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 recombinatio... See more...

Aliases for XRN1 Gene

Aliases for XRN1 Gene

  • 5'-3' Exoribonuclease 1 2 3 4 5
  • SEP1 2 3 4
  • Strand-Exchange Protein 1 Homolog 3 4
  • EC 3.1.13.- 4
  • XRN1 5

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. Diseases associated with XRN1 include Murray Valley Encephalitis and Sarcoma. Among its related pathways are Regulation of activated PAK-2p34 by proteasome mediated degradation and Gene Expression. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and exonuclease activity. An important paralog of this gene is XRN2.

UniProtKB/Swiss-Prot Summary 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 CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for XRN1 Gene

Genomics for XRN1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for XRN1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J142444 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 623.1 +1.0 1046 4.2 BRCA1 SP1 CREB1 PRDM10 ZNF629 NFKBIZ ZNF692 POLR2A ZNF7 BACH1 XRN1 lnc-ATR-2 PBX2P1 ATR RNU1-100P U2SURP RASA2 piR-33905-058 GK5
GH03J143118 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 27.5 -673.6 -673617 8.2 SP1 CTCF HNRNPL LEF1 IKZF1 KDM1A POLR2A LARP7 MTA2 PHF21A CHST2 ENSG00000241679 U2SURP XRN1 ATR PBX2P1 GK5 SLC9A9-AS1 lnc-SLC9A9-3 SLC9A9
GH03J141803 Enhancer 1.1 Ensembl dbSUPER 45.7 +643.0 642961 0.2 RNF2 LEF1 IKZF1 DDX20 MTA2 ZSCAN4 PKNOX1 MTA1 NR2C1 ZNF24 XRN1 ATR TRPC1 RASA2 YWHAQP6 piR-33905-057 piR-30847 GRK7 ENSG00000285558 ATP1B3
GH03J142997 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 22.7 -552.7 -552693 6.9 CEBPG SP1 HNRNPL CREB1 GATAD2A TEAD4 PRDM10 ZNF629 TFE3 LEF1 U2SURP ENSG00000268129 LOC100289361 XRN1 ATR PBX2P1 ST13P15 PAQR9 PAQR9-AS1 TFDP2
GH03J142594 Promoter/Enhancer 1.7 Ensembl ENCODE CraniofacialAtlas 21.6 -148.8 -148756 3.8 SP1 HNRNPL GATAD2A PRDM10 ZNF629 REST TFE3 SOX13 IKZF1 RFX5 PLS1 XRN1 ATR U2SURP YWHAQP6 PBX2P1 PLS1-AS1 TRPC1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around XRN1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for XRN1

Top Transcription factor binding sites by QIAGEN in the XRN1 gene promoter:
  • AP-1
  • c-Fos
  • c-Jun
  • C/EBPbeta
  • FosB
  • Fra-1
  • JunB
  • LCR-F1
  • MyoD
  • Nkx6-1

Genomic Locations for XRN1 Gene

Genomic Locations for XRN1 Gene
chr3:142,306,607-142,448,062
(GRCh38/hg38)
Size:
141,456 bases
Orientation:
Minus strand
chr3:142,025,449-142,166,904
(GRCh37/hg19)
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:
    • Found in a mRNP complex with UPF1, UPF2, UPF3B and XRN1 (PubMed:14527413). Associates with alpha and beta tubulins (By similarity). Interacts with DIS3L2 (PubMed:23756462). Interacts with ZC3HAV1 in an RNA-dependent manner (PubMed:21876179). Interacts with ZFP36L1 (PubMed:15687258). Interacts with TRIM71 (via NHL repeats) in an RNA-dependent manner (PubMed:23125361). Interacts with YTHDC2 (via ANK repeats) (PubMed:29033321).
    Miscellaneous:
    • Down-regulated in OGS biopsy.

    Alternative splice isoforms for XRN1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for XRN1 Gene

Post-translational modifications for XRN1 Gene

  • Ubiquitination at Lys79 and Lys847
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Abcam antibodies for XRN1
  • Boster Bio Antibodies for XRN1

No data available for DME Specific Peptides for XRN1 Gene

Domains & Families for XRN1 Gene

Gene Families for XRN1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for XRN1 Gene

InterPro:
Blocks:
  • Putative 5-3 exonuclease domain
ProtoNet:

Suggested Antigen Peptide Sequences for XRN1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ61552, highly similar to 5'-3' exoribonuclease 1 (EC 3.1.11.-) (B4E2K3_HUMAN)
  • Strand-exchange protein 1 homolog (XRN1_HUMAN)

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

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

Phenotypes From GWAS Catalog for XRN1 Gene

Gene Ontology (GO) - Molecular Function for XRN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002151 G-quadruplex RNA binding ISS --
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding IEA,IBA 21873635
GO:0004518 nuclease activity IEA --
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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for XRN1

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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for XRN1 gene
Compartment Confidence
cytosol 5
plasma membrane 4
nucleus 4
cytoskeleton 3
extracellular 2
mitochondrion 2
endoplasmic reticulum 2
golgi apparatus 2
peroxisome 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Plasma membrane (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for XRN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000932 P-body IEA --
GO:0005634 nucleus IEA,IBA 21873635
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0005886 plasma membrane IDA --
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 IEA,IMP 17545563
GO:0016075 rRNA catabolic process IMP 20368444
GO:0017148 negative regulation of translation IEA --
GO:0032211 negative regulation of telomere maintenance via telomerase IC 26950371
GO:0033574 response to testosterone IEA --
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

mRNA/cDNA for XRN1 Gene

4 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
14 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for XRN1

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

No ASD Table

Relevant External Links for XRN1 Gene

GeneLoc Exon Structure for
XRN1

Expression for XRN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE 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, MaxQB, and MOPED for XRN1 Gene



Protein tissue co-expression partners for XRN1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for XRN1

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.

