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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:TET2-LARP7 (FusionGDB2 ID:90172)

Fusion Gene Summary for TET2-LARP7

check button Fusion gene summary
Fusion gene informationFusion gene name: TET2-LARP7
Fusion gene ID: 90172
HgeneTgene
Gene symbol

TET2

LARP7

Gene ID

54790

51574

Gene nametet methylcytosine dioxygenase 2La ribonucleoprotein 7, transcriptional regulator
SynonymsKIAA1546|MDSALAZS|HDCMA18P|PIP7S
Cytomap

4q24

4q25

Type of geneprotein-codingprotein-coding
Descriptionmethylcytosine dioxygenase TET2probable methylcytosine dioxygenase TET2tet oncogene family member 2la-related protein 7La ribonucleoprotein domain family member 7P-TEFb-interaction protein for 7SK stability
Modification date2020032220200313
UniProtAcc.

Q4G0J3

Ensembl transtripts involved in fusion geneENST00000504042, ENST00000380013, 
ENST00000394764, ENST00000413648, 
ENST00000513237, ENST00000540549, 
ENST00000545826, ENST00000305737, 
ENST00000324052, ENST00000344442, 
ENST00000509061, ENST00000503898, 
Fusion gene scores* DoF score11 X 6 X 11=7266 X 6 X 3=108
# samples 156
** MAII scorelog2(15/726*10)=-2.27500704749987
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/108*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TET2 [Title/Abstract] AND LARP7 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTET2(106068136)-LARP7(113565824), # samples:2
Anticipated loss of major functional domain due to fusion event.
* 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
HgeneTET2

GO:0006211

5-methylcytosine catabolic process

24315485

HgeneTET2

GO:0006493

protein O-linked glycosylation

23222540

HgeneTET2

GO:0080111

DNA demethylation

24315485


check buttonFusion gene breakpoints across TET2 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across LARP7 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChimerDB4PRADTCGA-KK-A8I5-01ATET2chr4

106068136

-LARP7chr4

113565824

+
ChimerDB4PRADTCGA-KK-A8I5TET2chr4

106068136

+LARP7chr4

113565824

+


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Fusion Gene ORF analysis for TET2-LARP7

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-5UTRENST00000504042ENST00000324052TET2chr4

106068136

+LARP7chr4

113565824

+
3UTR-5UTRENST00000504042ENST00000344442TET2chr4

106068136

+LARP7chr4

113565824

+
3UTR-5UTRENST00000504042ENST00000509061TET2chr4

106068136

+LARP7chr4

113565824

+
3UTR-intronENST00000504042ENST00000503898TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-5UTRENST00000380013ENST00000324052TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-5UTRENST00000380013ENST00000344442TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-5UTRENST00000380013ENST00000509061TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-5UTRENST00000394764ENST00000324052TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-5UTRENST00000394764ENST00000344442TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-5UTRENST00000394764ENST00000509061TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-5UTRENST00000413648ENST00000324052TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-5UTRENST00000413648ENST00000344442TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-5UTRENST00000413648ENST00000509061TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-5UTRENST00000513237ENST00000324052TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-5UTRENST00000513237ENST00000344442TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-5UTRENST00000513237ENST00000509061TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-5UTRENST00000540549ENST00000324052TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-5UTRENST00000540549ENST00000344442TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-5UTRENST00000540549ENST00000509061TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-5UTRENST00000545826ENST00000324052TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-5UTRENST00000545826ENST00000344442TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-5UTRENST00000545826ENST00000509061TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-intronENST00000380013ENST00000503898TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-intronENST00000394764ENST00000503898TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-intronENST00000413648ENST00000503898TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-intronENST00000513237ENST00000503898TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-intronENST00000540549ENST00000503898TET2chr4

106068136

+LARP7chr4

113565824

+
5UTR-intronENST00000545826ENST00000503898TET2chr4

106068136

+LARP7chr4

113565824

+
intron-5UTRENST00000305737ENST00000324052TET2chr4

106068136

+LARP7chr4

113565824

+
intron-5UTRENST00000305737ENST00000344442TET2chr4

106068136

+LARP7chr4

113565824

+
intron-5UTRENST00000305737ENST00000509061TET2chr4

106068136

+LARP7chr4

113565824

+
intron-intronENST00000305737ENST00000503898TET2chr4

106068136

+LARP7chr4

113565824

+

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)

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

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Fusion Genomic Features for TET2-LARP7


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)
TET2chr4106068136+LARP7chr4113565823+0.0003544830.9996455
TET2chr4106068136+LARP7chr4113565823+0.0003544830.9996455

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.

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 TET2-LARP7


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/:106068136/:113565824)
- 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
.LARP7

Q4G0J3

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}.FUNCTION: RNA-binding protein that specifically binds distinct small nuclear RNA (snRNAs) and regulates their processing and function (PubMed:18249148, PubMed:32017898). Specifically binds the 7SK snRNA (7SK RNA) and acts as a core component of the 7SK ribonucleoprotein (RNP) complex, thereby acting as a negative regulator of transcription elongation by RNA polymerase II (PubMed:18249148, PubMed:18483487). The 7SK RNP complex sequesters the positive transcription elongation factor b (P-TEFb) in a large inactive 7SK RNP complex preventing RNA polymerase II phosphorylation and subsequent transcriptional elongation (PubMed:18249148, PubMed:18483487). The 7SK RNP complex also promotes snRNA gene transcription by RNA polymerase II via interaction with the little elongation complex (LEC) (PubMed:28254838). LARP7 specifically binds to the highly conserved 3'-terminal U-rich stretch of 7SK RNA; on stimulation, remains associated with 7SK RNA, whereas P-TEFb is released from the complex (PubMed:18483487, PubMed:18281698). LARP7 also acts as a regulator of mRNA splicing fidelity by promoting U6 snRNA processing (PubMed:32017898). Specifically binds U6 snRNAs and associates with a subset of box C/D RNP complexes: promotes U6 snRNA 2'-O-methylation by facilitating U6 snRNA loading into box C/D RNP complexes (PubMed:32017898). U6 snRNA 2'-O-methylation is required for mRNA splicing fidelity (PubMed:32017898). Binds U6 snRNAs with a 5'-CAGGG-3' sequence motif (PubMed:32017898). U6 snRNA processing is required for spermatogenesis (By similarity). {ECO:0000250|UniProtKB:Q05CL8, ECO:0000269|PubMed:18249148, ECO:0000269|PubMed:18281698, ECO:0000269|PubMed:18483487, ECO:0000269|PubMed:28254838, ECO:0000269|PubMed:32017898}.

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


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Fusion Gene Sequence for TET2-LARP7


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.

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Fusion Gene PPI Analysis for TET2-LARP7


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


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 TET2-LARP7


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 TET2-LARP7


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