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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:RAB1A-LUC7L3 (FusionGDB2 ID:71202)

Fusion Gene Summary for RAB1A-LUC7L3

check button Fusion gene summary
Fusion gene informationFusion gene name: RAB1A-LUC7L3
Fusion gene ID: 71202
HgeneTgene
Gene symbol

RAB1A

LUC7L3

Gene ID

5861

51747

Gene nameRAB1A, member RAS oncogene familyLUC7 like 3 pre-mRNA splicing factor
SynonymsRAB1|YPT1CRA|CREAP-1|CROP|LUC7A|OA48-18|hLuc7A
Cytomap

2p14

17q21.33

Type of geneprotein-codingprotein-coding
Descriptionras-related protein Rab-1AGTP binding protein Rab1aRAB1, member RAS oncogene familyRab GTPase YPT1 homologYPT1-related proteinluc7-like protein 3CRE-associated protein 1LUC7-like 3cAMP regulatory element-associated protein 1cisplatin resistance-associated-overexpressed proteinokadaic acid-inducible phosphoprotein OA48-18
Modification date2020032920200313
UniProtAcc.

O95232

Ensembl transtripts involved in fusion geneENST00000260638, ENST00000356214, 
ENST00000398529, ENST00000409751, 
ENST00000409784, ENST00000409892, 
ENST00000494188, 		ENST00000240304, 
ENST00000311571, ENST00000393227, 
ENST00000505658, ENST00000544170, 
ENST00000503798, 
Fusion gene scores* DoF score10 X 11 X 4=4408 X 8 X 5=320
# samples 139
** MAII scorelog2(13/440*10)=-1.7589919004962
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/320*10)=-1.83007499855769
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RAB1A [Title/Abstract] AND LUC7L3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRAB1A(65357209)-LUC7L3(48797049), # samples:2
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

check buttonFusion gene breakpoints across RAB1A (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 LUC7L3 (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/ABC000604RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
ChiTaRS5.0N/ABE276057RAB1Achr2

65357209

+LUC7L3chr17

48797049

+


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Fusion Gene ORF analysis for RAB1A-LUC7L3

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-5UTRENST00000260638ENST00000240304RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000260638ENST00000311571RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000260638ENST00000393227RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000260638ENST00000505658RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000260638ENST00000544170RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000356214ENST00000240304RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000356214ENST00000311571RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000356214ENST00000393227RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000356214ENST00000505658RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000356214ENST00000544170RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000398529ENST00000240304RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000398529ENST00000311571RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000398529ENST00000393227RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000398529ENST00000505658RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000398529ENST00000544170RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000409751ENST00000240304RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000409751ENST00000311571RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000409751ENST00000393227RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000409751ENST00000505658RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000409751ENST00000544170RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000409784ENST00000240304RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000409784ENST00000311571RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000409784ENST00000393227RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000409784ENST00000505658RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000409784ENST00000544170RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000409892ENST00000240304RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000409892ENST00000311571RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000409892ENST00000393227RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000409892ENST00000505658RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000409892ENST00000544170RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000494188ENST00000240304RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000494188ENST00000311571RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000494188ENST00000393227RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000494188ENST00000505658RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-5UTRENST00000494188ENST00000544170RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-intronENST00000260638ENST00000503798RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-intronENST00000356214ENST00000503798RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-intronENST00000398529ENST00000503798RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-intronENST00000409751ENST00000503798RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-intronENST00000409784ENST00000503798RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-intronENST00000409892ENST00000503798RAB1Achr2

65357209

+LUC7L3chr17

48797049

+
intron-intronENST00000494188ENST00000503798RAB1Achr2

65357209

+LUC7L3chr17

48797049

+

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 RAB1A-LUC7L3


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 RAB1A-LUC7L3


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/:65357209/:48797049)
- 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
.LUC7L3

O95232

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: Binds cAMP regulatory element DNA sequence. May play a role in RNA splicing. {ECO:0000269|PubMed:16462885}.

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 RAB1A-LUC7L3


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 RAB1A-LUC7L3


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 RAB1A-LUC7L3


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 RAB1A-LUC7L3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource