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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:RALY-MAP1LC3A (FusionGDB2 ID:71539)

Fusion Gene Summary for RALY-MAP1LC3A

check button Fusion gene summary
Fusion gene informationFusion gene name: RALY-MAP1LC3A
Fusion gene ID: 71539
HgeneTgene
Gene symbol

RALY

MAP1LC3A

Gene ID

22913

84557

Gene nameRALY heterogeneous nuclear ribonucleoproteinmicrotubule associated protein 1 light chain 3 alpha
SynonymsHNRPCL2|P542ATG8E|LC3|LC3A|MAP1ALC3|MAP1BLC3
Cytomap

20q11.22

20q11.22

Type of geneprotein-codingprotein-coding
DescriptionRNA-binding protein RalyRNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog)RNA-binding protein (autoantigenic)RNA-binding protein (autoantigenic, hnRNP-associated with lethal yellow)autoantigen p542heterogeneous nuclear rmicrotubule-associated proteins 1A/1B light chain 3AMAP1 light chain 3-like protein 1MAP1A/1B light chain 3 AMAP1A/MAP1B LC3 AMAP1A/MAP1B light chain 3 Aautophagy-related ubiquitin-like modifier LC3 Amicrotubule-associated proteins 1A/1B light chain
Modification date2020032720200329
UniProtAcc.

Q9H492

Ensembl transtripts involved in fusion geneENST00000375114, ENST00000246194, 
ENST00000493399, 		ENST00000374837, 
ENST00000360668, ENST00000397709, 
ENST00000476428, 
Fusion gene scores* DoF score28 X 14 X 15=58806 X 9 X 5=270
# samples 379
** MAII scorelog2(37/5880*10)=-3.99021897920741
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/270*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RALY [Title/Abstract] AND MAP1LC3A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRALY(32581937)-MAP1LC3A(33147012), # 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
TgeneMAP1LC3A

GO:0009267

cellular response to starvation

28223137

TgeneMAP1LC3A

GO:0016236

macroautophagy

28223137

TgeneMAP1LC3A

GO:0097352

autophagosome maturation

28223137


check buttonFusion gene breakpoints across RALY (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 MAP1LC3A (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
ChimerDB4BRCATCGA-D8-A1XD-01ARALYchr20

32581937

+MAP1LC3Achr20

33147012

+
ChimerDB4BRCATCGA-D8-A1XDRALYchr20

32581937

+MAP1LC3Achr20

33147011

+
ChimerDB4BRCATCGA-D8-A1XDRALYchr20

32581937

+MAP1LC3Achr20

33147150

+
ChimerDB4BRCATCGA-D8-A1XD-01ARALYchr20

32581937

+MAP1LC3Achr20

33147012

+
ChimerDB4BRCATCGA-D8-A1XD-01ARALYchr20

32581937

+MAP1LC3Achr20

33147151

+
ChimerDB4BRCATCGA-D8-A1XD-01ARALYchr20

32581937

+MAP1LC3Achr20

33137709

+


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Fusion Gene ORF analysis for RALY-MAP1LC3A

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-3CDSENST00000375114ENST00000374837RALYchr20

