
    NM_016381.5: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
  2. NM_033627.3: Suppressed sequence

    Description
    NM_033627.3: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript, which represents a rare readthrough event.
  3. NM_033628.2: Suppressed sequence

    Description
    NM_033628.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript, which represents a rare readthrough event.
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