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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:TNNT2-CPSF7 (FusionGDB2 ID:92136)

Fusion Gene Summary for TNNT2-CPSF7

check button Fusion gene summary
Fusion gene informationFusion gene name: TNNT2-CPSF7
Fusion gene ID: 92136
HgeneTgene
Gene symbol

TNNT2

CPSF7

Gene ID

7139

79869

Gene nametroponin T2, cardiac typecleavage and polyadenylation specific factor 7
SynonymsCMD1D|CMH2|CMPD2|LVNC6|RCM3|TnTC|cTnTCFIm59
Cytomap

1q32.1

11q12.2

Type of geneprotein-codingprotein-coding
Descriptiontroponin T, cardiac musclecardiomyopathy, dilated 1D (autosomal dominant)cardiomyopathy, hypertrophic 2troponin T type 2 (cardiac)truncated cardiac troponin Tcleavage and polyadenylation specificity factor subunit 7CPSF 59 kDa subunitcleavage and polyadenylation specificity factor 59 kDa subunitcleavage factor Im complex 59 kDa subunitpre-mRNA cleavage factor I, 59 kDa subunitpre-mRNA cleavage factor Im 5
Modification date2020032220200313
UniProtAcc.

Q8N684

Ensembl transtripts involved in fusion geneENST00000460780, ENST00000367318, 
ENST00000367322, ENST00000367315, 
ENST00000236918, ENST00000360372, 
ENST00000367317, ENST00000458432, 
ENST00000421663, ENST00000367320, 
ENST00000509001, 		ENST00000340437, 
ENST00000394888, ENST00000439958, 
ENST00000494016, ENST00000448745, 
ENST00000541963, 
Fusion gene scores* DoF score1 X 1 X 1=19 X 8 X 5=360
# samples 110
** MAII scorelog2(1/1*10)=3.32192809488736log2(10/360*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TNNT2 [Title/Abstract] AND CPSF7 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTNNT2(201328204)-CPSF7(61183821), # samples:1
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
HgeneTNNT2

GO:0030049

muscle filament sliding

12186860|15923195

HgeneTNNT2

GO:0032780

negative regulation of ATPase activity

10850966

HgeneTNNT2

GO:0032781

positive regulation of ATPase activity

10850966|12186860

HgeneTNNT2

GO:0060048

cardiac muscle contraction

25771144

TgeneCPSF7

GO:0051262

protein tetramerization

20695905

TgeneCPSF7

GO:0051290

protein heterotetramerization

23187700

TgeneCPSF7

GO:1990120

messenger ribonucleoprotein complex assembly

29276085


check buttonFusion gene breakpoints across TNNT2 (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 CPSF7 (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
ChiTaRS5.0N/AAI015129TNNT2chr1

201328204

+CPSF7chr11

61183821

+


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Fusion Gene ORF analysis for TNNT2-CPSF7

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
intron-3CDSENST00000460780ENST00000340437TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000460780ENST00000394888TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000460780ENST00000439958TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000460780ENST00000494016TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000460780ENST00000448745TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000460780ENST00000541963TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000367318ENST00000340437TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000367318ENST00000394888TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000367318ENST00000439958TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000367318ENST00000494016TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000367318ENST00000448745TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000367318ENST00000541963TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000367322ENST00000340437TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000367322ENST00000394888TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000367322ENST00000439958TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000367322ENST00000494016TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000367322ENST00000448745TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000367322ENST00000541963TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000367315ENST00000340437TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000367315ENST00000394888TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000367315ENST00000439958TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000367315ENST00000494016TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000367315ENST00000448745TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000367315ENST00000541963TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000236918ENST00000340437TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000236918ENST00000394888TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000236918ENST00000439958TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000236918ENST00000494016TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000236918ENST00000448745TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000236918ENST00000541963TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000360372ENST00000340437TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000360372ENST00000394888TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000360372ENST00000439958TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000360372ENST00000494016TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000360372ENST00000448745TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000360372ENST00000541963TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000367317ENST00000340437TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000367317ENST00000394888TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000367317ENST00000439958TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000367317ENST00000494016TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000367317ENST00000448745TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000367317ENST00000541963TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000458432ENST00000340437TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000458432ENST00000394888TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000458432ENST00000439958TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000458432ENST00000494016TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000458432ENST00000448745TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000458432ENST00000541963TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000421663ENST00000340437TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000421663ENST00000394888TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000421663ENST00000439958TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000421663ENST00000494016TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000421663ENST00000448745TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000421663ENST00000541963TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000367320ENST00000340437TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000367320ENST00000394888TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000367320ENST00000439958TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000367320ENST00000494016TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000367320ENST00000448745TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000367320ENST00000541963TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000509001ENST00000340437TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000509001ENST00000394888TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-3CDSENST00000509001ENST00000439958TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000509001ENST00000494016TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000509001ENST00000448745TNNT2chr1

201328204

+CPSF7chr11

61183821

+
intron-intronENST00000509001ENST00000541963TNNT2chr1

201328204

+CPSF7chr11

61183821

+

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 TNNT2-CPSF7


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)

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.

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Fusion Protein Features for TNNT2-CPSF7


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.CPSF7

Q8N684

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Component of the cleavage factor Im (CFIm) complex that functions as an activator of the pre-mRNA 3'-end cleavage and polyadenylation processing required for the maturation of pre-mRNA into functional mRNAs (PubMed:8626397, PubMed:17024186, PubMed:29276085). CFIm contributes to the recruitment of multiprotein complexes on specific sequences on the pre-mRNA 3'-end, so called cleavage and polyadenylation signals (pA signals) (PubMed:8626397, PubMed:17024186). Most pre-mRNAs contain multiple pA signals, resulting in alternative cleavage and polyadenylation (APA) producing mRNAs with variable 3'-end formation (PubMed:23187700, PubMed:29276085). The CFIm complex acts as a key regulator of cleavage and polyadenylation site choice during APA through its binding to 5'-UGUA-3' elements localized in the 3'-untranslated region (UTR) for a huge number of pre-mRNAs (PubMed:20695905, PubMed:29276085). CPSF7 activates directly the mRNA 3'-processing machinery (PubMed:29276085). Binds to pA signals in RNA substrates (PubMed:8626397, PubMed:17024186). {ECO:0000269|PubMed:17024186, ECO:0000269|PubMed:20695905, ECO:0000269|PubMed:23187700, ECO:0000269|PubMed:29276085, ECO:0000269|PubMed:8626397}.

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 TNNT2-CPSF7


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 TNNT2-CPSF7


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 TNNT2-CPSF7


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 TNNT2-CPSF7


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTNNT2C1861864Cardiomyopathy, Familial Hypertrophic, 216CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneTNNT2C0007194Hypertrophic Cardiomyopathy12CLINGEN;CTD_human;GENOMICS_ENGLAND
HgeneTNNT2C1832243CARDIOMYOPATHY, DILATED, 1D (disorder)8CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneTNNT2C2676271CARDIOMYOPATHY, FAMILIAL RESTRICTIVE, 3 (disorder)3CTD_human;GENOMICS_ENGLAND
HgeneTNNT2C0007193Cardiomyopathy, Dilated2CTD_human
HgeneTNNT2C0018801Heart failure2CTD_human
HgeneTNNT2C0018802Congestive heart failure2CTD_human
HgeneTNNT2C0023212Left-Sided Heart Failure2CTD_human
HgeneTNNT2C0033141Cardiomyopathies, Primary2CTD_human
HgeneTNNT2C0036529Myocardial Diseases, Secondary2CTD_human
HgeneTNNT2C0235527Heart Failure, Right-Sided2CTD_human
HgeneTNNT2C0340427Familial dilated cardiomyopathy2ORPHANET
HgeneTNNT2C0597124Obstructive asymmetric septal hypertrophy2CTD_human
HgeneTNNT2C0700053Idiopathic hypertrophic subaortic stenosis2CTD_human
HgeneTNNT2C0878544Cardiomyopathies2CTD_human;GENOMICS_ENGLAND
HgeneTNNT2C0949658Cardiomyopathy, Hypertrophic, Familial2CTD_human
HgeneTNNT2C1449563Cardiomyopathy, Familial Idiopathic2CTD_human
HgeneTNNT2C1959583Myocardial Failure2CTD_human
HgeneTNNT2C1961112Heart Decompensation2CTD_human
HgeneTNNT2C0007222Cardiovascular Diseases1CTD_human
HgeneTNNT2C0017921Glycogen storage disease type II1CTD_human
HgeneTNNT2C0018799Heart Diseases1CTD_human
HgeneTNNT2C0018800Cardiomegaly1CTD_human
HgeneTNNT2C0024117Chronic Obstructive Airway Disease1CTD_human
HgeneTNNT2C0027540Necrosis1CTD_human
HgeneTNNT2C0035220Respiratory Distress Syndrome, Newborn1CTD_human
HgeneTNNT2C0042514Tachycardia, Ventricular1CTD_human
HgeneTNNT2C0085298Sudden Cardiac Death1CTD_human
HgeneTNNT2C0151744Myocardial Ischemia1CTD_human
HgeneTNNT2C0242698Ventricular Dysfunction, Left1CTD_human
HgeneTNNT2C0342751Generalized glycogen storage disease of infants1CTD_human
HgeneTNNT2C0348616Other restrictive cardiomyopathy1ORPHANET
HgeneTNNT2C0751172Adult Glycogen Storage Disease Type II1CTD_human
HgeneTNNT2C0751173Glycogen Storage Disease Type II, Infantile1CTD_human
HgeneTNNT2C0751174Glycogen Storage Disease Type II, Juvenile1CTD_human
HgeneTNNT2C0948089Acute Coronary Syndrome1CTD_human
HgeneTNNT2C1383860Cardiac Hypertrophy1CTD_human
HgeneTNNT2C1527303Chronic Airflow Obstruction1CTD_human
HgeneTNNT2C1720824Sudden Cardiac Arrest1CTD_human
HgeneTNNT2C1960469Left ventricular noncompaction1ORPHANET
HgeneTNNT2C4551472Hypertrophic obstructive cardiomyopathy1CTD_human