Format

Send to:

Choose Destination

EXOSC2 exosome component 2 [ Homo sapiens (human) ]

Gene ID: 23404, updated on 6-Jan-2019

Summary

Official Symbol
EXOSC2provided by HGNC
Official Full Name
exosome component 2provided by HGNC
Primary source
HGNC:HGNC:17097
See related
Ensembl:ENSG00000130713 MIM:602238
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
p7; RRP4; SHRF; Rrp4p; hRrp4p
Expression
Ubiquitous expression in lymph node (RPKM 5.3), ovary (RPKM 5.1) and 25 other tissues See more
Orthologs

Genomic context

See EXOSC2 in Genome Data Viewer
Location:
9q34.12
Exon count:
9
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 9 NC_000009.12 (130693760..130704894)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (133569158..133580452)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein L19 pseudogene 15 Neighboring gene VISTA enhancer hs876 Neighboring gene PR/SET domain 12 Neighboring gene ABL breakpoint recombination region Neighboring gene ribosomal protein L37 pseudogene 17 Neighboring gene ABL proto-oncogene 1, non-receptor tyrosine kinase Neighboring gene pyroglutamylated RFamide peptide

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 FunctionsWhat's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of exosome component 2 (EXOSC2; RRP4) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • ATF4 activates genes, organism-specific biosystem (from REACTOME)
    ATF4 activates genes, organism-specific biosystemATF4 is a transcription factor and activates expression of IL-8, MCP1, IGFBP-1, CHOP, HERP1 and ATF3.
  • Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA, organism-specific biosystem (from REACTOME)
    Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA, organism-specific biosystemButyrate Response Factor 1 (BRF1, ZFP36L1, not to be confused with transcription factor IIIB) binds AU-rich elements in the 3' region of mRNAs. After binding, BRF1 recruits exonucleases (XRN1 and the...
  • Deadenylation-dependent mRNA decay, organism-specific biosystem (from REACTOME)
    Deadenylation-dependent mRNA decay, organism-specific biosystemAfter undergoing rounds of translation, mRNA is normally destroyed by the deadenylation-dependent pathway. Though the trigger is unclear, deadenylation likely proceeds in two steps: one catalyzed by...
  • Exosome, archaea, organism-specific biosystem (from KEGG)
    Exosome, archaea, organism-specific biosystemStructural complex; Genetic information processing; RNA processing
  • Exosome, archaea, conserved biosystem (from KEGG)
    Exosome, archaea, conserved biosystemStructural complex; Genetic information processing; RNA processing
  • Exosome, eukaryotes, organism-specific biosystem (from KEGG)
    Exosome, eukaryotes, organism-specific biosystemStructural complex; Genetic information processing; RNA processing
  • Exosome, eukaryotes, conserved biosystem (from KEGG)
    Exosome, eukaryotes, conserved biosystemStructural complex; Genetic information processing; RNA processing
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • KSRP (KHSRP) binds and destabilizes mRNA, organism-specific biosystem (from REACTOME)
    KSRP (KHSRP) binds and destabilizes mRNA, organism-specific biosystemKSRP binds to AU-rich sequences in the 3' untranslated regions of mRNAs. KSRP causes the bound mRNA to be targeted for hydrolysis by recruiting exonucleases and decapping enzymes. The activity of KSR...
  • Major pathway of rRNA processing in the nucleolus and cytosol, organism-specific biosystem (from REACTOME)
    Major pathway of rRNA processing in the nucleolus and cytosol, organism-specific biosystemIn humans, a 47S precursor rRNA (pre-rRNA) is transcribed by RNA polymerase I from rRNA-encoding genes (rDNA) at the boundary of the fibrillar center and the dense fibrillar components of the nucleol...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • PERK regulates gene expression, organism-specific biosystem (from REACTOME)
    PERK regulates gene expression, organism-specific biosystemPERK (EIF2AK3) is a single-pass transmembrane protein located in the endoplasmic reticulum (ER) membrane such that the N-terminus of PERK is luminal and the C-terminus is cytosolic. PERK is maintaine...
  • RNA degradation, organism-specific biosystem (from KEGG)
    RNA degradation, organism-specific biosystemThe correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes, two major pathways of mRNA decay e...
  • RNA degradation, conserved biosystem (from KEGG)
    RNA degradation, conserved biosystemThe correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes, two major pathways of mRNA decay e...
  • Regulation of mRNA stability by proteins that bind AU-rich elements, organism-specific biosystem (from REACTOME)
    Regulation of mRNA stability by proteins that bind AU-rich elements, organism-specific biosystemRNA elements rich in adenine and uracil residues (AU-rich elements) bind specific proteins which either target the RNA for degradation or, more rarely, stabilize the RNA. The activity of the AU-eleme...
  • Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA, organism-specific biosystem (from REACTOME)
    Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA, organism-specific biosystemTristetraproline (TTP) binds RNAs that contain AU-rich elements and recruits enzymes that degrade RNA. TTP interacts with the exosome (3' to 5' exonuclease), XRN1 (5' to 3' exonuclease), and the deca...
  • Unfolded Protein Response (UPR), organism-specific biosystem (from REACTOME)
    Unfolded Protein Response (UPR), organism-specific biosystemThe Unfolded Protein Response (UPR) is a regulatory system that protects the Endoplasmic Reticulum (ER) from overload. The UPR is provoked by the accumulation of improperly folded protein in the ER d...
  • mRNA decay by 3' to 5' exoribonuclease, organism-specific biosystem (from REACTOME)
    mRNA decay by 3' to 5' exoribonuclease, organism-specific biosystemThe degradation of mRNA from 3' to 5' occurs in two steps. First, the exosome exoribonuclease complex binds the 3' end of the oligoadenylated mRNA and hydrolyzes it from 3' to 5', yielding ribonucleo...
  • rRNA processing, organism-specific biosystem (from REACTOME)
    rRNA processing, organism-specific biosystemEach eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 2...
  • rRNA processing in the nucleus and cytosol, organism-specific biosystem (from REACTOME)
    rRNA processing in the nucleus and cytosol, organism-specific biosystemEach eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 2...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
3'-5'-exoribonuclease activity TAS
Traceable Author Statement
more info
PubMed 
7S RNA binding TAS
Traceable Author Statement
more info
PubMed 
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
NOT exoribonuclease activity IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
CUT catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U4 snRNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay TAS
Traceable Author Statement
more info
 
exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear polyadenylation-dependent rRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear polyadenylation-dependent tRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
polyadenylation-dependent snoRNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of cell growth IMP
Inferred from Mutant Phenotype
more info
PubMed 
rRNA processing TAS
Traceable Author Statement
more info
 
regulation of mRNA stability TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic exosome (RNase complex) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
exosome (RNase complex) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
exosome (RNase complex) IDA
Inferred from Direct Assay
more info
PubMed 
nuclear exosome (RNase complex) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear exosome (RNase complex) IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
exosome complex component RRP4
Names
exosome complex exonuclease RRP4
homolog of yeast RRP4 (ribosomal RNA processing 4), 3' 5' exoribonuclease (RRP4)
homolog of yeast RRP4 (ribosomal RNA processing 4), 3'-5'-exoribonuclease
ribosomal RNA-processing protein 4

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_001282708.1NP_001269637.1  exosome complex component RRP4 isoform 2

    See identical proteins and their annotated locations for NP_001269637.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region compared to variant 1. It encodes isoform 2 which is shorter than isoform 1.
    Source sequence(s)
    AK296605, AL359092, BU934039
    Consensus CDS
    CCDS65160.1
    UniProtKB/Swiss-Prot
    Q13868
    Related
    ENSP00000444917.1, ENST00000546165.5
    Conserved Domains (1) summary
    cl26026
    Location:22215
    ECR1_N; Exosome complex exonuclease RRP4 N-terminal region
  2. NM_001282709.1NP_001269638.1  exosome complex component RRP4 isoform 3

    See identical proteins and their annotated locations for NP_001269638.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the central coding region compared to variant 1. It encodes isoform 3 which is shorter than isoform 1.
    Source sequence(s)
    AL359092, AL573310, BU934039, DA813307
    Consensus CDS
    CCDS65161.1
    UniProtKB/Swiss-Prot
    Q13868
    Related
    ENSP00000361426.3, ENST00000372351.7
    Conserved Domains (1) summary
    cl26026
    Location:22211
    ECR1_N; Exosome complex exonuclease RRP4 N-terminal region
  3. NM_014285.7NP_055100.2  exosome complex component RRP4 isoform 1

    See identical proteins and their annotated locations for NP_055100.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AL359092, BC000747, BU934039
    Consensus CDS
    CCDS6935.1
    UniProtKB/Swiss-Prot
    Q13868
    Related
    ENSP00000361433.5, ENST00000372358.9
    Conserved Domains (1) summary
    cl26026
    Location:22241
    ECR1_N; Exosome complex exonuclease RRP4 N-terminal region

RNA

  1. NR_104230.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate internal exon and uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK303163, AL359092

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p12 Primary Assembly

    Range
    130693760..130704894
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017014558.1XP_016870047.1  exosome complex component RRP4 isoform X1

    UniProtKB/TrEMBL
    B3KQW2
    Conserved Domains (2) summary
    cd05789
    Location:254
    S1_Rrp4; S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in ...
    pfam15985
    Location:5797
    KH_6; KH domain
  2. XM_005272176.2XP_005272233.1  exosome complex component RRP4 isoform X1

    See identical proteins and their annotated locations for XP_005272233.1

    UniProtKB/TrEMBL
    B3KQW2
    Conserved Domains (2) summary
    cd05789
    Location:254
    S1_Rrp4; S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in ...
    pfam15985
    Location:5797
    KH_6; KH domain
  3. XM_006717023.2XP_006717086.1  exosome complex component RRP4 isoform X2

    Conserved Domains (2) summary
    pfam15985
    Location:3979
    KH_6; KH domain
    cl09927
    Location:136
    S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...

RNA

  1. XR_001746262.1 RNA Sequence

Support Center