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Aliases for EXOSC6 Gene

Aliases for EXOSC6 Gene

  • Exosome Component 6 2 3 4 5
  • MRNA Transport Regulator 3 Homolog 3 4
  • HMtr3 3 4
  • MTR3 3 4
  • P11 3 4
  • Mtr3 (MRNA Transport Regulator 3)-Homolog (Yeast) 2
  • Homolog Of Yeast MRNA Transport Regulator 3 3
  • Mtr3 (MRNA Transport Regulator 3)-Homolog 3
  • Exosome Complex Exonuclease MTR3 3
  • Exosome Complex Component MTR3 3
  • HMtr3p 3
  • Mtr3p 3
  • EAP4 3

External Ids for EXOSC6 Gene

Previous GeneCards Identifiers for EXOSC6 Gene

  • GC16M070061
  • GC16M068841
  • GC16M070284
  • GC16M056117

Summaries for EXOSC6 Gene

Entrez Gene Summary for EXOSC6 Gene

  • This gene product constitutes one of the subunits of the multisubunit particle called exosome, which mediates mRNA degradation. The composition of human exosome is similar to its yeast counterpart. This protein is homologous to the yeast Mtr3 protein. Its exact function is not known, however, it has been shown using a cell-free RNA decay system that the exosome is required for rapid degradation of unstable mRNAs containing AU-rich elements (AREs), but not for poly(A) shortening. The exosome does not recognize ARE-containing mRNAs on its own, but requires ARE-binding proteins that could interact with the exosome and recruit it to unstable mRNAs, thereby promoting their rapid degradation. [provided by RefSeq, Jul 2008]

GeneCards Summary for EXOSC6 Gene

EXOSC6 (Exosome Component 6) is a Protein Coding gene. Among its related pathways are CDK-mediated phosphorylation and removal of Cdc6 and Pyrimidine metabolism (KEGG). GO annotations related to this gene include poly(A) RNA binding and exoribonuclease activity. An important paralog of this gene is EXOSC4.

UniProtKB/Swiss-Prot for EXOSC6 Gene

  • 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.

Gene Wiki entry for EXOSC6 Gene

Additional gene information for EXOSC6 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for EXOSC6 Gene

Genomics for EXOSC6 Gene

Regulatory Elements for EXOSC6 Gene

Enhancers for EXOSC6 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH16H070403 1.5 Ensembl ENCODE dbSUPER 58.5 -152.6 -152577 1 HDGF PKNOX1 ATF1 TCF12 ZNF121 GATA2 ZNF143 FOS ATF7 RUNX3 EXOSC6 PDXDC2P-NPIPB14P LOC100506083 LOC105371329 ENSG00000260111
GH16H070250 1.1 ENCODE 69.6 +0.4 397 2 HDGF PKNOX1 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 EXOSC6 COG4 NPIPB14P DDX19B HYDIN SF3B3 PDPR NONOP1 LOC100506083 PDXDC2P-NPIPB14P
GH16H070346 1.1 ENCODE 61.7 -95.2 -95208 2 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 ZNF207 SP3 EXOSC6 NFAT5 NONOP1 LOC100506083 PDPR DDX19A SF3B3 LOC400541 DDX19B ENSG00000260111
GH16H070986 1.3 Ensembl ENCODE 38.9 -735.5 -735532 1 PKNOX1 ZNF133 GLI4 ZNF2 FOS SP3 YY2 REST TSHZ1 ZNF518A SF3B3 PDPR PDXDC2P-NPIPB14P DDX19A LOC400541 EXOSC6 HYDIN DDX19B NPIPB14P PDXDC2P
GH16H069402 2 FANTOM5 Ensembl ENCODE dbSUPER 19.8 +843.8 843753 11 PKNOX1 FOXA2 MLX ZFP64 ARID4B FEZF1 DMAP1 SLC30A9 ZNF302 FOS NFAT5 PDPR DDX19A LOC400541 PDXDC2P-NPIPB14P NONOP1 PDXDC2P NPIPB14P SNTB2 UTP4
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around EXOSC6 on UCSC Golden Path with GeneCards custom track

Promoters for EXOSC6 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000087547 530 1601 HDGF MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9

