Human Gene TNRC6A (ENST00000395799.8_9) from GENCODE V47lift37
  Description: trinucleotide repeat containing adaptor 6A, transcript variant 1 (from RefSeq NM_014494.4)
Gencode Transcript: ENST00000395799.8_9
Gencode Gene: ENSG00000090905.19_12
Transcript (Including UTRs)
   Position: hg19 chr16:24,740,972-24,837,539 Size: 96,568 Total Exon Count: 25 Strand: +
Coding Region
   Position: hg19 chr16:24,741,163-24,835,128 Size: 93,966 Coding Exon Count: 25 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
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 (chr16:24,740,972-24,837,539)mRNA (may differ from genome)Protein (1962 aa)
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-  Comments and Description Text from UniProtKB
  ID: TNR6A_HUMAN
DESCRIPTION: RecName: Full=Trinucleotide repeat-containing gene 6A protein; AltName: Full=CAG repeat protein 26; AltName: Full=EMSY interactor protein; AltName: Full=GW182 autoantigen; Short=Protein GW1; AltName: Full=Glycine-tryptophan protein of 182 kDa;
FUNCTION: Plays a role in RNA-mediated gene silencing by both micro-RNAs (miRNAs) and short interfering RNAs (siRNAs). Required for miRNA-dependent repression of translation and for siRNA- dependent endonucleolytic cleavage of complementary mRNAs by argonaute family proteins.
SUBUNIT: Interacts with EIF2C1/AGO1, EIF2C2/AGO2, EIF2C3/AGO3 and EIF2C4/AGO4.
SUBCELLULAR LOCATION: Cytoplasm, P-body. Note=Mammalian P-bodies are also known as GW bodies (GWBs).
TISSUE SPECIFICITY: Ubiquitous.
INDUCTION: By exogenous short interfering RNA (siRNA).
MISCELLANEOUS: Antibodies against TNRC6A are found in sera from patients with Sjoegren syndrome (SS), ataxia and sensor neuropathy diseases that developed autoantibodies against protein of the GWB structure. Autoantibodies were mapped to the GW-rich mid-part, the non-GW-rich region and the C-terminus of the protein.
SIMILARITY: Belongs to the GW182 family.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.
SEQUENCE CAUTION: Sequence=BAA91899.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAD28525.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
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           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: 27.93 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 651.09 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 -99.40191-0.520 Picture PostScript Text
3' UTR -586.102411-0.243 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
IPR019486 - Argonaute_hook_dom
IPR026804 - GW182_fam
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom
IPR009060 - UBA-like

Pfam Domains:
PF10427 - Argonaute hook
PF16608 - TNRC6-PABC binding domain

SCOP Domains:
46934 - UBA-like
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on Q8NDV7
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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
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0006417 regulation of translation
GO:0007223 Wnt signaling pathway, calcium modulating pathway
GO:0031047 gene silencing by RNA
GO:0035194 posttranscriptional gene silencing by RNA
GO:0035195 gene silencing by miRNA
GO:0035278 miRNA mediated inhibition of translation
GO:0045652 regulation of megakaryocyte differentiation
GO:0060964 regulation of gene silencing by miRNA

Cellular Component:
GO:0000932 P-body
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0035068 micro-ribonucleoprotein complex
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  U80739 - Homo sapiens CAGH26 mRNA, partial cds.
LP896012 - Sequence 876 from Patent EP3253886.
AB587316 - Synthetic construct DNA, clone: pF1KA1460, Homo sapiens TNRC6A gene for trinucleotide repeat containing 6A, without stop codon, in Flexi system.
BC172409 - Synthetic construct Homo sapiens clone IMAGE:100069103, MGC:199114 trinucleotide repeat containing 6A (TNRC6A) mRNA, encodes complete protein.
AJ492221 - Homo sapiens mRNA for EDIE protein (KIAA1460 gene).
JC506674 - Sequence 42 from Patent EP2733220.
JC737786 - Sequence 42 from Patent WO2014075939.
JC506661 - Sequence 29 from Patent EP2733220.
JC737773 - Sequence 29 from Patent WO2014075939.
JC506688 - Sequence 56 from Patent EP2733220.
JC737800 - Sequence 56 from Patent WO2014075939.
JC506666 - Sequence 34 from Patent EP2733220.
JC737778 - Sequence 34 from Patent WO2014075939.
JD387569 - Sequence 368593 from Patent EP1572962.
AY035864 - Homo sapiens GW182 autoantigen (GW1) mRNA, complete cds.
JD229199 - Sequence 210223 from Patent EP1572962.
JD289665 - Sequence 270689 from Patent EP1572962.
JD126780 - Sequence 107804 from Patent EP1572962.
AB040893 - Homo sapiens mRNA for KIAA1460 protein, partial cds.
AL833757 - Homo sapiens mRNA; cDNA DKFZp666E117 (from clone DKFZp666E117).
AK025696 - Homo sapiens cDNA: FLJ22043 fis, clone HEP09131.
AK299905 - Homo sapiens cDNA FLJ59141 complete cds, highly similar to Trinucleotide repeat-containing gene 6A protein.
JD023717 - Sequence 4741 from Patent EP1572962.
AL713750 - Homo sapiens mRNA; cDNA DKFZp566M143 (from clone DKFZp566M143).
AK094542 - Homo sapiens cDNA FLJ37223 fis, clone BRAMY1000157, highly similar to Trinucleotide repeat-containing gene 6A protein.
BC024324 - Homo sapiens trinucleotide repeat containing 6A, mRNA (cDNA clone IMAGE:4427559), partial cds.
AK001773 - Homo sapiens cDNA FLJ10911 fis, clone OVARC1000148.
AK025277 - Homo sapiens cDNA: FLJ21624 fis, clone COL08006.
BC068209 - Homo sapiens trinucleotide repeat containing 6A, mRNA (cDNA clone IMAGE:6197151).
CU686625 - Synthetic construct Homo sapiens gateway clone IMAGE:100022794 5' read TNRC6A mRNA.
KJ902470 - Synthetic construct Homo sapiens clone ccsbBroadEn_11864 TNRC6A gene, encodes complete protein.
JD079413 - Sequence 60437 from Patent EP1572962.
JD476156 - Sequence 457180 from Patent EP1572962.
JD458650 - Sequence 439674 from Patent EP1572962.
JD378970 - Sequence 359994 from Patent EP1572962.
JD501382 - Sequence 482406 from Patent EP1572962.
JD557757 - Sequence 538781 from Patent EP1572962.
JD464951 - Sequence 445975 from Patent EP1572962.
JD363510 - Sequence 344534 from Patent EP1572962.
JD199193 - Sequence 180217 from Patent EP1572962.
JD413957 - Sequence 394981 from Patent EP1572962.
JD510573 - Sequence 491597 from Patent EP1572962.

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

Protein Q8NDV7 (Reactome details) participates in the following event(s):

R-HSA-5578965 TNRC6A binds AGO2:miRNA
R-HSA-426489 RISC binds inexactly matching target RNAs
R-HSA-426522 Nonendonucleolytic RISC binds exactly matching target RNAs
R-HSA-3209151 miR-24 binds p16-INK4a and p14-ARF mRNAs
R-HSA-8935766 miR-378 binds RUNX1 mRNA
R-HSA-8937134 miR-27a binds RUNX1 mRNA
R-HSA-8938440 miR-17 binds RUNX1 mRNA
R-HSA-8938487 miR-20a binds RUNX1 mRNA
R-HSA-8938507 miR-106a binds RUNX1 mRNA
R-HSA-8944650 miR-214 microRNA binds PTEN mRNA
R-HSA-8944706 miR-21 nonendonucleolytic RISC binds PTEN mRNA
R-HSA-1606561 MIR449 microRNAs bind 3'UTR of NOTCH1 mRNA
R-HSA-1606682 MIR34 microRNAs bind 3'UTR of NOTCH1 mRNA
R-HSA-1912367 MIR34 microRNAs bind 3'UTR of NOTCH2 mRNA
R-HSA-1912366 MIR206 microRNA binds 3'UTR of NOTCH3 mRNA
R-HSA-1912363 MIR200B/C microRNAs bind NOTCH1 mRNA
R-HSA-1912368 MIR302A microRNA binds 3'UTR of NOTCH4 mRNA
R-HSA-1912364 MIR181C microRNA binds 3'UTR of NOTCH4 mRNA
R-HSA-1912362 MIR150 microRNA binds 3'UTR of NOTCH3 mRNA
R-HSA-2318752 miR-26A microRNAs bind PTEN mRNA
R-HSA-8935864 miR-302b binds RUNX1 mRNA
R-HSA-8935930 miR-18a binds RUNX1 mRNA
R-HSA-8936058 miR-675 binds RUNX1 mRNA
R-HSA-8944483 miR-17 microRNA binds PTEN mRNA
R-HSA-8948582 miR-17 microRNA binds VAPA mRNA
R-HSA-8948583 miR-17 microRNA binds CNOT6L mRNA
R-HSA-8939129 miR-215 binds RUNX1 mRNA
R-HSA-8948524 PTENP1 mRNA binds miR-19b RISC
R-HSA-8948569 miR-19b microRNA binds PTEN mRNA
R-HSA-8948612 miR-19b microRNA binds CNOT6L mRNA
R-HSA-8944538 miR-22 microRNA binds PTEN mRNA
R-HSA-8944569 miR-25 microRNA binds PTEN mRNA
R-HSA-8944599 miR-93 microRNA binds PTEN mRNA
R-HSA-8944632 miR-106 microRNAs bind PTEN mRNA
R-HSA-8948641 miR-106 microRNAs bind VAPA mRNA
R-HSA-8948651 miR-106a,(miR106b) microRNA binds CNOT6L mRNA
R-HSA-8944684 miR-205 microRNA binds PTEN mRNA
R-HSA-8945709 miR-20 microRNAs bind PTEN mRNA
R-HSA-8948536 PTENP1 mRNA binds miR-20 RISC
R-HSA-8948621 miR-20 microRNAs bind VAPA mRNA
R-HSA-8948623 miR-20 microRNAs bind CNOT6L mRNA
R-HSA-8944522 miR-19a microRNA binds PTEN mRNA
R-HSA-8948594 miR-19a microRNA binds VAPA mRNA
R-HSA-8948602 miR-19a microRNA binds CNOT6L mRNA
R-HSA-9011958 miR-26A and B bind to the 3'UTR of the GREB1 mRNA
R-HSA-9012203 miR-26A and B bind to the 3'UTR of the CHD11 mRNA
R-HSA-9012208 miR-26A and B bind to the 3'UTR of the KPNA2 mRNA
R-HSA-5578749 Transcriptional regulation by small RNAs
R-HSA-426496 Post-transcriptional silencing by small RNAs
R-HSA-211000 Gene Silencing by RNA
R-HSA-2559580 Oxidative Stress Induced Senescence
R-HSA-2559585 Oncogene Induced Senescence
R-HSA-8934593 Regulation of RUNX1 Expression and Activity
R-HSA-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-HSA-8943723 Regulation of PTEN mRNA translation
R-HSA-74160 Gene expression (Transcription)
R-HSA-1912408 Pre-NOTCH Transcription and Translation
R-HSA-5628897 TP53 Regulates Metabolic Genes
R-HSA-2559583 Cellular Senescence
R-HSA-4086398 Ca2+ pathway
R-HSA-5687128 MAPK6/MAPK4 signaling
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-8948700 Competing endogenous RNAs (ceRNAs) regulate PTEN translation
R-HSA-6807070 PTEN Regulation
R-HSA-1912422 Pre-NOTCH Expression and Processing
R-HSA-9018519 Estrogen-dependent gene expression
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-2262752 Cellular responses to stress
R-HSA-3858494 Beta-catenin independent WNT signaling
R-HSA-5683057 MAPK family signaling cascades
R-HSA-212436 Generic Transcription Pathway
R-HSA-1257604 PIP3 activates AKT signaling
R-HSA-157118 Signaling by NOTCH
R-HSA-8939211 ESR-mediated signaling
R-HSA-8953897 Cellular responses to external stimuli
R-HSA-195721 Signaling by WNT
R-HSA-162582 Signal Transduction
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-9006925 Intracellular signaling by second messengers
R-HSA-9006931 Signaling by Nuclear Receptors

-  Other Names for This Gene
  Alternate Gene Symbols: C9JAR8, CAGH26, ENST00000395799.1, ENST00000395799.2, ENST00000395799.3, ENST00000395799.4, ENST00000395799.5, ENST00000395799.6, ENST00000395799.7, KIAA1460, NM_014494, O15408, Q658L5, Q6NVB5, Q8NDV7, Q8NEZ0, Q8TBT8, Q8TCR0, Q9NV59, Q9P268, TNR6A_HUMAN, TNRC6, uc318xsq.1, uc318xsq.2
UCSC ID: ENST00000395799.8_9
RefSeq Accession: NM_014494.4
Protein: Q8NDV7 (aka TNR6A_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.