32581937

+MAP1LC3Achr20

33147012

+
5UTR-3CDSENST00000375114ENST00000360668RALYchr20

32581937

+MAP1LC3Achr20

33147012

+
5UTR-3CDSENST00000375114ENST00000397709RALYchr20

32581937

+MAP1LC3Achr20

33147012

+
5UTR-intronENST00000375114ENST00000476428RALYchr20

32581937

+MAP1LC3Achr20

33147012

+
5UTR-3CDSENST00000246194ENST00000374837RALYchr20

32581937

+MAP1LC3Achr20

33147012

+
5UTR-3CDSENST00000246194ENST00000360668RALYchr20

32581937

+MAP1LC3Achr20

33147012

+
5UTR-3CDSENST00000246194ENST00000397709RALYchr20

32581937

+MAP1LC3Achr20

33147012

+
5UTR-intronENST00000246194ENST00000476428RALYchr20

32581937

+MAP1LC3Achr20

33147012

+
intron-3CDSENST00000493399ENST00000374837RALYchr20

32581937

+MAP1LC3Achr20

33147012

+
intron-3CDSENST00000493399ENST00000360668RALYchr20

32581937

+MAP1LC3Achr20

33147012

+
intron-3CDSENST00000493399ENST00000397709RALYchr20

32581937

+MAP1LC3Achr20

33147012

+
intron-intronENST00000493399ENST00000476428RALYchr20

32581937

+MAP1LC3Achr20

33147012

+
5UTR-3CDSENST00000375114ENST00000374837RALYchr20

32581937

+MAP1LC3Achr20

33147011

+
5UTR-3CDSENST00000375114ENST00000360668RALYchr20

32581937

+MAP1LC3Achr20

33147011

+
5UTR-3CDSENST00000375114ENST00000397709RALYchr20

32581937

+MAP1LC3Achr20

33147011

+
5UTR-intronENST00000375114ENST00000476428RALYchr20

32581937

+MAP1LC3Achr20

33147011

+
5UTR-3CDSENST00000246194ENST00000374837RALYchr20

32581937

+MAP1LC3Achr20

33147011

+
5UTR-3CDSENST00000246194ENST00000360668RALYchr20

32581937

+MAP1LC3Achr20

33147011

+
5UTR-3CDSENST00000246194ENST00000397709RALYchr20

32581937

+MAP1LC3Achr20

33147011

+
5UTR-intronENST00000246194ENST00000476428RALYchr20

32581937

+MAP1LC3Achr20

33147011

+
intron-3CDSENST00000493399ENST00000374837RALYchr20

32581937

+MAP1LC3Achr20

33147011

+
intron-3CDSENST00000493399ENST00000360668RALYchr20

32581937

+MAP1LC3Achr20

33147011

+
intron-3CDSENST00000493399ENST00000397709RALYchr20

32581937

+MAP1LC3Achr20

33147011

+
intron-intronENST00000493399ENST00000476428RALYchr20

32581937

+MAP1LC3Achr20

33147011

+
5UTR-3CDSENST00000375114ENST00000374837RALYchr20

32581937

+MAP1LC3Achr20

33147150

+
5UTR-3CDSENST00000375114ENST00000360668RALYchr20

32581937

+MAP1LC3Achr20

33147150

+
5UTR-3CDSENST00000375114ENST00000397709RALYchr20

32581937

+MAP1LC3Achr20

33147150

+
5UTR-3UTRENST00000375114ENST00000476428RALYchr20

32581937

+MAP1LC3Achr20

33147150

+
5UTR-3CDSENST00000246194ENST00000374837RALYchr20

32581937

+MAP1LC3Achr20

33147150

+
5UTR-3CDSENST00000246194ENST00000360668RALYchr20

32581937

+MAP1LC3Achr20

33147150

+
5UTR-3CDSENST00000246194ENST00000397709RALYchr20

32581937

+MAP1LC3Achr20

33147150

+
5UTR-3UTRENST00000246194ENST00000476428RALYchr20

32581937

+MAP1LC3Achr20

33147150

+
intron-3CDSENST00000493399ENST00000374837RALYchr20

32581937

+MAP1LC3Achr20

33147150

+
intron-3CDSENST00000493399ENST00000360668RALYchr20

32581937

+MAP1LC3Achr20

33147150

+
intron-3CDSENST00000493399ENST00000397709RALYchr20

32581937

+MAP1LC3Achr20

33147150

+
intron-3UTRENST00000493399ENST00000476428RALYchr20

32581937

+MAP1LC3Achr20

33147150

+
5UTR-3CDSENST00000375114ENST00000374837RALYchr20

32581937

+MAP1LC3Achr20

33147151

+
5UTR-3CDSENST00000375114ENST00000360668RALYchr20

32581937

+MAP1LC3Achr20

33147151

+
5UTR-3CDSENST00000375114ENST00000397709RALYchr20

32581937

+MAP1LC3Achr20

33147151

+
5UTR-3UTRENST00000375114ENST00000476428RALYchr20

32581937

+MAP1LC3Achr20

33147151

+
5UTR-3CDSENST00000246194ENST00000374837RALYchr20

32581937

+MAP1LC3Achr20

33147151

+
5UTR-3CDSENST00000246194ENST00000360668RALYchr20

32581937

+MAP1LC3Achr20

33147151

+
