Human Gene EXOSC5 (uc002oqo.3)
  Description: Homo sapiens exosome component 5 (EXOSC5), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr19:41,892,276-41,903,256 Size: 10,981 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr19:41,892,538-41,903,233 Size: 10,696 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:41,892,276-41,903,256)mRNA (may differ from genome)Protein (235 aa)
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-  Comments and Description Text from UniProtKB
  ID: EXOS5_HUMAN
DESCRIPTION: RecName: Full=Exosome complex component RRP46; AltName: Full=Chronic myelogenous leukemia tumor antigen 28; AltName: Full=Exosome component 5; AltName: Full=Ribosomal RNA-processing protein 46; AltName: Full=p12B;
FUNCTION: Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes.
SUBUNIT: Component of the RNA exosome complex. Specifically part of the catalytically inactive RNA exosome core (Exo-9) complex which is believed to associate with catalytic subunits EXOSC10, and DIS3 or DIS3L in cytoplasmic- and nuclear-specific RNA exosome complex forms. Exo-9 is formed by a hexameric ring of RNase PH domain-containing subunits specifically containing the heterodimers EXOSC4-EXOSC9, EXOSC5-EXOSC8 and EXOSC6-EXOSC7, and peripheral S1 domain-containing components EXOSC1, EXOSC2 and EXOSC3 located on the top of the ring structure. Interacts with EXOSC1. Interacts with GTPBP1. Interacts with ZC3HAV1. Interacts with DDX17 only in the presence of ZC3HAV1 in an RNA-independent manner.
INTERACTION: Q9Y3B2:EXOSC1; NbExp=10; IntAct=EBI-371876, EBI-371892; Q9NQT5:EXOSC3; NbExp=7; IntAct=EBI-371876, EBI-371866; Q96B26:EXOSC8; NbExp=4; IntAct=EBI-371876, EBI-371922;
SUBCELLULAR LOCATION: Nucleus, nucleolus. Cytoplasm (Probable). Nucleus (Probable).
TISSUE SPECIFICITY: Highly expressed in a variety of hematopoietic and epithelial tumor cell lines, but not in normal hematopoietic tissues or other normal tissue, with the exception of testis.
SIMILARITY: Belongs to the RNase PH family.
CAUTION: The six exosome core subunits containing a RNase PH- domain are not phosphorolytically active.
SEQUENCE CAUTION: Sequence=AAM75154.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

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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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): EXOSC5
CDC HuGE Published Literature: EXOSC5

-  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: 32.94 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 532.12 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -6.0023-0.261 Picture PostScript Text
3' UTR -93.30262-0.356 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
IPR001247 - ExoRNase_PH_dom1
IPR015847 - ExoRNase_PH_dom2
IPR020568 - Ribosomal_S5_D2-typ_fold

Pfam Domains:
PF01138 - 3' exoribonuclease family, domain 1
PF03725 - 3' exoribonuclease family, domain 2

SCOP Domains:
55666 - Ribonuclease PH domain 2-like
54211 - Ribosomal protein S5 domain 2-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2NN6 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9NQT4
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-  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 orthologGenome BrowserNo orthologGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein Sequence Protein SequenceProtein SequenceProtein Sequence
 Alignment AlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000175 3'-5'-exoribonuclease activity
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0004532 exoribonuclease activity

Biological Process:
GO:0006364 rRNA processing
GO:0006401 RNA catabolic process
GO:0016075 rRNA catabolic process
GO:0031125 rRNA 3'-end processing
GO:0034427 nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'
GO:0034475 U4 snRNA 3'-end processing
GO:0043488 regulation of mRNA stability
GO:0043928 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay
GO:0045006 DNA deamination
GO:0051607 defense response to virus
GO:0071028 nuclear mRNA surveillance
GO:0071051 polyadenylation-dependent snoRNA 3'-end processing
GO:0090503 RNA phosphodiester bond hydrolysis, exonucleolytic

Cellular Component:
GO:0000176 nuclear exosome (RNase complex)
GO:0000177 cytoplasmic exosome (RNase complex)
GO:0000178 exosome (RNase complex)
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0035327 transcriptionally active chromatin


-  Descriptions from all associated GenBank mRNAs
  LF384229 - JP 2014500723-A/191732: Polycomb-Associated Non-Coding RNAs.
BC007742 - Homo sapiens exosome component 5, mRNA (cDNA clone MGC:12901 IMAGE:4308795), complete cds.
AF281134 - Homo sapiens exosome component Rrp46 mRNA, complete cds.
AF285785 - Homo sapiens chronic myelogenous leukemia tumor antigen 28 mRNA, complete cds.
BC107696 - Homo sapiens exosome component 5, mRNA (cDNA clone MGC:111224 IMAGE:6453881), complete cds.
JD082550 - Sequence 63574 from Patent EP1572962.
JD369864 - Sequence 350888 from Patent EP1572962.
JD263876 - Sequence 244900 from Patent EP1572962.
JD558922 - Sequence 539946 from Patent EP1572962.
JD126372 - Sequence 107396 from Patent EP1572962.
AK314941 - Homo sapiens cDNA, FLJ95853, highly similar to Homo sapiens exosome component Rrp46 (RRP46), mRNA.
JF432476 - Synthetic construct Homo sapiens clone IMAGE:100073697 exosome component 5 (EXOSC5) gene, encodes complete protein.
KJ899265 - Synthetic construct Homo sapiens clone ccsbBroadEn_08659 EXOSC5 gene, encodes complete protein.
AB463622 - Synthetic construct DNA, clone: pF1KB8248, Homo sapiens EXOSC5 gene for exosome component 5, without stop codon, in Flexi system.
LF367136 - JP 2014500723-A/174639: Polycomb-Associated Non-Coding RNAs.
JD025687 - Sequence 6711 from Patent EP1572962.
JD029233 - Sequence 10257 from Patent EP1572962.
MA619806 - JP 2018138019-A/191732: Polycomb-Associated Non-Coding RNAs.
MA602713 - JP 2018138019-A/174639: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03018 - RNA degradation

Reactome (by CSHL, EBI, and GO)

Protein Q9NQT4 (Reactome details) participates in the following event(s):

R-HSA-450422 KSRP recruits RNA degradation activities
R-HSA-450431 ZFP36 (TTP) recruits RNA degradation activities
R-HSA-450488 BRF1 Complex recruits RNA degradation activities
R-HSA-430028 Exosome Complex hydrolyzes mRNA by 3' to 5' exoribonuclease digestion
R-HSA-450604 KSRP (KHSRP) binds and destabilizes 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-6791226 Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-429958 mRNA decay by 3' to 5' exoribonuclease
R-HSA-8953854 Metabolism of RNA
R-HSA-8868773 rRNA processing in the nucleus and cytosol
R-HSA-429914 Deadenylation-dependent mRNA decay
R-HSA-72312 rRNA processing

-  Other Names for This Gene
  Alternate Gene Symbols: CML28, EXOS5_HUMAN, NM_020158, NP_064543, Q32Q81, Q8NG16, Q96I89, Q9NQT4, RRP46
UCSC ID: uc002oqo.3
RefSeq Accession: NM_020158
Protein: Q9NQT4 (aka EXOS5_HUMAN or RR46_HUMAN)
CCDS: CCDS12580.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_020158.3
exon count: 6CDS single in 3' UTR: no RNA size: 1006
ORF size: 708CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1616.00frame shift in genome: no % Coverage: 98.71
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.