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EXOSC5 exosome component 5 [ Homo sapiens (human) ]

Gene ID: 56915, updated on 5-Aug-2018

Summary

Official Symbol
EXOSC5provided by HGNC
Official Full Name
exosome component 5provided by HGNC
Primary source
HGNC:HGNC:24662
See related
Ensembl:ENSG00000077348 MIM:606492; Vega:OTTHUMG00000182759
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
p12B; RRP46; RRP41B; Rrp46p; hRrp46p
Expression
Ubiquitous expression in lymph node (RPKM 8.8), ovary (RPKM 8.2) and 25 other tissues See more
Orthologs

Genomic context

See EXOSC5 in Genome Data Viewer
Location:
19q13.2
Exon count:
6
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 19 NC_000019.10 (41386370..41397351, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (41892275..41903289, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene transforming growth factor beta 1 Neighboring gene B9 domain containing 2 Neighboring gene transmembrane protein 91 Neighboring gene branched chain keto acid dehydrogenase E1, alpha polypeptide Neighboring gene UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 8

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of exosome component 5 (EXOSC5) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed
Knockdown of exosome component 5 (EXOSC5) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Protein interactions

Protein Gene Interaction Pubs
Pr55(Gag) gag Knockdown of exosome component 5 (EXOSC5) affects HIV-1 Gag trafficking, leading to inhibit HIV-1 replication in Jurkat cells PubMed
Rev rev HIV-1 Rev interacting protein, exosome component 5 (EXOSC5), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with EXOSC5 is increased by RRE 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, 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

Clone Names

  • MGC12901, MGC111224

Gene Ontology Provided by GOA

Function Evidence Code Pubs
3'-5'-exoribonuclease activity NAS
Non-traceable Author Statement
more info
PubMed 
RNA binding IEA
Inferred from Electronic Annotation
more info
 
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
DNA deamination IDA
Inferred from Direct Assay
more info
PubMed 
RNA phosphodiester bond hydrolysis, exonucleolytic IEA
Inferred from Electronic Annotation
more info
 
U4 snRNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
defense response to virus IMP
Inferred from Mutant Phenotype
more info
PubMed 
exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay IMP
Inferred from Mutant Phenotype
more info
PubMed 
exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay TAS
Traceable Author Statement
more info
 
nuclear mRNA surveillance 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 
rRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
rRNA processing NAS
Non-traceable Author Statement
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 NAS
Non-traceable Author Statement
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) IDA
Inferred from Direct Assay
more info
PubMed 
nuclear exosome (RNase complex) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleolus NAS
Non-traceable Author Statement
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
 
transcriptionally active chromatin IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

Preferred Names
exosome complex component RRP46
Names
chronic myelogenous leukemia tumor antigen 28
exosome complex exonuclease RRP46
exosome component Rrp46
ribosomal RNA-processing protein 46

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_020158.3NP_064543.3  exosome complex component RRP46

    See identical proteins and their annotated locations for NP_064543.3

    Status: VALIDATED

    Source sequence(s)
    AF281134, BU683254
    Consensus CDS
    CCDS12580.1
    UniProtKB/Swiss-Prot
    Q9NQT4
    Related
    ENSP00000221233.3, OTTHUMP00000270084, ENST00000221233.8, OTTHUMT00000463492
    Conserved Domains (2) summary
    TIGR02065
    Location:28232
    ECX1; archaeal exosome-like complex exonuclease 1
    cd11372
    Location:28225
    RNase_PH_RRP46; RRP46 subunit of eukaryotic exosome

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p12 Primary Assembly

    Range
    41386370..41397351 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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