Evidence on tissue expression from TISSUES for XRN1 Gene

  • Liver(4.5)
  • Kidney(4.5)
  • Nervous system(4.5)
  • Intestine(4.4)
  • Skin(2.5)
  • Lung(2.4)
  • Muscle(2.3)
  • Spleen(2.3)
  • Blood(2.1)
  • Heart(2)
genes like me logo Genes that share expression patterns with XRN1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
Chimpanzee
(Pan troglodytes)
Mammalia XRN1 30 31
  • 99.65 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia XRN1 30 31
  • 93.45 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia XRN1 30 31
  • 92.48 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Xrn1 30
  • 88.05 (n)
Mouse
(Mus musculus)
Mammalia Xrn1 30 17 31
  • 88.03 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia XRN1 31
  • 82 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia XRN1 31
  • 75 (a)
OneToOne
Chicken
(Gallus gallus)
Aves XRN1 30 31
  • 77.5 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia XRN1 31
  • 72 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia xrn1 30
  • 70.49 (n)
Str.17672 30
Zebrafish
(Danio rerio)
Actinopterygii xrn1 30 31
  • 64.09 (n)
OneToOne
zgc63635 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004430 30
  • 51.29 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta pcm 30 31
  • 47.3 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea xrn-1 30 31
  • 49.06 (n)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes XRN1 30 31 33
  • 48.77 (n)
OneToOne
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_ADL046C 30
  • 48.23 (n)
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F22385g 30
  • 48.04 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes exo2 30
  • 51.13 (n)
Bread mold
(Neurospora crassa)
Ascomycetes NCU06678 30
  • 48.74 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 46 (a)
OneToOne
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.7993 30
Species where no ortholog for XRN1 was found in the sources mined by GeneCards:
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for XRN1: view image

Paralogs for XRN1 Gene

Paralogs for XRN1 Gene

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

  • XRN1_HUMAN
  • B4E2K3_HUMAN
  • C9JCZ8_HUMAN
  • F8WDA0_HUMAN
  • H7C583_HUMAN
  • H7C5E4_HUMAN
genes like me logo Genes that share paralogs with XRN1: view

Variants for XRN1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for XRN1 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
717836 Benign: not provided 142,329,608(-) A/G SYNONYMOUS_VARIANT
774607 Likely Benign: not provided 142,380,189(-) A/G INTRON_VARIANT
rs35214510 - p.Ser674Gly
rs35902661 - p.Val1259Ala

Additional dbSNP identifiers (rs#s) for XRN1 Gene

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

Variant ID Type Subtype PubMed ID
dgv1412e212 CNV gain 25503493
dgv299n21 CNV gain 19592680
dgv4912n100 CNV gain 25217958
dgv619n27 CNV gain 19166990
dgv8626n54 CNV gain 21841781
esv2759182 CNV gain 17122850
esv2763767 CNV gain 21179565
esv3310022 CNV mobile element insertion 20981092
esv3443267 CNV insertion 20981092
esv34483 CNV gain 17911159
esv3562643 CNV deletion 23714750
esv3597996 CNV gain 21293372
esv3598001 CNV gain 21293372
esv7548 CNV gain 19470904
nsv1011175 CNV gain 25217958
nsv1072719 CNV deletion 25765185
nsv237317 CNV insertion 16902084
nsv523596 CNV loss 19592680
nsv523945 CNV gain 19592680
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)

Additional Variant Information for XRN1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
XRN1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for XRN1 Gene

Disorders for XRN1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for XRN1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
murray valley encephalitis
  • australian encephalitis
sarcoma
  • connective and soft tissue neoplasm
osteogenic sarcoma
  • osteosarcoma; osrc
noonan syndrome 3
  • ns3
- elite association - COSMIC cancer census association via MalaCards
Search XRN1 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with XRN1: view

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

Publications for XRN1 Gene

  1. 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 4 23
  2. 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 (New York, N.Y.) 2002) 2 3 4
  3. Regulation of m6A Transcripts by the 3'→5' RNA Helicase YTHDC2 Is Essential for a Successful Meiotic Program in the Mammalian Germline. (PMID: 29033321) Wojtas MN … Pillai RS (Molecular cell 2017) 3 4
  4. The mammalian TRIM-NHL protein TRIM71/LIN-41 is a repressor of mRNA function. (PMID: 23125361) Loedige I … Filipowicz W (Nucleic acids research 2013) 3 4
  5. Exonuclease hDIS3L2 specifies an exosome-independent 3'-5' degradation pathway of human cytoplasmic mRNA. (PMID: 23756462) Lubas M … Dziembowski A (The EMBO journal 2013) 3 4

Products for XRN1 Gene

Sources for XRN1 Gene