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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:TNRC6A-METTL9 (FusionGDB2 ID:92854)

Fusion Gene Summary for TNRC6A-METTL9

check button Fusion gene summary
Fusion gene informationFusion gene name: TNRC6A-METTL9
Fusion gene ID: 92854
HgeneTgene
Gene symbol

TNRC6A

METTL9

Gene ID

27327

51108

Gene nametrinucleotide repeat containing adaptor 6Amethyltransferase like 9
SynonymsCAGH26|FAME6|GW1|GW182|TNRC6CGI-81|DREV|DREV1|PAP1
Cytomap

16p12.1

16p12.2

Type of geneprotein-codingprotein-coding
Descriptiontrinucleotide repeat-containing gene 6A proteinCAG repeat protein 26CTD-2540M10.1EDIEEMSY interactor proteinGW182 autoantigenglycine-tryptophan protein of 182 kDatrinucleotide repeat containing 6Amethyltransferase-like protein 9CTB-31N19.3DORA reverse strand protein 1p53 activated protein 1
Modification date2020031320200313
UniProtAcc.

Q9H1A3

Ensembl transtripts involved in fusion geneENST00000562829, ENST00000315183, 
ENST00000395799, ENST00000432286, 
ENST00000358154, ENST00000396014, 
ENST00000563026, 
Fusion gene scores* DoF score10 X 10 X 6=6006 X 5 X 6=180
# samples 126
** MAII scorelog2(12/600*10)=-2.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/180*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TNRC6A [Title/Abstract] AND METTL9 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTNRC6A(24741167)-METTL9(21666548), # samples:1
Anticipated loss of major functional domain due to fusion event.TNRC6A-METTL9 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneTNRC6A

GO:0035278

miRNA mediated inhibition of translation

17671087


check buttonFusion gene breakpoints across TNRC6A (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across METTL9 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4LUSCTCGA-O2-A52S-01ATNRC6Achr16

24741167

+METTL9chr16

21666548

+


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Fusion Gene ORF analysis for TNRC6A-METTL9

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
3UTR-3CDSENST00000562829ENST00000358154TNRC6Achr16

24741167

+METTL9chr16

21666548

+
3UTR-3CDSENST00000562829ENST00000396014TNRC6Achr16

24741167

+METTL9chr16

21666548

+
3UTR-intronENST00000562829ENST00000563026TNRC6Achr16

24741167

+METTL9chr16

21666548

+
5CDS-intronENST00000315183ENST00000563026TNRC6Achr16

24741167

+METTL9chr16

21666548

+
5CDS-intronENST00000395799ENST00000563026TNRC6Achr16

24741167

+METTL9chr16

21666548

+
Frame-shiftENST00000315183ENST00000396014TNRC6Achr16

24741167

+METTL9chr16

21666548

+
Frame-shiftENST00000395799ENST00000396014TNRC6Achr16

24741167

+METTL9chr16

21666548

+
In-frameENST00000315183ENST00000358154TNRC6Achr16

24741167

+METTL9chr16

21666548

+
In-frameENST00000395799ENST00000358154TNRC6Achr16

24741167

+METTL9chr16

21666548

+
intron-3CDSENST00000432286ENST00000358154TNRC6Achr16

24741167

+METTL9chr16

21666548

+
intron-3CDSENST00000432286ENST00000396014TNRC6Achr16

24741167

+METTL9chr16

21666548

+
intron-intronENST00000432286ENST00000563026TNRC6Achr16

24741167

+METTL9chr16

21666548

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000315183TNRC6Achr1624741167+ENST00000358154METTL9chr1621666548+239915223048785
ENST00000395799TNRC6Achr1624741167+ENST00000358154METTL9chr1621666548+238113421246985

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000315183ENST00000358154TNRC6Achr1624741167+METTL9chr1621666548+0.702020170.29797986
ENST00000395799ENST00000358154TNRC6Achr1624741167+METTL9chr1621666548+0.801949260.19805075

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Fusion Genomic Features for TNRC6A-METTL9


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
TNRC6Achr1624741167+METTL9chr1621666550+1.47E-060.99999857
TNRC6Achr1624741167+METTL9chr1621666550+1.47E-060.99999857

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.
genomic feature

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for TNRC6A-METTL9


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr16:24741167/chr16:21666548)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.METTL9

