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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:STUB1-MECP2 (FusionGDB2 ID:87164)

Fusion Gene Summary for STUB1-MECP2

check button Fusion gene summary
Fusion gene informationFusion gene name: STUB1-MECP2
Fusion gene ID: 87164
HgeneTgene
Gene symbol

STUB1

MECP2

Gene ID

10273

4204

Gene nameSTIP1 homology and U-box containing protein 1methyl-CpG binding protein 2
SynonymsCHIP|HSPABP2|NY-CO-7|SCA48|SCAR16|SDCCAG7|UBOX1AUTSX3|MRX16|MRX79|MRXS13|MRXSL|PPMX|RS|RTS|RTT
Cytomap

16p13.3

Xq28

Type of geneprotein-codingprotein-coding
DescriptionE3 ubiquitin-protein ligase CHIPCLL-associated antigen KW-8RING-type E3 ubiquitin transferase CHIPSTIP1 homology and U-box containing protein 1, E3 ubiquitin protein ligaseantigen NY-CO-7carboxy terminus of Hsp70-interacting proteinheat shock proteimethyl-CpG-binding protein 2meCp-2 protein
Modification date2020032920200315
UniProtAcc.

P51608

Ensembl transtripts involved in fusion geneENST00000565677, ENST00000219548, 
ENST00000564370, ENST00000566181, 
ENST00000303391, ENST00000453960, 
ENST00000407218, ENST00000460227, 
Fusion gene scores* DoF score5 X 4 X 3=608 X 7 X 5=280
# samples 510
** MAII scorelog2(5/60*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/280*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: STUB1 [Title/Abstract] AND MECP2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSTUB1(730684)-MECP2(153298008), # samples:3
Anticipated loss of major functional domain due to fusion event.STUB1-MECP2 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
STUB1-MECP2 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
STUB1-MECP2 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor 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
HgeneSTUB1

GO:0000209

protein polyubiquitination

15781469|16275660

HgeneSTUB1

GO:0006515

protein quality control for misfolded or incompletely synthesized proteins

16831871

HgeneSTUB1

GO:0016567

protein ubiquitination

14610072|16809764

HgeneSTUB1

GO:0030579

ubiquitin-dependent SMAD protein catabolic process

15781469

HgeneSTUB1

GO:0031398

positive regulation of protein ubiquitination

11146632|16831871

HgeneSTUB1

GO:0031647

regulation of protein stability

16809764

HgeneSTUB1

GO:0031943

regulation of glucocorticoid metabolic process

11146632

HgeneSTUB1

GO:0032436

positive regulation of proteasomal ubiquitin-dependent protein catabolic process

11146632

HgeneSTUB1

GO:0043161

proteasome-mediated ubiquitin-dependent protein catabolic process

15781469|24613385

HgeneSTUB1

GO:0051865

protein autoubiquitination

16307917|18042044

HgeneSTUB1

GO:0070534

protein K63-linked ubiquitination

16307917

HgeneSTUB1

GO:0071218

cellular response to misfolded protein

16831871

HgeneSTUB1

GO:0090035

positive regulation of chaperone-mediated protein complex assembly

16831871

TgeneMECP2

GO:0010629

negative regulation of gene expression

23960241

TgeneMECP2

GO:0043537

negative regulation of blood vessel endothelial cell migration

23960241

TgeneMECP2

GO:0045892

negative regulation of transcription, DNA-templated

11441023

TgeneMECP2

GO:1905643

positive regulation of DNA methylation

23960241


check buttonFusion gene breakpoints across STUB1 (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 MECP2 (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
ChimerDB4OVTCGA-57-1582-01ASTUB1chr16

730684

+MECP2chrX

153298008

-
ChimerDB4OVTCGA-57-1582STUB1chr16

730684

+MECP2chrX

153298008

-
ChimerDB4OVTCGA-57-1582-01ASTUB1chr16

730684

+MECP2chrX

153298008

-


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Fusion Gene ORF analysis for STUB1-MECP2

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
5UTR-3CDSENST00000565677ENST00000303391STUB1chr16