Genomic Location for EXOSC6 Gene

Chromosome:
16
Start:
70,246,778 bp from pter
End:
70,251,930 bp from pter
Size:
5,153 bases
Orientation:
Minus strand

Genomic View for EXOSC6 Gene

Genes around EXOSC6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EXOSC6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EXOSC6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for EXOSC6 Gene

Proteins for EXOSC6 Gene

  • Protein details for EXOSC6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5RKV6-EXOS6_HUMAN
    Recommended name:
    Exosome complex component MTR3
    Protein Accession:
    Q5RKV6

    Protein attributes for EXOSC6 Gene

    Size:
    272 amino acids
    Molecular mass:
    28235 Da
    Quaternary structure:
    • 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.

    Three dimensional structures from OCA and Proteopedia for EXOSC6 Gene

neXtProt entry for EXOSC6 Gene

Post-translational modifications for EXOSC6 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for EXOSC6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for EXOSC6 Gene

Domains & Families for EXOSC6 Gene

Gene Families for EXOSC6 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for EXOSC6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q5RKV6

UniProtKB/Swiss-Prot:

EXOS6_HUMAN :
  • Belongs to the RNase PH family.
Family:
  • Belongs to the RNase PH family.
genes like me logo Genes that share domains with EXOSC6: view

Function for EXOSC6 Gene

Molecular function for EXOSC6 Gene

UniProtKB/Swiss-Prot 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.

Phenotypes From GWAS Catalog for EXOSC6 Gene

Gene Ontology (GO) - Molecular Function for EXOSC6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA,IDA 22681889
GO:0004532 NOT exoribonuclease activity IDA 17174896
genes like me logo Genes that share ontologies with EXOSC6: view

Phenotypes for EXOSC6 Gene

genes like me logo Genes that share phenotypes with EXOSC6: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for EXOSC6
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for EXOSC6 Gene

Localization for EXOSC6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for EXOSC6 Gene

Cytoplasm. Nucleus, nucleolus. Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for EXOSC6 gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for EXOSC6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000176 nuclear exosome (RNase complex) IBA --
GO:0000177 cytoplasmic exosome (RNase complex) IBA --
GO:0000178 exosome (RNase complex) IEA,IDA 20531389
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with EXOSC6: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for EXOSC6 Gene

Pathways & Interactions for EXOSC6 Gene

genes like me logo Genes that share pathways with EXOSC6: view

Pathways by source for EXOSC6 Gene

Gene Ontology (GO) - Biological Process for EXOSC6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006364 rRNA processing TAS --
GO:0016075 rRNA catabolic process IBA --
GO:0031125 rRNA 3-end processing IBA --
GO:0034427 nuclear-transcribed mRNA catabolic process, exonucleolytic, 3-5 IBA --
GO:0034475 U4 snRNA 3-end processing IBA --
genes like me logo Genes that share ontologies with EXOSC6: view

No data available for SIGNOR curated interactions for EXOSC6 Gene

Drugs & Compounds for EXOSC6 Gene

No Compound Related Data Available

Transcripts for EXOSC6 Gene

mRNA/cDNA for EXOSC6 Gene

(1) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(96) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for EXOSC6 Gene

Exosome component 6:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for EXOSC6
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for EXOSC6 Gene

No ASD Table

Relevant External Links for EXOSC6 Gene

GeneLoc Exon Structure for
EXOSC6
ECgene alternative splicing isoforms for
EXOSC6

Expression for EXOSC6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for EXOSC6 Gene

Protein differential expression in normal tissues from HIPED for EXOSC6 Gene

This gene is overexpressed in Breast (32.6) and Peripheral blood mononuclear cells (8.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for EXOSC6 Gene



Protein tissue co-expression partners for EXOSC6 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of EXOSC6 Gene:

EXOSC6

SOURCE GeneReport for Unigene cluster for EXOSC6 Gene:

Hs.660633
genes like me logo Genes that share expression patterns with EXOSC6: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for EXOSC6 Gene

