Human Gene TNRC6B (ENST00000454349.7_10) from GENCODE V47lift37
  Description: trinucleotide repeat containing adaptor 6B, transcript variant 1 (from RefSeq NM_001162501.2)
Gencode Transcript: ENST00000454349.7_10
Gencode Gene: ENSG00000100354.22_15
Transcript (Including UTRs)
   Position: hg19 chr22:40,573,929-40,731,812 Size: 157,884 Total Exon Count: 23 Strand: +
Coding Region
   Position: hg19 chr22:40,574,140-40,719,245 Size: 145,106 Coding Exon Count: 23 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:40,573,929-40,731,812)mRNA (may differ from genome)Protein (1833 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TNR6B_HUMAN
DESCRIPTION: RecName: Full=Trinucleotide repeat-containing gene 6B protein;
FUNCTION: Plays a role in RNA-mediated gene silencing by both micro-RNAs (miRNAs) and short interfering RNAs (siRNAs). Required for miRNA-dependent translational repression and 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).
SIMILARITY: Belongs to the GW182 family.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.
SEQUENCE CAUTION: Sequence=BAA83045.2; Type=Erroneous initiation;

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: TNRC6B
Diseases sorted by gene-association score: uterine fibroid (7), uterine benign neoplasm (4)

-  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: 5.10 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 136.61 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 -41.20211-0.195 Picture PostScript Text
3' UTR -3536.2012567-0.281 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
IPR009060 - UBA-like

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

SCOP Domains:
46934 - UBA-like
47943 - Retrovirus capsid protein, N-terminal core domain
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on Q9UPQ9
FrontTopSide
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    
Gene SorterGene Sorter    
 RGD    
      
      

-  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:0035278 miRNA mediated inhibition of translation
GO:0045652 regulation of megakaryocyte differentiation
GO:0060213 positive regulation of nuclear-transcribed mRNA poly(A) tail shortening
GO:1900153 positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay

Cellular Component:
GO:0000932 P-body
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  BC028626 - Homo sapiens trinucleotide repeat containing 6B, mRNA (cDNA clone MGC:33627 IMAGE:4826787), complete cds.
BX647630 - Homo sapiens mRNA; cDNA DKFZp451C057 (from clone DKFZp451C057).
AK296590 - Homo sapiens cDNA FLJ60637 complete cds, highly similar to Trinucleotide repeat-containing 6B protein.
AK294519 - Homo sapiens cDNA FLJ61234 complete cds, highly similar to Trinucleotide repeat-containing 6B protein.
AB029016 - Homo sapiens KIAA1093 mRNA for KIAA1093 protein.
JD442230 - Sequence 423254 from Patent EP1572962.
JD512333 - Sequence 493357 from Patent EP1572962.
AB384110 - Synthetic construct DNA, clone: pF1KSDA1093, Homo sapiens TNRC6B gene for trinucleotide repeat-containing 6B protein, complete cds, without stop codon, in Flexi system.
AK304087 - Homo sapiens cDNA FLJ50360 complete cds, highly similar to Mus musculus trinucleotide repeat containing 6b (Tnrc6b), transcript variant 1, mRNA.
JD052132 - Sequence 33156 from Patent EP1572962.
JD349211 - Sequence 330235 from Patent EP1572962.
JD436216 - Sequence 417240 from Patent EP1572962.
BX537577 - Homo sapiens mRNA; cDNA DKFZp686K15150 (from clone DKFZp686K15150).
BC046218 - Homo sapiens cDNA clone IMAGE:6195280, partial cds.
AL831862 - Homo sapiens mRNA; cDNA DKFZp761I2317 (from clone DKFZp761I2317).
JD421943 - Sequence 402967 from Patent EP1572962.
JD446401 - Sequence 427425 from Patent EP1572962.
JD315273 - Sequence 296297 from Patent EP1572962.
JD092528 - Sequence 73552 from Patent EP1572962.
JD306268 - Sequence 287292 from Patent EP1572962.

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

Protein Q9UPQ9 (Reactome details) participates in the following event(s):

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-426496 Post-transcriptional silencing by small RNAs
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-211000 Gene Silencing by RNA
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-74160 Gene expression (Transcription)
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: B0QY73, B0QY78, B4DGC0, ENST00000454349.1, ENST00000454349.2, ENST00000454349.3, ENST00000454349.4, ENST00000454349.5, ENST00000454349.6, KIAA1093, NM_001162501, Q5TH52, Q8TBX2, Q9UPQ9, TNR6B_HUMAN, uc320vmm.1, uc320vmm.2
UCSC ID: ENST00000454349.7_10
RefSeq Accession: NM_001162501.2
Protein: Q9UPQ9 (aka TNR6B_HUMAN or TR6B_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.