730684

+MECP2chrX

153298008

-
5UTR-3CDSENST00000565677ENST00000453960STUB1chr16

730684

+MECP2chrX

153298008

-
5UTR-3CDSENST00000565677ENST00000407218STUB1chr16

730684

+MECP2chrX

153298008

-
5UTR-5UTRENST00000565677ENST00000460227STUB1chr16

730684

+MECP2chrX

153298008

-
Frame-shiftENST00000219548ENST00000303391STUB1chr16

730684

+MECP2chrX

153298008

-
Frame-shiftENST00000219548ENST00000453960STUB1chr16

730684

+MECP2chrX

153298008

-
Frame-shiftENST00000219548ENST00000407218STUB1chr16

730684

+MECP2chrX

153298008

-
5CDS-5UTRENST00000219548ENST00000460227STUB1chr16

730684

+MECP2chrX

153298008

-
intron-3CDSENST00000564370ENST00000303391STUB1chr16

730684

+MECP2chrX

153298008

-
intron-3CDSENST00000564370ENST00000453960STUB1chr16

730684

+MECP2chrX

153298008

-
intron-3CDSENST00000564370ENST00000407218STUB1chr16

730684

+MECP2chrX

153298008

-
intron-5UTRENST00000564370ENST00000460227STUB1chr16

730684

+MECP2chrX

153298008

-
intron-3CDSENST00000566181ENST00000303391STUB1chr16

730684

+MECP2chrX

153298008

-
intron-3CDSENST00000566181ENST00000453960STUB1chr16

730684

+MECP2chrX

153298008

-
intron-3CDSENST00000566181ENST00000407218STUB1chr16

730684

+MECP2chrX

153298008

-
intron-5UTRENST00000566181ENST00000460227STUB1chr16

730684

+MECP2chrX

153298008

-

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 STUB1-MECP2


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 STUB1-MECP2


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
.MECP2

P51608

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: Chromosomal protein that binds to methylated DNA. It can bind specifically to a single methyl-CpG pair. It is not influenced by sequences flanking the methyl-CpGs. Mediates transcriptional repression through interaction with histone deacetylase and the corepressor SIN3A. Binds both 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC)-containing DNA, with a preference for 5-methylcytosine (5mC). {ECO:0000250|UniProtKB:Q9Z2D6}.

