Human Gene EXOSC6 (ENST00000435634.3_7) from GENCODE V47lift37
  Description: exosome component 6 (from RefSeq NM_058219.3)
Gencode Transcript: ENST00000435634.3_7
Gencode Gene: ENSG00000223496.3_9
Transcript (Including UTRs)
   Position: hg19 chr16:70,280,681-70,285,843 Size: 5,163 Total Exon Count: 1 Strand: -
Coding Region
   Position: hg19 chr16:70,284,985-70,285,803 Size: 819 Coding Exon Count: 1 

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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 (chr16:70,280,681-70,285,843)mRNA (may differ from genome)Protein (272 aa)
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-  Comments and Description Text from UniProtKB
  ID: EXOS6_HUMAN
DESCRIPTION: RecName: Full=Exosome complex component MTR3; AltName: Full=Exosome component 6; AltName: Full=mRNA transport regulator 3 homolog; Short=hMtr3; AltName: Full=p11;
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.
SUBCELLULAR LOCATION: Cytoplasm (Probable). Nucleus, nucleolus (Probable). Nucleus (Probable).
SIMILARITY: Belongs to the RNase PH family.
CAUTION: The six exosome core subunits containing a RNase PH- domain are not phosphorolytically active.

-  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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 11.94 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 332.97 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 -12.5040-0.312 Picture PostScript Text
3' UTR -1320.904304-0.307 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

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 Q5RKV6
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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 orthologNo orthologNo ortholog
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0004532 exoribonuclease activity

Biological Process:
GO:0006364 rRNA processing
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:0045190 isotype switching
GO:0045830 positive regulation of isotype switching
GO:0071028 nuclear mRNA surveillance
GO:0071051 polyadenylation-dependent snoRNA 3'-end processing

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


-  Descriptions from all associated GenBank mRNAs
  AF126109 - Homo sapiens clone TA40 untranslated mRNA, complete sequence.
AF131796 - Homo sapiens clone 24852 mRNA sequence.
AK024276 - Homo sapiens cDNA FLJ14214 fis, clone NT2RP3003576.
JD267438 - Sequence 248462 from Patent EP1572962.
JD345618 - Sequence 326642 from Patent EP1572962.
JD394734 - Sequence 375758 from Patent EP1572962.
AK095542 - Homo sapiens cDNA FLJ38223 fis, clone FCBBF2003297.
JD365437 - Sequence 346461 from Patent EP1572962.
BC052252 - Homo sapiens exosome component 6, mRNA (cDNA clone MGC:59978 IMAGE:6256140), complete cds.
BC039194 - Homo sapiens cDNA clone IMAGE:4281687, **** WARNING: chimeric clone ****.
JD272839 - Sequence 253863 from Patent EP1572962.
JD156461 - Sequence 137485 from Patent EP1572962.
JD208110 - Sequence 189134 from Patent EP1572962.
JD181725 - Sequence 162749 from Patent EP1572962.
JD204290 - Sequence 185314 from Patent EP1572962.

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

Protein Q5RKV6 (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: ENST00000435634.1, ENST00000435634.2, EXOS6_HUMAN, MTR3, NM_058219, Q5RKV6, uc320ebo.1, uc320ebo.2
UCSC ID: ENST00000435634.3_7
RefSeq Accession: NM_058219.3
Protein: Q5RKV6 (aka EXOS6_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.