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Aliases for TREX1 Gene

Aliases for TREX1 Gene

  • Three Prime Repair Exonuclease 1 2 3 5
  • 3-5 Exonuclease TREX1 3 4
  • DNase III 3 4
  • Aicardi-Goutieres Syndrome 1 2
  • 3 Repair Exonuclease 1 3
  • Deoxyribonuclease III 3
  • EC 3.1.11.2 4
  • HERNS 3
  • AGS1 3
  • DRN3 3
  • CRV 3

External Ids for TREX1 Gene

Previous HGNC Symbols for TREX1 Gene

  • AGS1

Previous GeneCards Identifiers for TREX1 Gene

  • GC03P048289
  • GC03P047770
  • GC03P048448
  • GC03P048463
  • GC03P048482

Summaries for TREX1 Gene

Entrez Gene Summary for TREX1 Gene

  • 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]

GeneCards Summary for TREX1 Gene

TREX1 (Three Prime Repair Exonuclease 1) is a Protein Coding gene. Diseases associated with TREX1 include Chilblain Lupus and Aicardi-Goutieres Syndrome 1, Dominant And Recessive. Among its related pathways are p53 Pathway (RnD) and Chks in Checkpoint Regulation. GO annotations related to this gene include nucleic acid binding and double-stranded DNA binding. An important paralog of this gene is TREX2.

UniProtKB/Swiss-Prot for TREX1 Gene

  • Major cellular 3-to-5 DNA exonuclease which digests single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with mismatched 3 termini. Prevents cell-intrinsic initiation of autoimmunity. Acts by metabolizing DNA fragments from endogenous retroelements, including L1, LTR and SINE elements. Unless degraded, these DNA fragments accumulate in the cytosol and activate the IFN-stimulatory DNA (ISD) response and innate immune signaling. Prevents chronic ATM-dependent checkpoint activation, by processing ssDNA polynucleotide species arising from the processing of aberrant DNA replication intermediates. Inefficiently degrades oxidized DNA, such as that generated upon antimicrobial reactive oxygen production or upon absorption of UV light. During GZMA-mediated cell death, contributes to DNA damage in concert with NME1. NME1 nicks one strand of DNA and TREX1 removes bases from the free 3 end to enhance DNA damage and prevent DNA end reannealing and rapid repair.

Gene Wiki entry for TREX1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TREX1 Gene

Genomics for TREX1 Gene

Regulatory Elements for TREX1 Gene

Enhancers for TREX1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around TREX1 on UCSC Golden Path with GeneCards custom track

Promoters for TREX1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around TREX1 on UCSC Golden Path with GeneCards custom track

Genomic Location for TREX1 Gene

Chromosome:
3
Start:
48,465,520 bp from pter
End:
48,467,645 bp from pter
Size:
2,126 bases
Orientation:
Plus strand

Genomic View for TREX1 Gene

Genes around TREX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TREX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TREX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TREX1 Gene

Proteins for TREX1 Gene

  • Protein details for TREX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NSU2-TREX1_HUMAN
    Recommended name:
    Three-prime repair exonuclease 1
    Protein Accession:
    Q9NSU2
    Secondary Accessions:
    • B2RCN9
    • Q8TEU2
    • Q9BPW1
    • Q9Y4X2

    Protein attributes for TREX1 Gene

    Size:
    369 amino acids
    Molecular mass:
    38923 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Homodimer. Interacts (via proline-rich region) with TCERG1/CA150 (via the second WW domain). Component of the SET complex, composed of at least ANP32A, APEX1, HMGB2, NME1, SET and TREX1. Within this complex, directly interacts with SET; this interaction does not result in TREX1 inhibition. Also interacts with NME1, but only following translocation to the nucleus. Directly interacts with UBQLN1 (via ubiquitin-like domain); the interaction may control TREX1 subcellular location.
    • Homodimer. Interacts (via proline-rich region) with TCERG1/CA150 (via the second WW domain). Component of the SET complex, composed of at least ANP32A, APEX1, HMGB2, NME1, SET and TREX1. Within this complex, directly interacts with SET; this interaction does not result in TREX1 inhibition. Also interacts with NME1, but only following translocation to the nucleus. Directly interacts with UBQLN1 (via ubiquitin-like domain); the interaction may control TREX1 subcellular location.
    SequenceCaution:
    • Sequence=AAD48774.2; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for TREX1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TREX1 Gene