Orthologs for EXOSC6 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for EXOSC6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia EXOSC6 33 34
  • 99.51 (n)
dog
(Canis familiaris)
Mammalia EXOSC6 33
  • 92.31 (n)
mouse
(Mus musculus)
Mammalia Exosc6 33 16
  • 86.67 (n)
rat
(Rattus norvegicus)
Mammalia Exosc6 33
  • 84.74 (n)
oppossum
(Monodelphis domestica)
Mammalia EXOSC6 34
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rarg 33
  • 60.78 (n)
Str.64 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.6653 33
zebrafish
(Danio rerio)
Actinopterygii exosc6 33 34
  • 58.37 (n)
idibd1130 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011906 33
  • 49.59 (n)
fruit fly
(Drosophila melanogaster)
Insecta Mtr3 34
  • 20 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea exos-4.2 34
  • 22 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SKI6 34
  • 23 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G27490 33
  • 40.76 (n)
rice
(Oryza sativa)
Liliopsida Os08g0116800 33
  • 45.56 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU08026 33
  • 41.19 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 35 (a)
OneToOne
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPBC211.08c 33
  • 34.69 (n)
Species where no ortholog for EXOSC6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for EXOSC6 Gene

ENSEMBL:
Gene Tree for EXOSC6 (if available)
TreeFam:
Gene Tree for EXOSC6 (if available)

Paralogs for EXOSC6 Gene

Paralogs for EXOSC6 Gene

Pseudogenes.org Pseudogenes for EXOSC6 Gene

genes like me logo Genes that share paralogs with EXOSC6: view

Variants for EXOSC6 Gene

Sequence variations from dbSNP and Humsavar for EXOSC6 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
rs11537663 Likely benign 70,252,647(+) AAGAT(A/T)CAAAT nc-transcript-variant, upstream-variant-2KB, utr-variant-3-prime
rs116553521 Likely benign 70,252,470(+) AGCCG(G/T)TATCT nc-transcript-variant, upstream-variant-2KB, utr-variant-3-prime
rs149377346 Likely benign 70,252,837(+) ACCAC(C/T)TTTAC nc-transcript-variant, upstream-variant-2KB, reference, missense
rs150625194 Likely benign 70,252,508(+) AATGC(A/G)GGGTT nc-transcript-variant, upstream-variant-2KB, utr-variant-3-prime
rs35744709 Likely benign 70,252,728(-) TGTAA(A/T)GAACT nc-transcript-variant, upstream-variant-2KB, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for EXOSC6 Gene

Variant ID Type Subtype PubMed ID
esv25519 CNV gain+loss 19812545
esv2758652 CNV gain+loss 17122850
esv33745 CNV gain+loss 17666407
nsv1061286 CNV gain 25217958
nsv428328 CNV gain+loss 18775914
nsv7285 OTHER inversion 18451855
nsv833271 CNV gain+loss 17160897
nsv978165 CNV duplication 23825009

Variation tolerance for EXOSC6 Gene

Gene Damage Index Score: 4.33; 63.12% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for EXOSC6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
EXOSC6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EXOSC6 Gene

Disorders for EXOSC6 Gene

Relevant External Links for EXOSC6

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
EXOSC6

No disorders were found for EXOSC6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for EXOSC6 Gene

Publications for EXOSC6 Gene

  1. Protein-protein interactions between human exosome components support the assembly of RNase PH-type subunits into a six-membered PNPase-like ring. (PMID: 12419256) Raijmakers R … Pruijn GJ (Journal of molecular biology 2002) 2 3 4 60
  2. AU binding proteins recruit the exosome to degrade ARE-containing mRNAs. (PMID: 11719186) Chen CY … Karin M (Cell 2001) 2 3 4 60
  3. The RNA exosome targets the AID cytidine deaminase to both strands of transcribed duplex DNA substrates. (PMID: 21255825) Basu U … Alt FW (Cell 2011) 3 4 60
  4. Dis3-like 1: a novel exoribonuclease associated with the human exosome. (PMID: 20531389) Staals RH … Pruijn GJ (The EMBO journal 2010) 3 4 60
  5. Reconstitution, activities, and structure of the eukaryotic RNA exosome. (PMID: 17174896) Liu Q … Lima CD (Cell 2006) 3 4 60

Products for EXOSC6 Gene

Sources for EXOSC6 Gene

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