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Aliases for TNRC6C Gene

Aliases for TNRC6C Gene

  • Trinucleotide Repeat Containing 6C 2 3 5
  • KIAA1582 4

External Ids for TNRC6C Gene

Previous GeneCards Identifiers for TNRC6C Gene

  • GC17P073557
  • GC17P076002
  • GC17P071424
  • GC17P078004

Summaries for TNRC6C Gene

GeneCards Summary for TNRC6C Gene

TNRC6C (Trinucleotide Repeat Containing 6C) is a Protein Coding gene. Among its related pathways are RET signaling and Innate Immune System. Gene Ontology (GO) annotations related to this gene include RNA binding and nucleotide binding. An important paralog of this gene is TNRC6A.

UniProtKB/Swiss-Prot for TNRC6C Gene

  • Plays a role in RNA-mediated gene silencing by micro-RNAs (miRNAs). Required for miRNA-dependent translational repression of complementary mRNAs by argonaute family proteins. As scaffoldng protein associates with argonaute proteins bound to partially complementary mRNAs and simultaneously can recruit CCR4-NOT and PAN deadenylase complexes.

Additional gene information for TNRC6C Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TNRC6C Gene

Genomics for TNRC6C Gene

GeneHancer (GH) Regulatory Elements for TNRC6C Gene

Promoters and enhancers for TNRC6C Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17I078039 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 560.5 +81.6 81555 3.4 SMAD1 NFIB SIN3A YBX1 RFX5 YY1 ZNF366 ZNF207 ZNF143 RCOR1 TNRC6C RNU6-625P TMEM235 RNU1-80P UBE2V2P2 ENSG00000279600
GH17I077957 Promoter/Enhancer 1.9 FANTOM5 Ensembl ENCODE 566.1 -0.2 -206 3.8 HDGF SMAD1 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 POLR2B TNRC6C SNHG20 USP36 TMC8 TMC6 SOCS3 TMEM235 PGS1 LOC105371909
GH17I078004 Promoter 0.5 EPDnew 550.2 +45.8 45781 0.1 TNRC6C RNU1-80P LINC01973 RNU6-625P ENSG00000279600 GC17P077979
GH17I077961 Enhancer 0.3 Ensembl 550.8 +1.9 1861 0.2 MLLT1 TNRC6C RNU1-80P LINC01973 GC17P077979
GH17I077233 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 48.1 -724.4 -724405 3.3 PKNOX1 ARNT SIN3A FEZF1 ZNF2 CBX5 ZNF213 ZNF302 E2F8 ZNF416 SRSF2 TNRC6C METTL23 ENSG00000267546 SEPT9 PRPSAP1 SNHG20 RNU4-47P ENSG00000267543 MFSD11
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TNRC6C on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TNRC6C gene promoter:

Genomic Locations for TNRC6C Gene

Genomic Locations for TNRC6C Gene
chr17:77,959,240-78,108,835
(GRCh38/hg38)
Size:
149,596 bases
Orientation:
Plus strand
chr17:76,000,249-76,104,916
(GRCh37/hg19)

Genomic View for TNRC6C Gene

Genes around TNRC6C on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TNRC6C Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TNRC6C Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TNRC6C Gene

Proteins for TNRC6C Gene

  • Protein details for TNRC6C Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HCJ0-TNR6C_HUMAN
    Recommended name:
    Trinucleotide repeat-containing gene 6C protein
    Protein Accession:
    Q9HCJ0
    Secondary Accessions:
    • G3XAB8
    • Q86UE5
    • Q8N3D8
    • Q96MU9

    Protein attributes for TNRC6C Gene

    Size:
    1690 amino acids
    Molecular mass:
    175964 Da
    Quaternary structure:
    • Interacts with one or more of the argonaute family proteins AGO1, AGO2, AGO3 and AGO4. Interacts with PABPC1 and EIF4G1. Interacts with CNOT1; the interaction is direct and mediates the association with the CCR4-NOT complex. Interacts with PAN3; the interaction mediates the association with the PAN complex.
    SequenceCaution:
    • Sequence=BAB13408.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAB71179.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for TNRC6C Gene