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 STUB1-MECP2


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 STUB1-MECP2


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 STUB1-MECP2


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 STUB1-MECP2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSTUB1C4014261SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 166GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneMECP2C0035372Rett Syndrome50CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneMECP2C1968550Mental Retardation, X-Linked, Syndromic 1311CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneMECP2C0024141Lupus Erythematosus, Systemic5ORPHANET
TgeneMECP2C0004352Autistic Disorder3CTD_human
TgeneMECP2C1968556ENCEPHALOPATHY, NEONATAL SEVERE, DUE TO MECP2 MUTATIONS3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneMECP2C0020796Profound Mental Retardation2CTD_human
TgeneMECP2C0025363Mental Retardation, Psychosocial2CTD_human
TgeneMECP2C0917816Mental deficiency2CTD_human
TgeneMECP2C1535926Neurodevelopmental Disorders2CTD_human
TgeneMECP2C2749007Chromosome Xq28 Duplication Syndrome2GENOMICS_ENGLAND
TgeneMECP2C3714756Intellectual Disability2CTD_human
TgeneMECP2C0003469Anxiety Disorders1CTD_human
TgeneMECP2C0008073Developmental Disabilities1CTD_human
TgeneMECP2C0008074Child Development Disorders, Pervasive1CTD_human
TgeneMECP2C0009171Cocaine Abuse1CTD_human
TgeneMECP2C0014544Epilepsy1CTD_human
TgeneMECP2C0021712Myoclonus, Intention1CTD_human
TgeneMECP2C0022333Jacksonian Seizure1CTD_human
TgeneMECP2C0023186Learning Disorders1CTD_human
TgeneMECP2C0026825Flaccid Muscle Tone1CTD_human
TgeneMECP2C0026827Muscle hypotonia1CTD_human
TgeneMECP2C0027066Myoclonus1CTD_human
TgeneMECP2C0030214Myoclonus, Palatal1CTD_human
TgeneMECP2C0033922Psychomotor Disorders1CTD_human
TgeneMECP2C0034069Pulmonary Fibrosis1CTD_human
TgeneMECP2C0035229Respiratory Insufficiency1CTD_human
TgeneMECP2C0036572Seizures1CTD_human
TgeneMECP2C0085996Child Development Deviations1CTD_human
TgeneMECP2C0085997Child Development Disorders, Specific1CTD_human
TgeneMECP2C0086237Epilepsy, Cryptogenic1CTD_human
TgeneMECP2C0149958Complex partial seizures1CTD_human
TgeneMECP2C0234533Generalized seizures1CTD_human
TgeneMECP2C0234535Clonic Seizures1CTD_human
TgeneMECP2C0235063Respiratory Depression1CTD_human
TgeneMECP2C0236018Aura1CTD_human
TgeneMECP2C0236736Cocaine-Related Disorders1CTD_human
TgeneMECP2C0270824Visual seizure1CTD_human
TgeneMECP2C0270844Tonic Seizures1CTD_human
TgeneMECP2C0270846Epileptic drop attack1CTD_human
TgeneMECP2C0376280Anxiety States, Neurotic1CTD_human
TgeneMECP2C0376634Craniofacial Abnormalities1CTD_human
TgeneMECP2C0422850Seizures, Somatosensory1CTD_human
TgeneMECP2C0422852Seizures, Auditory1CTD_human
TgeneMECP2C0422853Olfactory seizure1CTD_human
TgeneMECP2C0422854Gustatory seizure1CTD_human
TgeneMECP2C0422855Vertiginous seizure1CTD_human
TgeneMECP2C0424230Motor retardation1CTD_human
TgeneMECP2C0427201Floppy Muscles1CTD_human
TgeneMECP2C0427202Muscle Tone Atonic1CTD_human
TgeneMECP2C0494475Tonic - clonic seizures1CTD_human
TgeneMECP2C0524528Pervasive Development Disorder1CTD_human
TgeneMECP2C0585540Myoclonus, Oculopalatal1CTD_human
TgeneMECP2C0600427Cocaine Dependence1CTD_human
TgeneMECP2C0751056Non-epileptic convulsion1CTD_human
TgeneMECP2C0751110Single Seizure1CTD_human
TgeneMECP2C0751111Awakening Epilepsy1CTD_human
TgeneMECP2C0751123Atonic Absence Seizures1CTD_human
TgeneMECP2C0751262Adult Learning Disorders1CTD_human
TgeneMECP2C0751263Learning Disturbance1CTD_human
TgeneMECP2C0751265Learning Disabilities1CTD_human
TgeneMECP2C0751330Unilateral Hypotonia1CTD_human
TgeneMECP2C0751348Myoclonus Simplex1CTD_human
TgeneMECP2C0751349Myoclonus, Eyelid1CTD_human
TgeneMECP2C0751350Myoclonus, Lower Extremity1CTD_human
TgeneMECP2C0751351Myoclonus, Segmental1CTD_human
TgeneMECP2C0751352Myoclonus, Nocturnal1CTD_human
TgeneMECP2C0751353Myoclonus, Upper Extremity1CTD_human
TgeneMECP2C0751354Myoclonus, Action1CTD_human
TgeneMECP2C0751355Polymyoclonus1CTD_human
TgeneMECP2C0751456Developmental Psychomotor Disorders1CTD_human
TgeneMECP2C0751494Convulsive Seizures1CTD_human
TgeneMECP2C0751495Seizures, Focal1CTD_human
TgeneMECP2C0751496Seizures, Sensory1CTD_human
TgeneMECP2C1145670Respiratory Failure1CTD_human
TgeneMECP2C1279420Anxiety neurosis (finding)1CTD_human
TgeneMECP2C1330966Developmental Academic Disorder1CTD_human
TgeneMECP2C1846058Lubs X-linked mental retardation syndrome1CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneMECP2C2239176Liver carcinoma1CTD_human
TgeneMECP2C2267233Neonatal Hypotonia1CTD_human
TgeneMECP2C2931498Mental Retardation, X-Linked 11ORPHANET
TgeneMECP2C3495874Nonepileptic Seizures1CTD_human
TgeneMECP2C3713418Ppm-X Syndrome1ORPHANET
TgeneMECP2C4048158Convulsions1CTD_human
TgeneMECP2C4316903Absence Seizures1CTD_human
TgeneMECP2C4317109Epileptic Seizures1CTD_human
TgeneMECP2C4317123Myoclonic Seizures1CTD_human
TgeneMECP2C4505436Generalized Absence Seizures1CTD_human
TgeneMECP2C4721507Alveolitis, Fibrosing1CTD_human