Proteomics data for TREX1 Gene at MOPED

Post-translational modifications for TREX1 Gene

  • Ubiquitinated, but not targeted to proteasomal degradation. Ubiquitination may be important for interaction with UBQLN1.
  • Ubiquitination at Lys 230
  • Modification sites at PhosphoSitePlus

Other Protein References for TREX1 Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for TREX1 (TREX1)

No data available for DME Specific Peptides for TREX1 Gene

Domains & Families for TREX1 Gene

Gene Families for TREX1 Gene

Protein Domains for TREX1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for TREX1 Gene

Graphical View of Domain Structure for InterPro Entry

Q9NSU2

UniProtKB/Swiss-Prot:

TREX1_HUMAN :
  • Belongs to the exonuclease superfamily. TREX family.
Family:
  • Belongs to the exonuclease superfamily. TREX family.
genes like me logo Genes that share domains with TREX1: view

Function for TREX1 Gene

Molecular function for TREX1 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Exonucleolytic cleavage in the 3- to 5-direction to yield nucleoside 5-phosphates.
UniProtKB/Swiss-Prot Function:
Major cellular 3-to-5 DNA exonuclease which digests single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with mismatched 3 termini. Prevents cell-intrinsic initiation of autoimmunity. Acts by metabolizing DNA fragments from endogenous retroelements, including L1, LTR and SINE elements. Unless degraded, these DNA fragments accumulate in the cytosol and activate the IFN-stimulatory DNA (ISD) response and innate immune signaling. Prevents chronic ATM-dependent checkpoint activation, by processing ssDNA polynucleotide species arising from the processing of aberrant DNA replication intermediates. Inefficiently degrades oxidized DNA, such as that generated upon antimicrobial reactive oxygen production or upon absorption of UV light. During GZMA-mediated cell death, contributes to DNA damage in concert with NME1. NME1 nicks one strand of DNA and TREX1 removes bases from the free 3 end to enhance DNA damage and prevent DNA end reannealing and rapid repair.
UniProtKB/Swiss-Prot Induction:
Induced by cytosolic DNA. Induced by inflammatory stimuli such as IFN-alpha and IFN-gamma in B cells and also by LPS and viral and bacterial DNA (via TLR9) in dendritic cells and macrophages (By similarity).

Enzyme Numbers (IUBMB) for TREX1 Gene

Gene Ontology (GO) - Molecular Function for TREX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003697 single-stranded DNA binding TAS 10391904
GO:0008408 3-5 exonuclease activity TAS 11278605
GO:0008853 exodeoxyribonuclease III activity IEA --
GO:0032405 MutLalpha complex binding IDA 16713580
genes like me logo Genes that share ontologies with TREX1: view
genes like me logo Genes that share phenotypes with TREX1: view

Human Phenotype Ontology for TREX1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for TREX1 Gene

MGI Knock Outs for TREX1:

Animal Model Products

No data available for miRNA , Transcription Factor Targets and HOMER Transcription for TREX1 Gene

Localization for TREX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TREX1 Gene

Nucleus. Cytoplasm, cytosol. Endoplasmic reticulum membrane; Peripheral membrane protein. Note=Retained in the cytoplasm through the C-terminal region (By similarity). In response to DNA damage, translocates to the nucleus where it is specifically recruited to replication foci. Translocation to the nucleus also occurs during GZMA-mediated cell death. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for TREX1 Gene COMPARTMENTS Subcellular localization image for TREX1 gene
Compartment Confidence
cytosol 5
endoplasmic reticulum 5
nucleus 5
lysosome 1
mitochondrion 1
peroxisome 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for TREX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol IEA --
genes like me logo Genes that share ontologies with TREX1: view

Pathways & Interactions for TREX1 Gene

genes like me logo Genes that share pathways with TREX1: view

Pathways by source for TREX1 Gene

1 R&D Systems pathway for TREX1 Gene
1 Qiagen pathway for TREX1 Gene

Interacting Proteins for TREX1 Gene

Gene Ontology (GO) - Biological Process for TREX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006260 DNA replication NAS 10391904
GO:0032481 positive regulation of type I interferon production TAS --
GO:0090305 nucleic acid phosphodiester bond hydrolysis TAS 10393201
genes like me logo Genes that share ontologies with TREX1: view