5UTR-3CDSENST00000246194ENST00000397709RALYchr20

32581937

+MAP1LC3Achr20

33147151

+
5UTR-3UTRENST00000246194ENST00000476428RALYchr20

32581937

+MAP1LC3Achr20

33147151

+
intron-3CDSENST00000493399ENST00000374837RALYchr20

32581937

+MAP1LC3Achr20

33147151

+
intron-3CDSENST00000493399ENST00000360668RALYchr20

32581937

+MAP1LC3Achr20

33147151

+
intron-3CDSENST00000493399ENST00000397709RALYchr20

32581937

+MAP1LC3Achr20

33147151

+
intron-3UTRENST00000493399ENST00000476428RALYchr20

32581937

+MAP1LC3Achr20

33147151

+
5UTR-5UTRENST00000375114ENST00000374837RALYchr20

32581937

+MAP1LC3Achr20

33137709

+
5UTR-intronENST00000375114ENST00000360668RALYchr20

32581937

+MAP1LC3Achr20

33137709

+
5UTR-intronENST00000375114ENST00000397709RALYchr20

32581937

+MAP1LC3Achr20

33137709

+
5UTR-intronENST00000375114ENST00000476428RALYchr20

32581937

+MAP1LC3Achr20

33137709

+
5UTR-5UTRENST00000246194ENST00000374837RALYchr20

32581937

+MAP1LC3Achr20

33137709

+
5UTR-intronENST00000246194ENST00000360668RALYchr20

32581937

+MAP1LC3Achr20

33137709

+
5UTR-intronENST00000246194ENST00000397709RALYchr20

32581937

+MAP1LC3Achr20

33137709

+
5UTR-intronENST00000246194ENST00000476428RALYchr20

32581937

+MAP1LC3Achr20

33137709

+
intron-5UTRENST00000493399ENST00000374837RALYchr20

32581937

+MAP1LC3Achr20

33137709

+
intron-intronENST00000493399ENST00000360668RALYchr20

32581937

+MAP1LC3Achr20

33137709

+
intron-intronENST00000493399ENST00000397709RALYchr20

32581937

+MAP1LC3Achr20

33137709

+
intron-intronENST00000493399ENST00000476428RALYchr20

32581937

+MAP1LC3Achr20

33137709

+

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 RALY-MAP1LC3A


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)
RALYchr2032581937+MAP1LC3Achr2033137708+6.48E-060.99999356
RALYchr2032581937+MAP1LC3Achr2033147011+6.24E-080.9999999
RALYchr2032581937+MAP1LC3Achr2033147011+6.24E-080.9999999
RALYchr2032581937+MAP1LC3Achr2033147150+3.89E-101
RALYchr2032581937+MAP1LC3Achr2033147150+3.89E-101
RALYchr2032581937+MAP1LC3Achr2033137708+6.48E-060.99999356
RALYchr2032581937+MAP1LC3Achr2033147011+6.24E-080.9999999
RALYchr2032581937+MAP1LC3Achr2033147011+6.24E-080.9999999
RALYchr2032581937+MAP1LC3Achr2033147150+3.89E-101
RALYchr2032581937+MAP1LC3Achr2033147150+3.89E-101

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 RALY-MAP1LC3A


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
.MAP1LC3A

Q9H492

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: Ubiquitin-like modifier involved in formation of autophagosomal vacuoles (autophagosomes) (PubMed:20713600, PubMed:24290141). While LC3s are involved in elongation of the phagophore membrane, the GABARAP/GATE-16 subfamily is essential for a later stage in autophagosome maturation (PubMed:20713600). Through its interaction with the reticulophagy receptor TEX264, participates in the remodeling of subdomains of the endoplasmic reticulum into autophagosomes upon nutrient stress, which then fuse with lysosomes for endoplasmic reticulum turnover (PubMed:31006538, PubMed:31006537). {ECO:0000269|PubMed:20713600, ECO:0000269|PubMed:24290141, ECO:0000269|PubMed:31006537, ECO:0000269|PubMed:31006538}.

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 RALY-MAP1LC3A


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 RALY-MAP1LC3A


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 RALY-MAP1LC3A


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 RALY-MAP1LC3A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRALYC0236733Amphetamine-Related Disorders1CTD_human
HgeneRALYC0236804Amphetamine Addiction1CTD_human
HgeneRALYC0236807Amphetamine Abuse1CTD_human
TgeneMAP1LC3AC0023893Liver Cirrhosis, Experimental1CTD_human