    Alternative splice isoforms for TNRC6C Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TNRC6C Gene

Post-translational modifications for TNRC6C Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for TNRC6C Gene

Domains & Families for TNRC6C Gene

Gene Families for TNRC6C Gene

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

Suggested Antigen Peptide Sequences for TNRC6C Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9HCJ0

UniProtKB/Swiss-Prot:

TNR6C_HUMAN :
  • The silencing domain, also known as C-terminal effector domain (CED), can act in autonomous repression, including both translational inhibition and mRNA degradation.
  • Belongs to the GW182 family.
Domain:
  • The silencing domain, also known as C-terminal effector domain (CED), can act in autonomous repression, including both translational inhibition and mRNA degradation.
Family:
  • Belongs to the GW182 family.
genes like me logo Genes that share domains with TNRC6C: view

Function for TNRC6C Gene

Molecular function for TNRC6C Gene

UniProtKB/Swiss-Prot Function:
Plays a role in RNA-mediated gene silencing by micro-RNAs (miRNAs). Required for miRNA-dependent translational repression of complementary mRNAs by argonaute family proteins. As scaffoldng protein associates with argonaute proteins bound to partially complementary mRNAs and simultaneously can recruit CCR4-NOT and PAN deadenylase complexes.

Phenotypes From GWAS Catalog for TNRC6C Gene

Gene Ontology (GO) - Molecular Function for TNRC6C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA --
GO:0005515 protein binding IPI 19383768
genes like me logo Genes that share ontologies with TNRC6C: view
genes like me logo Genes that share phenotypes with TNRC6C: view

Animal Model Products

miRNA for TNRC6C Gene

miRTarBase miRNAs that target TNRC6C

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TNRC6C Gene

Localization for TNRC6C Gene

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 TNRC6C gene
Compartment Confidence
cytosol 5
nucleus 3

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for TNRC6C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with TNRC6C: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for TNRC6C Gene

Pathways & Interactions for TNRC6C Gene

genes like me logo Genes that share pathways with TNRC6C: view

Pathways by source for TNRC6C Gene

Gene Ontology (GO) - Biological Process for TNRC6C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006417 regulation of translation IEA --
GO:0007223 Wnt signaling pathway, calcium modulating pathway TAS --
GO:0031047 gene silencing by RNA IEA --
GO:0035194 posttranscriptional gene silencing by RNA TAS --
GO:0035195 gene silencing by miRNA IGI 23172285
genes like me logo Genes that share ontologies with TNRC6C: view

No data available for SIGNOR curated interactions for TNRC6C Gene

Drugs & Compounds for TNRC6C Gene

No Compound Related Data Available

Transcripts for TNRC6C Gene

Unigene Clusters for TNRC6C Gene

Trinucleotide repeat containing 6C:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TNRC6C Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19a · 19b
SP1: - - - -
SP2: - - - -
SP3: -
SP4:

Relevant External Links for TNRC6C Gene

GeneLoc Exon Structure for
TNRC6C
ECgene alternative splicing isoforms for
TNRC6C

Expression for TNRC6C Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TNRC6C Gene

Protein differential expression in normal tissues from HIPED for TNRC6C Gene

This gene is overexpressed in Breast (51.7) and Heart (11.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TNRC6C Gene



NURSA nuclear receptor signaling pathways regulating expression of TNRC6C Gene:

TNRC6C

SOURCE GeneReport for Unigene cluster for TNRC6C Gene:

Hs.569831

Evidence on tissue expression from TISSUES for TNRC6C Gene

  • Nervous system(4.7)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with TNRC6C: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TNRC6C Gene

Orthologs for TNRC6C Gene

This gene was present in the common ancestor of animals.

Orthologs for TNRC6C Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TNRC6C 33 34
  • 99.52 (n)
dog
(Canis familiaris)
Mammalia TNRC6C 33 34
  • 91.11 (n)
mouse
(Mus musculus)
Mammalia Tnrc6c 33 16 34
  • 90.11 (n)
rat
(Rattus norvegicus)
Mammalia Tnrc6c 33
  • 89.81 (n)
cow
(Bos Taurus)
Mammalia TNRC6C 33 34
  • 87.16 (n)
oppossum
(Monodelphis domestica)
Mammalia TNRC6C 34
  • 78 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TNRC6C 34
  • 60 (a)
OneToOne
chicken
(Gallus gallus)
Aves TNRC6C 33 34
  • 86.95 (n)
lizard
(Anolis carolinensis)
Reptilia TNRC6C 34
  • 78 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tnrc6c 33
  • 78.35 (n)
zebrafish
(Danio rerio)
Actinopterygii tnrc6c 33
  • 65.39 (n)
TNRC6C (2 of 5) 34
  • 54 (a)
OneToMany
TNRC6C (4 of 5) 34
  • 53 (a)
OneToMany
TNRC6C (5 of 5) 34
  • 53 (a)
OneToMany
TNRC6C (3 of 5) 34
  • 33 (a)
OneToMany
tnrc6b 34
  • 26 (a)
OneToMany
Dr.12790 33
fruit fly
(Drosophila melanogaster)
Insecta gw 34
  • 24 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 32 (a)
OneToMany
Species where no ortholog for TNRC6C was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for TNRC6C Gene

ENSEMBL:
Gene Tree for TNRC6C (if available)
TreeFam:
Gene Tree for TNRC6C (if available)

Paralogs for TNRC6C Gene

Paralogs for TNRC6C Gene

(2) SIMAP similar genes for TNRC6C Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with TNRC6C: view

Variants for TNRC6C Gene

Sequence variations from dbSNP and Humsavar for TNRC6C Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1000023578 -- 77,985,844(+) G/C genic_upstream_transcript_variant, intron_variant
rs1000026329 -- 78,107,351(+) A/C 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1000049646 -- 78,033,869(+) T/A genic_upstream_transcript_variant, intron_variant
rs1000053833 -- 77,996,331(+) G/A genic_upstream_transcript_variant, intron_variant
rs1000136001 -- 78,101,870(+) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for TNRC6C Gene

Variant ID Type Subtype PubMed ID
dgv570e199 CNV deletion 23128226
esv3641322 CNV loss 21293372
esv3641323 CNV loss 21293372
nsv1064772 CNV gain 25217958
nsv2153 CNV deletion 18451855
nsv833554 CNV gain+loss 17160897

Variation tolerance for TNRC6C Gene

Residual Variation Intolerance Score: 3.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.89; 79.56% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TNRC6C Gene

Human Gene Mutation Database (HGMD)
TNRC6C
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TNRC6C

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TNRC6C Gene

Disorders for TNRC6C Gene

Additional Disease Information for TNRC6C

No disorders were found for TNRC6C Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for TNRC6C Gene

Publications for TNRC6C Gene

  1. Early origin and adaptive evolution of the GW182 protein family, the key component of RNA silencing in animals. (PMID: 26106978) Zielezinski A … Karlowski WM (RNA biology 2015) 2 3 58
  2. GW182 proteins directly recruit cytoplasmic deadenylase complexes to miRNA targets. (PMID: 21981923) Braun JE … Izaurralde E (Molecular cell 2011) 3 4 58
  3. miRNA repression involves GW182-mediated recruitment of CCR4-NOT through conserved W-containing motifs. (PMID: 21984184) Chekulaeva M … Filipowicz W (Nature structural & molecular biology 2011) 3 4 58
  4. miRNA-mediated deadenylation is orchestrated by GW182 through two conserved motifs that interact with CCR4-NOT. (PMID: 21984185) Fabian MR … Sonenberg N (Nature structural & molecular biology 2011) 3 4 58
  5. Functional dissection of the human TNRC6 (GW182-related) family of proteins. (PMID: 19470757) Baillat D … Shiekhattar R (Molecular and cellular biology 2009) 2 3 58

Products for TNRC6C Gene

Sources for TNRC6C Gene

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