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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:KTN1-MECP2 (FusionGDB2 ID:HG3895TG4204)

Fusion Gene Summary for KTN1-MECP2

check button Fusion gene summary
Fusion gene informationFusion gene name: KTN1-MECP2
Fusion gene ID: hg3895tg4204
HgeneTgene
Gene symbol

KTN1

MECP2

Gene ID

3895

4204

Gene namekinectin 1methyl-CpG binding protein 2
SynonymsCG1|KNT|MU-RMS-40.19AUTSX3|MRX16|MRX79|MRXS13|MRXSL|PPMX|RS|RTS|RTT
Cytomap('KTN1')('MECP2')

14q22.3

Xq28

Type of geneprotein-codingprotein-coding
DescriptionkinectinCG-1 antigenkinesin receptormethyl-CpG-binding protein 2meCp-2 protein
Modification date2020031320200315
UniProtAcc

Q86UP2

P51608

Ensembl transtripts involved in fusion geneENST00000395308, ENST00000395309, 
ENST00000395311, ENST00000395314, 
ENST00000413890, ENST00000416613, 
ENST00000438792, ENST00000554507, 
ENST00000555573, 
Fusion gene scores* DoF score17 X 19 X 8=25848 X 7 X 5=280
# samples 2010
** MAII scorelog2(20/2584*10)=-3.6915341649192
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: KTN1 [Title/Abstract] AND MECP2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKTN1(56078842)-MECP2(153287905), # 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
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 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/ABF761248KTN1chr14

56078842

-MECP2chrX

153287905

-


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Fusion Gene ORF analysis for KTN1-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
5CDS-3UTRENST00000395308ENST00000303391KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-3UTRENST00000395309ENST00000303391KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-3UTRENST00000395311ENST00000303391KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-3UTRENST00000395314ENST00000303391KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-3UTRENST00000413890ENST00000303391KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-3UTRENST00000416613ENST00000303391KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-3UTRENST00000438792ENST00000303391KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-intronENST00000395308ENST00000407218KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-intronENST00000395308ENST00000453960KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-intronENST00000395308ENST00000460227KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-intronENST00000395309ENST00000407218KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-intronENST00000395309ENST00000453960KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-intronENST00000395309ENST00000460227KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-intronENST00000395311ENST00000407218KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-intronENST00000395311ENST00000453960KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-intronENST00000395311ENST00000460227KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-intronENST00000395314ENST00000407218KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-intronENST00000395314ENST00000453960KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-intronENST00000395314ENST00000460227KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-intronENST00000413890ENST00000407218KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-intronENST00000413890ENST00000453960KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-intronENST00000413890ENST00000460227KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-intronENST00000416613ENST00000407218KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-intronENST00000416613ENST00000453960KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-intronENST00000416613ENST00000460227KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-intronENST00000438792ENST00000407218KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-intronENST00000438792ENST00000453960KTN1chr14

56078842

-MECP2chrX

153287905

-
5CDS-intronENST00000438792ENST00000460227KTN1chr14

56078842

-MECP2chrX

153287905

-
intron-3UTRENST00000554507ENST00000303391KTN1chr14

56078842

-MECP2chrX

153287905

-
intron-3UTRENST00000555573ENST00000303391KTN1chr14

56078842

-MECP2chrX

153287905

-
intron-intronENST00000554507ENST00000407218KTN1chr14

56078842

-MECP2chrX

153287905

-
intron-intronENST00000554507ENST00000453960KTN1chr14

56078842

-MECP2chrX

153287905

-
intron-intronENST00000554507ENST00000460227KTN1chr14

56078842

-MECP2chrX

153287905

-
intron-intronENST00000555573ENST00000407218KTN1chr14

56078842

-MECP2chrX

153287905

-
intron-intronENST00000555573ENST00000453960KTN1chr14

56078842

-MECP2chrX

153287905

-
intron-intronENST00000555573ENST00000460227KTN1chr14

56078842

-MECP2chrX

153287905

-

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 KTN1-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)


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Fusion Protein Features for KTN1-MECP2


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/:56078842/:153287905)
- 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
KTN1