Q9H1A3

FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page


* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneTNRC6Achr16:24741167chr16:21666548ENST00000315183+1247_5411914.0Coiled coilOntology_term=ECO:0000255
HgeneTNRC6Achr16:24741167chr16:21666548ENST00000395799+1257_5411963.0Coiled coilOntology_term=ECO:0000255
HgeneTNRC6Achr16:24741167chr16:21666548ENST00000315183+124192_36511914.0Compositional biasNote=Ser-rich
HgeneTNRC6Achr16:24741167chr16:21666548ENST00000315183+12493_12711914.0Compositional biasNote=Gln-rich
HgeneTNRC6Achr16:24741167chr16:21666548ENST00000395799+125192_36511963.0Compositional biasNote=Ser-rich
HgeneTNRC6Achr16:24741167chr16:21666548ENST00000395799+12593_12711963.0Compositional biasNote=Gln-rich
HgeneTNRC6Achr16:24741167chr16:21666548ENST00000315183+1241781_185311914.0DomainNote=RRM
HgeneTNRC6Achr16:24741167chr16:21666548ENST00000395799+1251781_185311963.0DomainNote=RRM
HgeneTNRC6Achr16:24741167chr16:21666548ENST00000315183+1241604_162211914.0RegionNote=PABPC1-interacting motif-2 (PAM2)
HgeneTNRC6Achr16:24741167chr16:21666548ENST00000395799+1251604_162211963.0RegionNote=PABPC1-interacting motif-2 (PAM2)
TgeneMETTL9chr16:24741167chr16:21666548ENST000003581543544_47250319.0Compositional biasNote=Poly-Ala
TgeneMETTL9chr16:24741167chr16:21666548ENST000003960143544_47250318.0Compositional biasNote=Poly-Ala


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Fusion Gene Sequence for TNRC6A-METTL9


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>92854_92854_1_TNRC6A-METTL9_TNRC6A_chr16_24741167_ENST00000315183_METTL9_chr16_21666548_ENST00000358154_length(transcript)=2399nt_BP=152nt
GGCGGCGGCGGCGGCGGCGGCGGCAGCGGGTCGGTGTAGAAAATGGCGCTGGTGCAGCGGCTCGGGCCTCTCCCCGCGGCGCTGCGGAGG
GCTTGAGGCTCGCGAGCCTCCTTCGCCGCGCCCCACTTGCTCGTGCACTTTACACACATGAGTAGGTGGCAAGTGGGAGAAACCATCAGA
AATTTTGGAAATCAAAGGACAGAACTGGGAAGAACAAGTGAATAGTCTGCCTGAAGTTTTCAGAAAAGCTGGTTTTGTTATCGAAGCTTT
CACCAGACTACCATACCTGTGTGAAGGCGACATGTATAATGACTACTACGTTCTGGATGACGCTGTCTTTGTTCTCAAACCAGTATAAAC
ACGTGGAGGTCGAAGTCTTCAGAGTCCGCACCCTCCGGGATGTGCCCTTGGAAGAGGGTCTGTGTTCACAATTACGTGAAGGGAGGACCC
TTGGGGACCGCCATTCTAAATATCATGTAGGAATTTAAAAAGCCAAAATACTAATTATTTCTTTGTAGTGTGTAAAGGAATGTTTTTAAA
AGACAAAAACCCAACTCTTTGTGGATTTTTATCAACTCTTTACTCAGAGCCACTCTCCAATGCAGGTCACACTCCAATTATGATGGAAGA
TATTTTTTATACTTAATTGCAGTAGGGACTCATTCCCAGACAAAGCAATAGTCACGACTTCATGGAACCAATCAATGGATTGTTTTTTGA
AGACTGGCAATAAAGCTGTCCATTCAATTCCAAATACTGGTTTTAAGGTATAGCCACTGATATTCTTTCATGTTTAGAAATTCTTTCTGT
TATTATTCAAGAAAATGTTTTTAATCATGCTAATAAACTTTTTTGGAGATGACTTTGGCATCATGTTTGAATTCATATAAAGCTCCCCTA
GCATTTTTTATTGGTTTGGCTTCAGGAGTACCCAAATAGTAGCATTATGAGAATGACGCAGACAATTTGAATAGGGGGGAAGGAAGGCTT
CAGACTTGGGGGAAGGGGAGATTATTGCAAATTGCAGTGAACACTGAGTCAGTAAAAAAAAAAAACAGAAACAAAAACCCAGCCTCATTC
AGATACAGAACTTCAGGGACCCCTCCCCCCACCCCCCCAGTTAATGCTGCTGTGAAAAATGCAAAATAACCTGGTTCTGACTTTGTGATC
ACTCATGTCCCATACACTGAACTTTGTTTTTTTCTGGACAATCTCAGGTTCTCAGAATTGAAACATTCAGTTTTGTCTACTGACAAAATG
CAACTAAAAATGTTTTAATTCAACTTCTTACTCTACACTTATATACCTCTCTCCCAGAGCTTGGCTCTTCCCTGAAATCCTTAAAGGAGT
TTATTATTTGCCAAGAATATGGTTTGATGAAGACCGTGTCAGACTCATGCATTCTGGAATCCGTGAGTGCCTCCAACCATAAACCCAGAA
ATGCTGCCATAGAGGAACCCATTAGCAAGATCAATAACCATCGTGGATATTCCAAAGAGCAGAGCATTTAACCCAGAATCTGAAATCTCA
GTAATAACAGAAATGTCAATATGAGATTGTGGTTATTAACAATATGTTATCCTCACTACTTTATTTCTTTTTTCATCCAGGTGTTTCATT
AAGTATTCTCATTTATATGCTCATAGAAGTCATCAGATCAACACATTCACTCCAACACCTGGGTATAAAGGCGAATTAAAACCTGAAGAA
TTACTTTATTATTCATTAAGAACTGCATTCCCACATCCTCACACCAATATCTTCCACTGTTACTGTGCAGTCATAATAAGAGTTGGGTTA
TGTGATTTATGCAAAATTGTTATTGGTGTGTTCTAATGATTTTTTTCCAGGAATTCAAGTAAGTGAAGTACAAATACTTAGCACCATAGA
TTGTAAAAATAGAAAGAGGAAATGAGAAAACTTAATGTCGTTCTTGTACAGTTGAGTTTTGCTTCTTTATAAACTGTCTGTTAAAATCAG
GGGTTGCTGTTAGACTGTCAAGCAGAAGTGATGGATGTTCAAGGAGGCAGGTTGCCCCAAAGTGTTTTCTAACTTTCAAGTAGAGAACTT
TATGCTCTAATAAGAAAAATACAACTCATTCTTAACCACCCCCCCAAAACAGAGAAAACACATACATTTATGCATTTTAAAGATAAAAAG
TAGTTTCTCAAAAAAATCTGAAGTTCTCTGAAAACCAGCTTATTAAAAGTGCTGTTTTGTGGTGAAAATTGAAACCAAATCCACTCACAT
TTCCTATCGGGTCTTGAAATTCTTGGTGGTGTGTCACCATTCCACTAGATGGCAGTGTTGCTTACTGAGTGTCAATGGCTTTTTTCCCCG

>92854_92854_1_TNRC6A-METTL9_TNRC6A_chr16_24741167_ENST00000315183_METTL9_chr16_21666548_ENST00000358154_length(amino acids)=85AA_BP=

--------------------------------------------------------------
>92854_92854_2_TNRC6A-METTL9_TNRC6A_chr16_24741167_ENST00000395799_METTL9_chr16_21666548_ENST00000358154_length(transcript)=2381nt_BP=134nt
GGCGGCAGCGGGTCGGTGTAGAAAATGGCGCTGGTGCAGCGGCTCGGGCCTCTCCCCGCGGCGCTGCGGAGGGCTTGAGGCTCGCGAGCC
TCCTTCGCCGCGCCCCACTTGCTCGTGCACTTTACACACATGAGTAGGTGGCAAGTGGGAGAAACCATCAGAAATTTTGGAAATCAAAGG
ACAGAACTGGGAAGAACAAGTGAATAGTCTGCCTGAAGTTTTCAGAAAAGCTGGTTTTGTTATCGAAGCTTTCACCAGACTACCATACCT
GTGTGAAGGCGACATGTATAATGACTACTACGTTCTGGATGACGCTGTCTTTGTTCTCAAACCAGTATAAACACGTGGAGGTCGAAGTCT
TCAGAGTCCGCACCCTCCGGGATGTGCCCTTGGAAGAGGGTCTGTGTTCACAATTACGTGAAGGGAGGACCCTTGGGGACCGCCATTCTA
AATATCATGTAGGAATTTAAAAAGCCAAAATACTAATTATTTCTTTGTAGTGTGTAAAGGAATGTTTTTAAAAGACAAAAACCCAACTCT
TTGTGGATTTTTATCAACTCTTTACTCAGAGCCACTCTCCAATGCAGGTCACACTCCAATTATGATGGAAGATATTTTTTATACTTAATT
GCAGTAGGGACTCATTCCCAGACAAAGCAATAGTCACGACTTCATGGAACCAATCAATGGATTGTTTTTTGAAGACTGGCAATAAAGCTG
TCCATTCAATTCCAAATACTGGTTTTAAGGTATAGCCACTGATATTCTTTCATGTTTAGAAATTCTTTCTGTTATTATTCAAGAAAATGT
TTTTAATCATGCTAATAAACTTTTTTGGAGATGACTTTGGCATCATGTTTGAATTCATATAAAGCTCCCCTAGCATTTTTTATTGGTTTG
GCTTCAGGAGTACCCAAATAGTAGCATTATGAGAATGACGCAGACAATTTGAATAGGGGGGAAGGAAGGCTTCAGACTTGGGGGAAGGGG
AGATTATTGCAAATTGCAGTGAACACTGAGTCAGTAAAAAAAAAAAACAGAAACAAAAACCCAGCCTCATTCAGATACAGAACTTCAGGG
ACCCCTCCCCCCACCCCCCCAGTTAATGCTGCTGTGAAAAATGCAAAATAACCTGGTTCTGACTTTGTGATCACTCATGTCCCATACACT
GAACTTTGTTTTTTTCTGGACAATCTCAGGTTCTCAGAATTGAAACATTCAGTTTTGTCTACTGACAAAATGCAACTAAAAATGTTTTAA
TTCAACTTCTTACTCTACACTTATATACCTCTCTCCCAGAGCTTGGCTCTTCCCTGAAATCCTTAAAGGAGTTTATTATTTGCCAAGAAT
ATGGTTTGATGAAGACCGTGTCAGACTCATGCATTCTGGAATCCGTGAGTGCCTCCAACCATAAACCCAGAAATGCTGCCATAGAGGAAC
CCATTAGCAAGATCAATAACCATCGTGGATATTCCAAAGAGCAGAGCATTTAACCCAGAATCTGAAATCTCAGTAATAACAGAAATGTCA
ATATGAGATTGTGGTTATTAACAATATGTTATCCTCACTACTTTATTTCTTTTTTCATCCAGGTGTTTCATTAAGTATTCTCATTTATAT
GCTCATAGAAGTCATCAGATCAACACATTCACTCCAACACCTGGGTATAAAGGCGAATTAAAACCTGAAGAATTACTTTATTATTCATTA
AGAACTGCATTCCCACATCCTCACACCAATATCTTCCACTGTTACTGTGCAGTCATAATAAGAGTTGGGTTATGTGATTTATGCAAAATT
GTTATTGGTGTGTTCTAATGATTTTTTTCCAGGAATTCAAGTAAGTGAAGTACAAATACTTAGCACCATAGATTGTAAAAATAGAAAGAG
GAAATGAGAAAACTTAATGTCGTTCTTGTACAGTTGAGTTTTGCTTCTTTATAAACTGTCTGTTAAAATCAGGGGTTGCTGTTAGACTGT
CAAGCAGAAGTGATGGATGTTCAAGGAGGCAGGTTGCCCCAAAGTGTTTTCTAACTTTCAAGTAGAGAACTTTATGCTCTAATAAGAAAA
ATACAACTCATTCTTAACCACCCCCCCAAAACAGAGAAAACACATACATTTATGCATTTTAAAGATAAAAAGTAGTTTCTCAAAAAAATC
TGAAGTTCTCTGAAAACCAGCTTATTAAAAGTGCTGTTTTGTGGTGAAAATTGAAACCAAATCCACTCACATTTCCTATCGGGTCTTGAA
ATTCTTGGTGGTGTGTCACCATTCCACTAGATGGCAGTGTTGCTTACTGAGTGTCAATGGCTTTTTTCCCCGTAAATGGAATCATGTTTT

>92854_92854_2_TNRC6A-METTL9_TNRC6A_chr16_24741167_ENST00000395799_METTL9_chr16_21666548_ENST00000358154_length(amino acids)=85AA_BP=

--------------------------------------------------------------

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Fusion Gene PPI Analysis for TNRC6A-METTL9


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with
HgeneTNRC6Achr16:24741167chr16:21666548ENST00000315183+1241_9321.66666666666666671914.0argonaute family proteins
HgeneTNRC6Achr16:24741167chr16:21666548ENST00000395799+1251_9321.66666666666666671963.0argonaute family proteins


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for TNRC6A-METTL9


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for TNRC6A-METTL9


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource