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XRN1 5'-3' exoribonuclease 1 [ Homo sapiens (human) ]

Gene ID: 54464, updated on 4-May-2020

Summary

Official Symbol
XRN1provided by HGNC
Official Full Name
5'-3' exoribonuclease 1provided by HGNC
Primary source
HGNC:HGNC:30654
See related
Ensembl:ENSG00000114127 MIM:607994
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
SEP1
Summary
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]
Expression
Ubiquitous expression in appendix (RPKM 6.9), lymph node (RPKM 6.5) and 25 other tissues See more
Orthologs

Genomic context

See XRN1 in Genome Data Viewer
Location:
3q23
Exon count:
43
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (142306610..142448062, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (142025449..142166904, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene glycerol kinase 5 Neighboring gene Sharpr-MPRA regulatory region 12219 Neighboring gene RNA, U6 small nuclear 1294, pseudogene Neighboring gene RNA, U1 small nuclear 100, pseudogene Neighboring gene eukaryotic translation initiation factor 2 alpha kinase 1 pseudogene Neighboring gene ATR serine/threonine kinase Neighboring gene SUCLG2 pseudogene 1

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 Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Pr55(Gag) gag Cellular biotinylated 5'-3' exoribonuclease 1 protein (XRN1) is incorporated into HIV-1 Gag virus-like particles PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ41903, DKFZp434P0721, DKFZp686B22225, DKFZp686F19113

Gene Ontology Provided by GOA

Function Evidence Code Pubs
5'-3' exoribonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
5'-3' exoribonuclease activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
5'-3' exoribonuclease activity ISS
Inferred from Sequence or Structural Similarity
more info
 
G-quadruplex DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
G-quadruplex RNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
RNA binding HDA PubMed 
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
telomerase RNA binding IC
Inferred by Curator
more info
PubMed 
Process Evidence Code Pubs
RNA phosphodiester bond hydrolysis, exonucleolytic ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular response to cycloheximide IEA
Inferred from Electronic Annotation
more info
 
cellular response to puromycin IEA
Inferred from Electronic Annotation
more info
 
histone mRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of telomere maintenance via telomerase IC
Inferred by Curator
more info
PubMed 
negative regulation of translation IEA
Inferred from Electronic Annotation
more info
 
nuclear mRNA surveillance IMP
Inferred from Mutant Phenotype
more info
PubMed 
nuclear-transcribed mRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear-transcribed mRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
rRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
rRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of mRNA stability TAS
Traceable Author Statement
more info
 
response to testosterone IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
P-body IEA
Inferred from Electronic Annotation
more info
 
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
dendrite IEA
Inferred from Electronic Annotation
more info
 
membrane HDA PubMed 
neuronal cell body IEA
Inferred from Electronic Annotation
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IDA
Inferred from Direct Assay
more info
 
synapse IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
5'-3' exoribonuclease 1
Names
strand-exchange protein 1 homolog
NP_001269786.1
NP_001269788.1
NP_061874.3
XP_006713736.1
XP_011511221.1
XP_011511222.1
XP_011511224.1
XP_016862129.1
XP_016862130.1
XP_016862131.1

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.

mRNA and Protein(s)

  1. NM_001282857.2NP_001269786.1  5'-3' exoribonuclease 1 isoform c

    See identical proteins and their annotated locations for NP_001269786.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (c) is shorter, compared to isoform a.
    Source sequence(s)
    AC023508, AC109992, AK096177
    Consensus CDS
    CCDS63801.1
    UniProtKB/Swiss-Prot
    Q8IZH2
    Related
    ENSP00000376707.2, ENST00000392981.6
    Conserved Domains (2) summary
    COG5049
    Location:1735
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]
    pfam03159
    Location:1226
    XRN_N; XRN 5'-3' exonuclease N-terminus
  2. NM_001282859.1NP_001269788.1  5'-3' exoribonuclease 1 isoform d

    See identical proteins and their annotated locations for NP_001269788.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks several exons and its 3' terminal exon extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (d) has a shorter and distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AK096177, BC039314
    Consensus CDS
    CCDS75028.1
    UniProtKB/Swiss-Prot
    Q8IZH2
    Related
    ENSP00000418404.1, ENST00000463916.5
    Conserved Domains (1) summary
    pfam03159
    Location:1226
    XRN_N; XRN 5'-3' exonuclease N-terminus
  3. NM_019001.5NP_061874.3  5'-3' exoribonuclease 1 isoform a

    See identical proteins and their annotated locations for NP_061874.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC023508, AK096177, AL133623, AY137776
    Consensus CDS
    CCDS3123.1
    UniProtKB/Swiss-Prot
    Q8IZH2
    Related
    ENSP00000264951.4, ENST00000264951.8
    Conserved Domains (2) summary
    COG5049
    Location:1735
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]
    pfam03159
    Location:1226
    XRN_N; XRN 5'-3' exonuclease N-terminus

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    142306610..142448062 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017006640.1XP_016862129.1  5'-3' exoribonuclease 1 isoform X2

  2. XM_017006641.1XP_016862130.1  5'-3' exoribonuclease 1 isoform X4

  3. XM_011512920.2XP_011511222.1  5'-3' exoribonuclease 1 isoform X3

    Conserved Domains (2) summary
    COG5049
    Location:1735
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]
    pfam03159
    Location:1226
    XRN_N; XRN 5'-3' exonuclease N-terminus
  4. XM_011512919.2XP_011511221.1  5'-3' exoribonuclease 1 isoform X1

    Conserved Domains (2) summary
    COG5049
    Location:1735
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]
    pfam03159
    Location:1226
    XRN_N; XRN 5'-3' exonuclease N-terminus
  5. XM_011512922.2XP_011511224.1  5'-3' exoribonuclease 1 isoform X5

    Conserved Domains (1) summary
    COG5049
    Location:1525
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]
  6. XM_017006642.1XP_016862131.1  5'-3' exoribonuclease 1 isoform X6

  7. XM_006713673.2XP_006713736.1  5'-3' exoribonuclease 1 isoform X7

    Conserved Domains (2) summary
    COG5049
    Location:1735
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]
    pfam03159
    Location:1226
    XRN_N; XRN 5'-3' exonuclease N-terminus

RNA

  1. XR_001740178.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001042604.1: Suppressed sequence

    Description
    NM_001042604.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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