No data available for SIGNOR curated interactions for TREX1 Gene

Drugs & Compounds for TREX1 Gene

(1) Drugs for TREX1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Magnesium Nutra 0

(4) Additional Compounds for TREX1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with TREX1: view

Transcripts for TREX1 Gene

Unigene Clusters for TREX1 Gene

Three prime repair exonuclease 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for TREX1 Gene

No ASD Table

Relevant External Links for TREX1 Gene

GeneLoc Exon Structure for
TREX1
ECgene alternative splicing isoforms for
TREX1

Expression for TREX1 Gene

mRNA expression in normal human tissues for TREX1 Gene

Protein differential expression in normal tissues from HIPED for TREX1 Gene

This gene is overexpressed in Nasal epithelium (64.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MOPED, and MaxQB for TREX1 Gene



SOURCE GeneReport for Unigene cluster for TREX1 Gene Hs.707026

mRNA Expression by UniProt/SwissProt for TREX1 Gene

Q9NSU2-TREX1_HUMAN
Tissue specificity: Detected in thymus, spleen, liver, brain, heart, small intestine and colon.
genes like me logo Genes that share expression patterns with TREX1: view

Protein tissue co-expression partners for TREX1 Gene

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for TREX1 Gene

Orthologs for TREX1 Gene

This gene was present in the common ancestor of animals.

Orthologs for TREX1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia TREX1 35
  • 81.63 (n)
  • 76.75 (a)
TREX1 36
  • 77 (a)
OneToOne
dog
(Canis familiaris)
Mammalia TREX1 35
  • 85.65 (n)
  • 81.96 (a)
mouse
(Mus musculus)
Mammalia Trex1 35
  • 80.09 (n)
  • 73.8 (a)
Trex1 16
Trex1 36
  • 74 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia TREX1 35
  • 98.74 (n)
  • 98.37 (a)
TREX1 36
  • 98 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Trex1 35
  • 80.72 (n)
  • 75.08 (a)
oppossum
(Monodelphis domestica)
Mammalia TREX1 36
  • 66 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TREX1 36
  • 45 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TREX1 36
  • 45 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.1185 35
fruit fly
(Drosophila melanogaster)
Insecta CG3165 36
  • 21 (a)
OneToMany
Species with no ortholog for TREX1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for TREX1 Gene

ENSEMBL:
Gene Tree for TREX1 (if available)
TreeFam:
Gene Tree for TREX1 (if available)

Paralogs for TREX1 Gene

Paralogs for TREX1 Gene

(1) SIMAP similar genes for TREX1 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with TREX1: view

Variants for TREX1 Gene

Sequence variations from dbSNP and Humsavar for TREX1 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
VAR_028319 Aicardi-Goutieres syndrome 1 (AGS1)
VAR_028319 Systemic lupus erythematosus (SLE)
VAR_028321 Aicardi-Goutieres syndrome 1 (AGS1)
VAR_032940 Aicardi-Goutieres syndrome 1 (AGS1)
VAR_037948 Aicardi-Goutieres syndrome 1 (AGS1)

Structural Variations from Database of Genomic Variants (DGV) for TREX1 Gene

Variant ID Type Subtype PubMed ID
nsv834684 CNV Gain 17160897
nsv508917 CNV Insertion 20534489

Variation tolerance for TREX1 Gene

Residual Variation Intolerance Score: 21.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.95; 19.61% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TREX1 Gene

Human Gene Mutation Database (HGMD)
TREX1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TREX1 Gene

Disorders for TREX1 Gene

MalaCards: The human disease database

(18) MalaCards diseases for TREX1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
chilblain lupus
  • chilblain lupus 1
aicardi-goutieres syndrome 1, dominant and recessive
  • aicardi-goutieres syndrome 5
vasculopathy, retinal, with cerebral leukodystrophy
  • herns
aicardi-goutieres syndrome
  • cree encephalitis
systemic lupus erythematosus
  • lupus nephritis
- elite association - COSMIC cancer census association via MalaCards
Search TREX1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

