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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:COL1A2-TCF4 (FusionGDB2 ID:HG1278TG6925)

Fusion Gene Summary for COL1A2-TCF4

check button Fusion gene summary
Fusion gene informationFusion gene name: COL1A2-TCF4
Fusion gene ID: hg1278tg6925
HgeneTgene
Gene symbol

COL1A2

TCF4

Gene ID

1278

6925

Gene namecollagen type I alpha 2 chaintranscription factor 4
SynonymsEDSARTH2|EDSCV|OI4E2-2|FECD3|ITF-2|ITF2|PTHS|SEF-2|SEF2|SEF2-1|SEF2-1A|SEF2-1B|SEF2-1D|TCF-4|bHLHb19
Cytomap('COL1A2')('TCF4')

7q21.3

18q21.2

Type of geneprotein-codingprotein-coding
Descriptioncollagen alpha-2(I) chainalpha 2 type I procollagenalpha 2(I) procollagenalpha 2(I)-collagenalpha-2 type I collagencollagen I, alpha-2 polypeptidecollagen of skin, tendon and bone, alpha-2 chaincollagen, type I, alpha 2epididymis secretory sperm btranscription factor 4SL3-3 enhancer factor 2class B basic helix-loop-helix protein 19immunoglobulin transcription factor 2
Modification date2020032220200329
UniProtAcc

P08123

.
Ensembl transtripts involved in fusion geneENST00000297268, 
Fusion gene scores* DoF score47 X 49 X 10=2303011 X 10 X 4=440
# samples 5811
** MAII scorelog2(58/23030*10)=-5.31131770066527
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/440*10)=-2
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: COL1A2 [Title/Abstract] AND TCF4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCOL1A2(94060127)-TCF4(52894388), # 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
HgeneCOL1A2

GO:0007179

transforming growth factor beta receptor signaling pathway

17217948

HgeneCOL1A2

GO:0007266

Rho protein signal transduction

17217948

TgeneTCF4

GO:0045893

positive regulation of transcription, DNA-templated

2105528|12651860



check button Fusion gene information
* 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


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Fusion Gene ORF analysis for COL1A2-TCF4

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

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 COL1A2-TCF4


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)


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Fusion Protein Features for COL1A2-TCF4


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/:94060127/:52894388)
- 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
COL1A2

P08123

.
FUNCTION: Type I collagen is a member of group I collagen (fibrillar forming collagen).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


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Fusion Gene Sequence for COL1A2-TCF4


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 COL1A2-TCF4


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 COL1A2-TCF4


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 COL1A2-TCF4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCOL1A2C0268358Osteogenesis imperfecta, dominant perinatal lethal16CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCOL1A2C0268362Osteogenesis imperfecta type III (disorder)16CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCOL1A2C0268363Osteogenesis imperfecta type IV (disorder)11GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCOL1A2C0023931Lobstein Disease6ORPHANET;UNIPROT
HgeneCOL1A2C1857034Ehlers-Danlos syndrome, cardiac valvular form3CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneCOL1A2C0268345EHLERS-DANLOS SYNDROME, ARTHROCHALASIA TYPE2ORPHANET
HgeneCOL1A2C0000786Spontaneous abortion1CTD_human
HgeneCOL1A2C0000822Abortion, Tubal1CTD_human
HgeneCOL1A2C0016059Fibrosis1CTD_human
HgeneCOL1A2C0018824Heart valve disease1CTD_human
HgeneCOL1A2C0023890Liver Cirrhosis1CTD_human
HgeneCOL1A2C0023893Liver Cirrhosis, Experimental1CTD_human
HgeneCOL1A2C0029172Oral Submucous Fibrosis1CTD_human
HgeneCOL1A2C0029408Degenerative polyarthritis1CTD_human
HgeneCOL1A2C0036421Systemic Scleroderma1CTD_human
HgeneCOL1A2C0086743Osteoarthrosis Deformans1CTD_human
HgeneCOL1A2C0239946Fibrosis, Liver1CTD_human
HgeneCOL1A2C1623038Cirrhosis1CTD_human
HgeneCOL1A2C3830362Early Pregnancy Loss1CTD_human
HgeneCOL1A2C4303789Ehlers-Danlos syndrome cardiac valvular type1GENOMICS_ENGLAND
HgeneCOL1A2C4551623EHLERS-DANLOS SYNDROME, ARTHROCHALASIA TYPE, 11GENOMICS_ENGLAND
HgeneCOL1A2C4552766Miscarriage1CTD_human
TgeneC1970431PITT-HOPKINS SYNDROME14CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0005586Bipolar Disorder5PSYGENET
TgeneC0036341Schizophrenia4PSYGENET
TgeneC0016781Fuchs Endothelial Dystrophy1ORPHANET
TgeneC0018799Heart Diseases1CTD_human
TgeneC0022333Jacksonian Seizure1CTD_human
TgeneC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneC0023903Liver neoplasms1CTD_human
TgeneC0025958Microcephaly1CTD_human
TgeneC0033975Psychotic Disorders1PSYGENET
TgeneC0036572Seizures1CTD_human
TgeneC0149958Complex partial seizures1CTD_human
TgeneC0234533Generalized seizures1CTD_human
TgeneC0234535Clonic Seizures1CTD_human
TgeneC0270824Visual seizure1CTD_human
TgeneC0270844Tonic Seizures1CTD_human
TgeneC0270846Epileptic drop attack1CTD_human
TgeneC0345904Malignant neoplasm of liver1CTD_human
TgeneC0349204Nonorganic psychosis1PSYGENET
TgeneC0376634Craniofacial Abnormalities1CTD_human
TgeneC0422850Seizures, Somatosensory1CTD_human
TgeneC0422852Seizures, Auditory1CTD_human
TgeneC0422853Olfactory seizure1CTD_human
TgeneC0422854Gustatory seizure1CTD_human
TgeneC0422855Vertiginous seizure1CTD_human
TgeneC0494475Tonic - clonic seizures1CTD_human
TgeneC0566602Primary sclerosing cholangitis1ORPHANET
TgeneC0751056Non-epileptic convulsion1CTD_human
TgeneC0751110Single Seizure1CTD_human
TgeneC0751123Atonic Absence Seizures1CTD_human
TgeneC0751494Convulsive Seizures1CTD_human
TgeneC0751495Seizures, Focal1CTD_human
TgeneC0751496Seizures, Sensory1CTD_human
TgeneC1456784Paranoia1PSYGENET
TgeneC1535926Neurodevelopmental Disorders1CTD_human
TgeneC1956147Microlissencephaly1CTD_human
TgeneC2750451CORNEAL DYSTROPHY, FUCHS ENDOTHELIAL, 31CTD_human;GENOMICS_ENGLAND
TgeneC2931456Prostate cancer, familial1CTD_human
TgeneC3495874Nonepileptic Seizures1CTD_human
TgeneC3853041Severe Congenital Microcephaly1CTD_human
TgeneC4048158Convulsions1CTD_human
TgeneC4316903Absence Seizures1CTD_human
TgeneC4317109Epileptic Seizures1CTD_human
TgeneC4317123Myoclonic Seizures1CTD_human
TgeneC4505436Generalized Absence Seizures1CTD_human
TgeneC4721453Peripheral Nervous System Diseases1CTD_human
TgeneC4722327PROSTATE CANCER, HEREDITARY, 11CTD_human