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Aliases for XRN1 Gene

Aliases for XRN1 Gene

  • 5'-3' Exoribonuclease 1 2
  • 5-3 Exoribonuclease 1 2 3 5
  • Strand-Exchange Protein 1 Homolog 3 4
  • SEP1 3 4
  • EC 3.1.13.- 4

External Ids for XRN1 Gene

Previous GeneCards Identifiers for XRN1 Gene

  • GC03M139058
  • GC03M143508
  • GC03M142025
  • GC03M139398

Summaries for XRN1 Gene

Entrez Gene Summary for XRN1 Gene

  • This gene encodes a member of the 5'-3' exonuclease family. The encoded protein may be involved in replication-dependent histone mRNA degradation, and interacts directly with the enhancer of mRNA-decapping protein 4. In addition to mRNA metabolism, a similar protein in yeast has been implicated in a variety of nuclear and cytoplasmic functions, including homologous recombination, meiosis, telomere maintenance, and microtubule assembly. Mutations in this gene are associated with osteosarcoma, suggesting that the encoded protein may also play a role in bone formation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

GeneCards Summary for XRN1 Gene

XRN1 (5'-3' Exoribonuclease 1) is a Protein Coding gene. Among its related pathways are Deadenylation-dependent mRNA decay and Gene Expression. GO annotations related to this gene include nucleic acid binding and exonuclease activity.

UniProtKB/Swiss-Prot for XRN1 Gene

  • Major 5-3 exoribonuclease involved in mRNA decay. Required for the 5-3-processing of the G4 tetraplex-containing DNA and RNA substrates. The kinetic of hydrolysis is faster for G4 RNA tetraplex than for G4 DNA tetraplex and monomeric RNA tetraplex. Binds to RNA and DNA (By similarity). Plays a role in replication-dependent histone mRNA degradation. May act as a tumor suppressor protein in osteogenic sarcoma (OGS).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for XRN1 Gene

Genomics for XRN1 Gene

Regulatory Elements for XRN1 Gene

Enhancers for XRN1 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 XRN1 on UCSC Golden Path with GeneCards custom track

Promoters for XRN1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around XRN1 on UCSC Golden Path with GeneCards custom track

Genomic Location for XRN1 Gene

Chromosome:
3
Start:
142,306,607 bp from pter
End:
142,448,062 bp from pter
Size:
141,456 bases
Orientation:
Minus strand

Genomic View for XRN1 Gene

Genes around XRN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
XRN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for XRN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for XRN1 Gene

Proteins for XRN1 Gene

  • Protein details for XRN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IZH2-XRN1_HUMAN
    Recommended name:
    5-3 exoribonuclease 1
    Protein Accession:
    Q8IZH2
    Secondary Accessions:
    • Q4G0S3
    • Q68D88
    • Q6AI24
    • Q6MZS8
    • Q86WS7
    • Q8N8U4
    • Q9UF39

    Protein attributes for XRN1 Gene

    Size:
    1706 amino acids
    Molecular mass:
    194107 Da
    Quaternary structure:
    • Associates with alpha and beta tubulins (By similarity). Found in a mRNP complex with UPF1, UPF2, UPF3B and XRN1. Interacts with ZC3HAV1 in an RNA-dependent manner. Interacts with DIS3L2.
    Miscellaneous:
    • Down-regulated in OGS biopsy.

    Alternative splice isoforms for XRN1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for XRN1 Gene

Proteomics data for XRN1 Gene at MOPED

Post-translational modifications for XRN1 Gene

  • Ubiquitination at Lys 79 and Lys 847
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Abcam antibodies for Xrn1

No data available for DME Specific Peptides for XRN1 Gene

Domains & Families for XRN1 Gene

Protein Domains for XRN1 Gene

Suggested Antigen Peptide Sequences for XRN1 Gene

Graphical View of Domain Structure for InterPro Entry

Q8IZH2

UniProtKB/Swiss-Prot:

XRN1_HUMAN :
  • Belongs to the 5-3 exonuclease family.
Family:
  • Belongs to the 5-3 exonuclease family.
genes like me logo Genes that share domains with XRN1: view

No data available for Gene Families for XRN1 Gene

Function for XRN1 Gene

Molecular function for XRN1 Gene

UniProtKB/Swiss-Prot Function:
Major 5-3 exoribonuclease involved in mRNA decay. Required for the 5-3-processing of the G4 tetraplex-containing DNA and RNA substrates. The kinetic of hydrolysis is faster for G4 RNA tetraplex than for G4 DNA tetraplex and monomeric RNA tetraplex. Binds to RNA and DNA (By similarity). Plays a role in replication-dependent histone mRNA degradation. May act as a tumor suppressor protein in osteogenic sarcoma (OGS).
UniProtKB/Swiss-Prot Induction:
By GDNF/glial cell line-derived neurotrophic factor.

Enzyme Numbers (IUBMB) for XRN1 Gene

Gene Ontology (GO) - Molecular Function for XRN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0004527 exonuclease activity IEA --
GO:0044822 poly(A) RNA binding IDA 22658674
genes like me logo Genes that share ontologies with XRN1: view
genes like me logo Genes that share phenotypes with XRN1: view

Animal Model Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for XRN1 Gene

Localization for XRN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for XRN1 Gene

Cytoplasm. Note=Discrete foci at the inner surface of the cell membrane.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for XRN1 Gene COMPARTMENTS Subcellular localization image for XRN1 gene
Compartment Confidence
cytoskeleton 5
cytosol 5
golgi apparatus 5
nucleus 5
plasma membrane 5
extracellular 2

Gene Ontology (GO) - Cellular Components for XRN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
GO:0016020 membrane IDA 19946888
genes like me logo Genes that share ontologies with XRN1: view

Pathways & Interactions for XRN1 Gene

genes like me logo Genes that share pathways with XRN1: view

Gene Ontology (GO) - Biological Process for XRN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000956 nuclear-transcribed mRNA catabolic process IMP 17545563
GO:0043928 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay TAS --
genes like me logo Genes that share ontologies with XRN1: view

No data available for SIGNOR curated interactions for XRN1 Gene

Drugs & Compounds for XRN1 Gene

No Compound Related Data Available

Transcripts for XRN1 Gene

Unigene Clusters for XRN1 Gene

5-3 exoribonuclease 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for XRN1 Gene

No ASD Table

Relevant External Links for XRN1 Gene

GeneLoc Exon Structure for
XRN1
ECgene alternative splicing isoforms for
XRN1

Expression for XRN1 Gene

mRNA expression in normal human tissues for XRN1 Gene

Protein differential expression in normal tissues from HIPED for XRN1 Gene

This gene is overexpressed in Amniocyte (21.8) and Heart (13.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for XRN1 Gene



SOURCE GeneReport for Unigene cluster for XRN1 Gene Hs.435103

mRNA Expression by UniProt/SwissProt for XRN1 Gene

Q8IZH2-XRN1_HUMAN
Tissue specificity: Expressed in heart, brain, pancreas, spleen, testis, osteogenic sarcoma (OGS) biopsy and primary cell lines.
genes like me logo Genes that share expression patterns with XRN1: view

Protein tissue co-expression partners for XRN1 Gene

- Elite partner

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 XRN1 Gene

Orthologs for XRN1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for XRN1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia XRN1 35
  • 92.48 (n)
  • 92.13 (a)
XRN1 36
  • 90 (a)
OneToOne
dog
(Canis familiaris)
Mammalia XRN1 35
  • 93.45 (n)
  • 93.78 (a)
XRN1 36
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Xrn1 35
  • 88.03 (n)
  • 88.55 (a)
Xrn1 16
Xrn1 36
  • 86 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia XRN1 35
  • 99.65 (n)
  • 99.24 (a)
XRN1 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Xrn1 35
  • 88.05 (n)
  • 89.14 (a)
oppossum
(Monodelphis domestica)
Mammalia XRN1 36
  • 82 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia XRN1 36
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves XRN1 35
  • 77.5 (n)
  • 78.88 (a)
XRN1 36
  • 76 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia XRN1 36
  • 72 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.17672 35
xrn1 35
  • 70.49 (n)
  • 71.67 (a)
zebrafish
(Danio rerio)
Actinopterygii xrn1 35
  • 64.09 (n)
  • 67.56 (a)
zgc63635 35
xrn1 36
  • 64 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004430 35
  • 51.29 (n)
  • 46.55 (a)
fruit fly
(Drosophila melanogaster)
Insecta pcm 35
  • 47.3 (n)
  • 43.14 (a)
pcm 36
  • 34 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea xrn-1 35
  • 49.06 (n)
  • 44.25 (a)
xrn-1 36
  • 34 (a)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ADL046C 35
  • 48.23 (n)
  • 39.21 (a)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F22385g 35
  • 48.04 (n)
  • 37.09 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes XRN1 35
  • 48.77 (n)
  • 38.58 (a)
XRN1 36
  • 31 (a)
OneToOne
XRN1 38
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.7993 35
bread mold
(Neurospora crassa)
Ascomycetes NCU06678 35
  • 48.74 (n)
  • 40.93 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes exo2 35
  • 51.13 (n)
  • 41.69 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 46 (a)
OneToOne
Species with no ortholog for XRN1:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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 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)

Evolution for XRN1 Gene

ENSEMBL:
Gene Tree for XRN1 (if available)
TreeFam:
Gene Tree for XRN1 (if available)

Paralogs for XRN1 Gene

(1) SIMAP similar genes for XRN1 Gene using alignment to 6 proteins:

genes like me logo Genes that share paralogs with XRN1: view

No data available for Paralogs for XRN1 Gene

Variants for XRN1 Gene

Sequence variations from dbSNP and Humsavar for XRN1 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs35214510 - 142,403,757(-) AGAAA(A/G)GTGGT reference, missense
rs35902661 - 142,347,335(-) TGCAG(C/T)TCTAC reference, missense
rs723100 -- 142,347,092(-) tcaca(A/C)aattg intron-variant
rs2291362 -- 142,329,702(+) GAGCA(A/C)GCAGG intron-variant
rs2291363 -- 142,397,309(+) ATTAA(A/G)TACTT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for XRN1 Gene

Variant ID Type Subtype PubMed ID
dgv1514e1 CNV Complex 17122850
dgv299n21 CNV Gain 19592680
dgv619n27 CNV Gain 19166990
esv34483 CNV Gain 17911159
nsv877556 CNV Loss 21882294
nsv523945 CNV Gain 19592680
esv7548 CNV Gain 19470904
nsv877557 CNV Loss 21882294
dgv5266n71 CNV Loss 21882294
esv274294 CNV Insertion 20981092
nsv523596 CNV Loss 19592680
nsv237317 CNV Insertion 16902084
nsv528954 CNV Loss 19592680

Variation tolerance for XRN1 Gene

Residual Variation Intolerance Score: 9.52% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.50; 77.60% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for XRN1 Gene

Disorders for XRN1 Gene

Relevant External Links for XRN1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
XRN1

No disorders were found for XRN1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for XRN1 Gene

Publications for XRN1 Gene

  1. The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci. (PMID: 12515382) Ingelfinger D. … Achsel T. (RNA 2002) 2 3 4 67
  2. Identification of human SEP1 as a glial cell line-derived neurotrophic factor-inducible protein and its expression in the nervous system. (PMID: 14580940) Shimoyama Y. … Takahashi M. (Neuroscience 2003) 3 23
  3. Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes. (PMID: 25281560) Lambert J.P. … Gingras A.C. (J Proteomics 2015) 3
  4. Analysis of HIV-1 Gag protein interactions via biotin ligase tagging. (PMID: 25631074) Ritchie C. … Barklis E. (J. Virol. 2015) 3
  5. Dissecting the roles of the 5' exoribonucleases Xrn1 and Xrn2 in restricting hepatitis C virus replication. (PMID: 25673723) Li Y. … Lemon S.M. (J. Virol. 2015) 3

Products for XRN1 Gene

Sources for XRN1 Gene

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