Human Gene XRN1 (ENST00000392981.7_10) from GENCODE V47lift37
  Description: 5'-3' exoribonuclease 1, transcript variant 3 (from RefSeq NM_001282857.2)
Gencode Transcript: ENST00000392981.7_10
Gencode Gene: ENSG00000114127.11_16
Transcript (Including UTRs)
   Position: hg19 chr3:142,025,452-142,166,879 Size: 141,428 Total Exon Count: 41 Strand: -
Coding Region
   Position: hg19 chr3:142,030,353-142,166,786 Size: 136,434 Coding Exon Count: 41 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:142,025,452-142,166,879)mRNA (may differ from genome)Protein (1694 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: XRN1_HUMAN
DESCRIPTION: RecName: Full=5'-3' exoribonuclease 1; EC=3.1.11.-; AltName: Full=Strand-exchange protein 1 homolog;
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).
SUBUNIT: 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.
SUBCELLULAR LOCATION: Cytoplasm. Note=Discrete foci at the inner surface of the cell membrane.
TISSUE SPECIFICITY: Expressed in heart, brain, pancreas, spleen, testis, osteogenic sarcoma (OGS) biopsy and primary cell lines.
INDUCTION: By GDNF/glial cell line-derived neurotrophic factor.
MISCELLANEOUS: Down-regulated in OGS biopsy.
SIMILARITY: Belongs to the 5'-3' exonuclease family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.03 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 216.87 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -36.5093-0.392 Picture PostScript Text
3' UTR -1182.204901-0.241 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR016494 - 5_3_exoribonuclease_1
IPR004859 - Put_53exo

Pfam Domains:
PF03159 - XRN 5'-3' exonuclease N-terminus
PF17846 - Xrn1 helical domain
PF18129 - Xrn1 SH3-like domain
PF18332 - Exoribonuclease Xrn1 D1 domain
PF18334 - Exoribonuclease Xrn1 D2/D3 domain

SCOP Domains:
88723 - PIN domain-like
54768 - dsRNA-binding domain-like

ModBase Predicted Comparative 3D Structure on Q8IZH2
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details  Gene DetailsGene Details
Gene SorterGene Sorter  Gene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0002151 G-quadruplex RNA binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0004518 nuclease activity
GO:0004527 exonuclease activity
GO:0004534 5'-3' exoribonuclease activity
GO:0005515 protein binding
GO:0008409 5'-3' exonuclease activity
GO:0016787 hydrolase activity
GO:0051880 G-quadruplex DNA binding
GO:0070034 telomerase RNA binding

Biological Process:
GO:0000956 nuclear-transcribed mRNA catabolic process
GO:0016075 rRNA catabolic process
GO:0017148 negative regulation of translation
GO:0032211 negative regulation of telomere maintenance via telomerase
GO:0033574 response to testosterone
GO:0043488 regulation of mRNA stability
GO:0071028 nuclear mRNA surveillance
GO:0071044 histone mRNA catabolic process
GO:0071409 cellular response to cycloheximide
GO:0090503 RNA phosphodiester bond hydrolysis, exonucleolytic

Cellular Component:
GO:0000932 P-body
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0030425 dendrite
GO:0043025 neuronal cell body
GO:0045202 synapse


