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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:L1CAM-TEX28 (FusionGDB2 ID:HG3897TG1527)

Fusion Gene Summary for L1CAM-TEX28

check button Fusion gene summary
Fusion gene informationFusion gene name: L1CAM-TEX28
Fusion gene ID: hg3897tg1527
HgeneTgene
Gene symbol

L1CAM

TEX28

Gene ID

3897

1527

Gene nameL1 cell adhesion moleculetestis expressed 28
SynonymsCAML1|CD171|HSAS|HSAS1|MASA|MIC5|N-CAM-L1|N-CAML1|NCAM-L1|S10|SPG1CXorf2|MRX99|TEX28P1|TEX28P2|fTEX
Cytomap('L1CAM')('TEX28')

Xq28

Xq28

Type of geneprotein-codingprotein-coding
Descriptionneural cell adhesion molecule L1antigen identified by monoclonal antibody R1testis-specific protein TEX28
Modification date2020032220200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000361699, ENST00000361981, 
ENST00000370055, ENST00000370057, 
ENST00000370060, ENST00000484587, 
ENST00000538883, ENST00000543994, 
Fusion gene scores* DoF score2 X 2 X 1=41 X 1 X 1=1
# samples 21
** MAII scorelog2(2/4*10)=2.32192809488736log2(1/1*10)=3.32192809488736
Context

PubMed: L1CAM [Title/Abstract] AND TEX28 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointL1CAM(153128225)-TEX28(153499436), # 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
HgeneL1CAM

GO:0007160

cell-matrix adhesion

22973895

HgeneL1CAM

GO:0007411

axon guidance

24155914

HgeneL1CAM

GO:0016477

cell migration

22973895

HgeneL1CAM

GO:0031175

neuron projection development

22973895

HgeneL1CAM

GO:0050808

synapse organization

24155914

HgeneL1CAM

GO:0061564

axon development

20621658



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-30-1857-01AL1CAMchrX

153128225

-TEX28chrX

153499436

-


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Fusion Gene ORF analysis for L1CAM-TEX28

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-3CDSENST00000361699ENST00000369926L1CAMchrX

153128225

-TEX28chrX

153499436

-
intron-3CDSENST00000361981ENST00000369926L1CAMchrX

153128225

-TEX28chrX

153499436

-
intron-3CDSENST00000370055ENST00000369926L1CAMchrX

153128225

-TEX28chrX

153499436

-
intron-3CDSENST00000370057ENST00000369926L1CAMchrX

153128225

-TEX28chrX

153499436

-
intron-3CDSENST00000370060ENST00000369926L1CAMchrX

153128225

-TEX28chrX

153499436

-
intron-3CDSENST00000484587ENST00000369926L1CAMchrX

153128225

-TEX28chrX

153499436

-
intron-3CDSENST00000538883ENST00000369926L1CAMchrX

153128225

-TEX28chrX

153499436

-
intron-3CDSENST00000543994ENST00000369926L1CAMchrX

153128225

-TEX28chrX

153499436

-

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 L1CAM-TEX28


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 L1CAM-TEX28


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/:153128225/:153499436)
- 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
..
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: 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 L1CAM-TEX28


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 L1CAM-TEX28


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 L1CAM-TEX28


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 L1CAM-TEX28


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneL1CAMC0265216X-linked hydrocephalus syndrome27CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneL1CAMC0795953MASA SYNDROME (disorder)24CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneL1CAMC1839909CORPUS CALLOSUM, PARTIAL AGENESIS OF, X-LINKED2CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneL1CAMC0003537Aphasia1CTD_human
HgeneL1CAMC0003546Aphasia, Acquired1CTD_human
HgeneL1CAMC0003886Arthrogryposis1GENOMICS_ENGLAND
HgeneL1CAMC0007134Renal Cell Carcinoma1CTD_human
HgeneL1CAMC0018566Congenital Hand Deformities1CTD_human
HgeneL1CAMC0037773Spastic Paraplegia, Hereditary1GENOMICS_ENGLAND
HgeneL1CAMC0231686Gait, Unsteady1CTD_human
HgeneL1CAMC0231687Spastic gait1CTD_human
HgeneL1CAMC0231688Gait, Shuffling1CTD_human
HgeneL1CAMC0231689Gait, Athetotic1CTD_human
HgeneL1CAMC0231693Charcot Gait1CTD_human
HgeneL1CAMC0231694Gait, Festinating1CTD_human
HgeneL1CAMC0231695Cerebellar ataxic gait1CTD_human
HgeneL1CAMC0231696Gait, Hemiplegic1CTD_human
HgeneL1CAMC0231698Gait, Scissors1CTD_human
HgeneL1CAMC0231712Waddling gait1CTD_human
HgeneL1CAMC0234462Aphasia, Ageusic1CTD_human
HgeneL1CAMC0234469Aphasia, Global1CTD_human
HgeneL1CAMC0234472Aphasia, Functional1CTD_human
HgeneL1CAMC0234474Aphasia, Graphomotor1CTD_human
HgeneL1CAMC0234476Aphasia, Intellectual1CTD_human
HgeneL1CAMC0234482Aphasia, Semantic1CTD_human
HgeneL1CAMC0234484Aphasia, Syntactical1CTD_human
HgeneL1CAMC0234996Gait, Rigid1CTD_human
HgeneL1CAMC0235000Gait, Broadened1CTD_human
HgeneL1CAMC0279702Conventional (Clear Cell) Renal Cell Carcinoma1CTD_human
HgeneL1CAMC0337210Gait, Stumbling1CTD_human
HgeneL1CAMC0338457Aphasia, Progressive1CTD_human
HgeneL1CAMC0427128Rapid Fatigue of Gait1CTD_human
HgeneL1CAMC0427149Gait, Drop Foot1CTD_human
HgeneL1CAMC0427169Marche a Petit Pas1CTD_human
HgeneL1CAMC0427177Gait, Hysterical1CTD_human
HgeneL1CAMC0431368Partial agenesis of corpus callosum1GENOMICS_ENGLAND
HgeneL1CAMC0454576Aphasia, Mixed1CTD_human
HgeneL1CAMC0750917Aphasia, Auditory Discriminatory1CTD_human
HgeneL1CAMC0750918Aphasia, Commisural1CTD_human
HgeneL1CAMC0750919Aphasia, Post-Ictal1CTD_human
HgeneL1CAMC0750920Aphasia, Post-Traumatic1CTD_human
HgeneL1CAMC0750921Dejerine-Lichtheim Phenomenon1CTD_human
HgeneL1CAMC0751829Gait Disorder, Sensorimotor1CTD_human
HgeneL1CAMC0751830Gait Disorders, Neurologic1CTD_human
HgeneL1CAMC0751831Gait, Frontal1CTD_human
HgeneL1CAMC0751832Gait, Widebased1CTD_human
HgeneL1CAMC0973461Dysphasia1CTD_human
HgeneL1CAMC1266042Chromophobe Renal Cell Carcinoma1CTD_human
HgeneL1CAMC1266043Sarcomatoid Renal Cell Carcinoma1CTD_human
HgeneL1CAMC1266044Collecting Duct Carcinoma of the Kidney1CTD_human
HgeneL1CAMC1306837Papillary Renal Cell Carcinoma1CTD_human