TREX1_HUMAN
  • Aicardi-Goutieres syndrome 1 (AGS1) [MIM:225750]: A form of Aicardi-Goutieres syndrome, a genetically heterogeneous disease characterized by cerebral atrophy, leukoencephalopathy, intracranial calcifications, chronic cerebrospinal fluid (CSF) lymphocytosis, increased CSF alpha-interferon, and negative serologic investigations for common prenatal infection. Clinical features as thrombocytopenia, hepatosplenomegaly and elevated hepatic transaminases along with intermittent fever may erroneously suggest an infective process. Severe neurological dysfunctions manifest in infancy as progressive microcephaly, spasticity, dystonic posturing and profound psychomotor retardation. Death often occurs in early childhood. {ECO:0000269 PubMed:16845398, ECO:0000269 PubMed:17357087, ECO:0000269 PubMed:17846997, ECO:0000269 PubMed:20131292, ECO:0000269 PubMed:20799324}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Chilblain lupus 1 (CHBL1) [MIM:610448]: A rare cutaneous form of lupus erythematosus. Affected individuals present with painful bluish-red papular or nodular lesions of the skin in acral locations precipitated by cold and wet exposure at temperatures less than 10 degrees centigrade. {ECO:0000269 PubMed:17357087, ECO:0000269 PubMed:17440703}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Systemic lupus erythematosus (SLE) [MIM:152700]: A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys and serosal membranes. It is of unknown etiology, but is thought to represent a failure of the regulatory mechanisms of the autoimmune system. The disease is marked by a wide range of system dysfunctions, an elevated erythrocyte sedimentation rate, and the formation of LE cells in the blood or bone marrow. {ECO:0000269 PubMed:17660818, ECO:0000269 PubMed:20131292}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. Enhanced immune sensing of oxidized DNA may be involved in the phototoxicity experienced by SLE patients. Exposure to UV-light produces DNA oxidative damage. Oxidized DNA being a poor TREX1 substrate, it accumulates in skin, leading to enhanced auto-immune reactivity and eventually skin lesions (PubMed:23993650). {ECO:0000269 PubMed:23993650}.
  • Vasculopathy, retinal, with cerebral leukodystrophy (RVCL) [MIM:192315]: A microvascular endotheliopathy resulting in central nervous system degeneration and retinopathy, with progressive loss of vision, stroke, motor impairment, and cognitive decline. The ocular manifestations are characterized by telangiectasias, microaneurysms and retinal capillary obliteration starting in the macula. Diseased cerebral white matter has prominent small infarcts that often coalesce to pseudotumors. {ECO:0000269 PubMed:17660820}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for TREX1

Genetic Association Database (GAD)
TREX1
Human Genome Epidemiology (HuGE) Navigator
TREX1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TREX1
genes like me logo Genes that share disorders with TREX1: view

No data available for Genatlas for TREX1 Gene

Publications for TREX1 Gene

  1. Mutations in the gene encoding the 3'-5' DNA exonuclease TREX1 cause Aicardi-Goutieres syndrome at the AGS1 locus. (PMID: 16845398) Crow Y.J. … Lindahl T. (Nat. Genet. 2006) 2 3 4 67
  2. Biochemical properties of mammalian TREX1 and its association with DNA replication and inherited inflammatory disease. (PMID: 19442247) Lindahl T. … Robins P. (Biochem. Soc. Trans. 2009) 3 23
  3. TREX1 polymorphisms associated with autoantibodies in patients with systemic lupus erythematosus. (PMID: 18092167) Hur J.W. … Bae S.C. (Rheumatol. Int. 2008) 3 23
  4. WRN exonuclease activity is blocked by DNA termini harboring 3' obstructive groups. (PMID: 17224176) Harrigan J.A. … Wilson D.M. (Mech. Ageing Dev. 2007) 3 23
  5. The crystal structure of TREX1 explains the 3' nucleotide specificity and reveals a polyproline II helix for protein partnering. (PMID: 17293595) de Silva U. … Hollis T. (J. Biol. Chem. 2007) 3 23

Products for TREX1 Gene

Sources for TREX1 Gene

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