-  Descriptions from all associated GenBank mRNAs
  LF384583 - JP 2014500723-A/192086: Polycomb-Associated Non-Coding RNAs.
AL133623 - Homo sapiens mRNA; cDNA DKFZp434P0721 (from clone DKFZp434P0721); partial cds.
BX640905 - Homo sapiens mRNA; cDNA DKFZp686L17106 (from clone DKFZp686L17106); complete cds.
CR627396 - Homo sapiens mRNA; cDNA DKFZp686F19113 (from clone DKFZp686F19113).
CR749518 - Homo sapiens mRNA; cDNA DKFZp686B22225 (from clone DKFZp686B22225).
AY137776 - Homo sapiens DNA strand-exchange protein SEP1 mRNA, complete cds.
BC141555 - Synthetic construct Homo sapiens clone IMAGE:100014585, MGC:175319 5'-3' exoribonuclease 1 (XRN1) mRNA, encodes complete protein.
AB527239 - Synthetic construct DNA, clone: pF1KB7307, Homo sapiens XRN1 gene for 5'-3' exoribonuclease 1, without stop codon, in Flexi system.
MA620160 - JP 2018138019-A/192086: Polycomb-Associated Non-Coding RNAs.
CR627160 - Homo sapiens mRNA; cDNA DKFZp686G09164 (from clone DKFZp686G09164).
JD314240 - Sequence 295264 from Patent EP1572962.
AL117516 - Homo sapiens mRNA; cDNA DKFZp434L1935 (from clone DKFZp434L1935).
JD546767 - Sequence 527791 from Patent EP1572962.
JD516727 - Sequence 497751 from Patent EP1572962.
JD065627 - Sequence 46651 from Patent EP1572962.
JD375383 - Sequence 356407 from Patent EP1572962.
JD300530 - Sequence 281554 from Patent EP1572962.
JD462417 - Sequence 443441 from Patent EP1572962.
JD082300 - Sequence 63324 from Patent EP1572962.
JD536522 - Sequence 517546 from Patent EP1572962.
MF281493 - Homo sapiens miAB2_pre miRNA, complete sequence.
MF281455 - Homo sapiens miAB2 miRNA, complete sequence.
JD510160 - Sequence 491184 from Patent EP1572962.
JD111935 - Sequence 92959 from Patent EP1572962.
LF378172 - JP 2014500723-A/185675: Polycomb-Associated Non-Coding RNAs.
LF378167 - JP 2014500723-A/185670: Polycomb-Associated Non-Coding RNAs.
MA613749 - JP 2018138019-A/185675: Polycomb-Associated Non-Coding RNAs.
MA613744 - JP 2018138019-A/185670: Polycomb-Associated Non-Coding RNAs.
AK123897 - Homo sapiens cDNA FLJ41903 fis, clone PEBLM2005183, highly similar to 5'-3' exoribonuclease 1 (EC 3.1.11.-).
DQ571195 - Homo sapiens piRNA piR-31307, complete sequence.
BC078146 - Homo sapiens 5'-3' exoribonuclease 1, mRNA (cDNA clone IMAGE:6015120).
AK096177 - Homo sapiens cDNA FLJ38858 fis, clone MESAN2011627, highly similar to 5'-3' exoribonuclease 1.
BC039314 - Homo sapiens 5'-3' exoribonuclease 1, mRNA (cDNA clone IMAGE:5296715), complete cds.
BC048104 - Homo sapiens 5'-3' exoribonuclease 1, mRNA (cDNA clone IMAGE:4820049), complete cds.
AK304312 - Homo sapiens cDNA FLJ61552 complete cds, highly similar to 5'-3' exoribonuclease 1 (EC 3.1.11.-).
LF208585 - JP 2014500723-A/16088: Polycomb-Associated Non-Coding RNAs.
MA444162 - JP 2018138019-A/16088: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8IZH2 (Reactome details) participates in the following event(s):

R-HSA-450431 ZFP36 (TTP) recruits RNA degradation activities
R-HSA-450488 BRF1 Complex recruits RNA degradation activities
R-HSA-429845 5' to 3' exoribonuclease hydrolyzes decapped mRNA
R-HSA-450513 Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA
R-HSA-450385 Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA
R-HSA-450531 Regulation of mRNA stability by proteins that bind AU-rich elements
R-HSA-430039 mRNA decay by 5' to 3' exoribonuclease
R-HSA-8953854 Metabolism of RNA
R-HSA-429914 Deadenylation-dependent mRNA decay

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000392981.1, ENST00000392981.2, ENST00000392981.3, ENST00000392981.4, ENST00000392981.5, ENST00000392981.6, NM_001282857, Q4G0S3, Q68D88, Q6AI24, Q6MZS8, Q86WS7, Q8IZH2, Q8N8U4, Q9UF39, SEP1 , uc318vmy.1, uc318vmy.2, XRN1 , XRN1_HUMAN
UCSC ID: ENST00000392981.7_10
RefSeq Accession: NM_001282857.2
Protein: Q8IZH2 (aka XRN1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.