Q86UP2

MECP2

P51608

FUNCTION: Receptor for kinesin thus involved in kinesin-driven vesicle motility. Accumulates in integrin-based adhesion complexes (IAC) upon integrin aggregation by fibronectin.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 KTN1-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 KTN1-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 KTN1-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 KTN1-MECP2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneKTN1C0023893Liver Cirrhosis, Experimental1CTD_human
TgeneC0035372Rett Syndrome50CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC1968550Mental Retardation, X-Linked, Syndromic 1311CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0024141Lupus Erythematosus, Systemic5ORPHANET
TgeneC0004352Autistic Disorder3CTD_human
TgeneC1968556ENCEPHALOPATHY, NEONATAL SEVERE, DUE TO MECP2 MUTATIONS3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0020796Profound Mental Retardation2CTD_human
TgeneC0025363Mental Retardation, Psychosocial2CTD_human
TgeneC0917816Mental deficiency2CTD_human
TgeneC1535926Neurodevelopmental Disorders2CTD_human
TgeneC2749007Chromosome Xq28 Duplication Syndrome2GENOMICS_ENGLAND
TgeneC3714756Intellectual Disability2CTD_human
TgeneC0003469Anxiety Disorders1CTD_human
TgeneC0008073Developmental Disabilities1CTD_human
TgeneC0008074Child Development Disorders, Pervasive1CTD_human
TgeneC0009171Cocaine Abuse1CTD_human
TgeneC0014544Epilepsy1CTD_human
TgeneC0021712Myoclonus, Intention1CTD_human
TgeneC0022333Jacksonian Seizure1CTD_human
TgeneC0023186Learning Disorders1CTD_human
TgeneC0026825Flaccid Muscle Tone1CTD_human
TgeneC0026827Muscle hypotonia1CTD_human
TgeneC0027066Myoclonus1CTD_human
TgeneC0030214Myoclonus, Palatal1CTD_human
TgeneC0033922Psychomotor Disorders1CTD_human
TgeneC0034069Pulmonary Fibrosis1CTD_human
TgeneC0035229Respiratory Insufficiency1CTD_human
TgeneC0036572Seizures1CTD_human
TgeneC0085996Child Development Deviations1CTD_human
TgeneC0085997Child Development Disorders, Specific1CTD_human
TgeneC0086237Epilepsy, Cryptogenic1CTD_human
TgeneC0149958Complex partial seizures1CTD_human
TgeneC0234533Generalized seizures1CTD_human
TgeneC0234535Clonic Seizures1CTD_human
TgeneC0235063Respiratory Depression1CTD_human
TgeneC0236018Aura1CTD_human
TgeneC0236736Cocaine-Related Disorders1CTD_human
TgeneC0270824Visual seizure1CTD_human
TgeneC0270844Tonic Seizures1CTD_human
TgeneC0270846Epileptic drop attack1CTD_human
TgeneC0376280Anxiety States, Neurotic1CTD_human
TgeneC0376634Craniofacial Abnormalities1CTD_human
TgeneC0422850Seizures, Somatosensory1CTD_human
TgeneC0422852Seizures, Auditory1CTD_human
TgeneC0422853Olfactory seizure1CTD_human
TgeneC0422854Gustatory seizure1CTD_human
TgeneC0422855Vertiginous seizure1CTD_human
TgeneC0424230Motor retardation1CTD_human
TgeneC0427201Floppy Muscles1CTD_human
TgeneC0427202Muscle Tone Atonic1CTD_human
TgeneC0494475Tonic - clonic seizures1CTD_human
TgeneC0524528Pervasive Development Disorder1CTD_human
TgeneC0585540Myoclonus, Oculopalatal1CTD_human
TgeneC0600427Cocaine Dependence1CTD_human
TgeneC0751056Non-epileptic convulsion1CTD_human
TgeneC0751110Single Seizure1CTD_human
TgeneC0751111Awakening Epilepsy1CTD_human
TgeneC0751123Atonic Absence Seizures1CTD_human
TgeneC0751262Adult Learning Disorders1CTD_human
TgeneC0751263Learning Disturbance1CTD_human
TgeneC0751265Learning Disabilities1CTD_human
TgeneC0751330Unilateral Hypotonia1CTD_human
TgeneC0751348Myoclonus Simplex1CTD_human
TgeneC0751349Myoclonus, Eyelid1CTD_human
TgeneC0751350Myoclonus, Lower Extremity1CTD_human
TgeneC0751351Myoclonus, Segmental1CTD_human
TgeneC0751352Myoclonus, Nocturnal1CTD_human
TgeneC0751353Myoclonus, Upper Extremity1CTD_human
TgeneC0751354Myoclonus, Action1CTD_human
TgeneC0751355Polymyoclonus1CTD_human
TgeneC0751456Developmental Psychomotor Disorders1CTD_human
TgeneC0751494Convulsive Seizures1CTD_human
TgeneC0751495Seizures, Focal1CTD_human
TgeneC0751496Seizures, Sensory1CTD_human
TgeneC1145670Respiratory Failure1CTD_human
TgeneC1279420Anxiety neurosis (finding)1CTD_human
TgeneC1330966Developmental Academic Disorder1CTD_human
TgeneC1846058Lubs X-linked mental retardation syndrome1CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC2239176Liver carcinoma1CTD_human
TgeneC2267233Neonatal Hypotonia1CTD_human
TgeneC2931498Mental Retardation, X-Linked 11ORPHANET
TgeneC3495874Nonepileptic Seizures1CTD_human
TgeneC3713418Ppm-X Syndrome1ORPHANET
TgeneC4048158Convulsions1CTD_human
TgeneC4316903Absence Seizures1CTD_human
TgeneC4317109Epileptic Seizures1CTD_human
TgeneC4317123Myoclonic Seizures1CTD_human
TgeneC4505436Generalized Absence Seizures1CTD_human
TgeneC4721507Alveolitis, Fibrosing1CTD_human