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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:LDHB-RARB (FusionGDB2 ID:44346)

Fusion Gene Summary for LDHB-RARB

check button Fusion gene summary
Fusion gene informationFusion gene name: LDHB-RARB
Fusion gene ID: 44346
HgeneTgene
Gene symbol

LDHB

RARB

Gene ID

3945

5915

Gene namelactate dehydrogenase Bretinoic acid receptor beta
SynonymsHEL-S-281|LDH-B|LDH-H|LDHBD|TRG-5HAP|MCOPS12|NR1B2|RARbeta1|RRB2
Cytomap

12p12.1

3p24.2

Type of geneprotein-codingprotein-coding
DescriptionL-lactate dehydrogenase B chainLDH heart subunitepididymis secretory protein Li 281lactate dehydrogenase H chainrenal carcinoma antigen NY-REN-46testicular secretory protein Li 25retinoic acid receptor betaHBV-activated proteinRAR-betaRAR-epsilonhepatitis B virus activated proteinnuclear receptor subfamily 1 group B member 2retinoic acid receptor, beta polypeptide
Modification date2020032620200328
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000350669, ENST00000396076, 
ENST00000535112, 		ENST00000458646, 
ENST00000462272, ENST00000330688, 
ENST00000404969, ENST00000437042, 
Fusion gene scores* DoF score10 X 8 X 6=4804 X 4 X 2=32
# samples 104
** MAII scorelog2(10/480*10)=-2.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/32*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: LDHB [Title/Abstract] AND RARB [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLDHB(21790005)-RARB(25637911), # samples:1
Anticipated loss of major functional domain due to fusion event.LDHB-RARB seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
LDHB-RARB seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
LDHB-RARB seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
LDHB-RARB seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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

check buttonFusion gene breakpoints across LDHB (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across RARB (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4UCSTCGA-N5-A4R8-01ALDHBchr12

21790005

-RARBchr3

25637911

+


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Fusion Gene ORF analysis for LDHB-RARB

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-3UTRENST00000350669ENST00000458646LDHBchr12

21790005

-RARBchr3

25637911

+
5CDS-3UTRENST00000350669ENST00000462272LDHBchr12

21790005

-RARBchr3

25637911

+
5CDS-3UTRENST00000396076ENST00000458646LDHBchr12

21790005

-RARBchr3

25637911

+
5CDS-3UTRENST00000396076ENST00000462272LDHBchr12

21790005

-RARBchr3

25637911

+
Frame-shiftENST00000350669ENST00000330688LDHBchr12

21790005

-RARBchr3

25637911

+
Frame-shiftENST00000350669ENST00000404969LDHBchr12

21790005

-RARBchr3

25637911

+
Frame-shiftENST00000350669ENST00000437042LDHBchr12

21790005

-RARBchr3

25637911

+
Frame-shiftENST00000396076ENST00000330688LDHBchr12

21790005

-RARBchr3

25637911

+
Frame-shiftENST00000396076ENST00000437042LDHBchr12

21790005

-RARBchr3

25637911

+
In-frameENST00000396076ENST00000404969LDHBchr12

21790005

-RARBchr3

25637911

+
intron-3CDSENST00000535112ENST00000330688LDHBchr12

21790005

-RARBchr3

25637911

+
intron-3CDSENST00000535112ENST00000404969LDHBchr12

21790005

-RARBchr3

25637911

+
intron-3CDSENST00000535112ENST00000437042LDHBchr12

21790005

-RARBchr3

25637911

+
intron-3UTRENST00000535112ENST00000458646LDHBchr12

21790005

-RARBchr3

25637911

+
intron-3UTRENST00000535112ENST00000462272LDHBchr12

21790005

-RARBchr3

25637911

+

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)
ENST00000396076LDHBchr1221790005-ENST00000404969RARBchr325637911+136711701711184337

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
ENST00000396076ENST00000404969LDHBchr1221790005-RARBchr325637911+0.0037607090.9962393

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Fusion Genomic Features for LDHB-RARB


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)
LDHBchr1221790004-RARBchr325637910+0.0002172410.99978274
LDHBchr1221790004-RARBchr325637910+0.0002172410.99978274

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.
genomic feature

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.
genomic feature of top 1%

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Fusion Protein Features for LDHB-RARB


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/chr12:21790005/chr3:25637911)
- 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
HgeneLDHBchr12:21790005chr3:25637911ENST00000350669-7831_53279335.0Nucleotide bindingNAD
HgeneLDHBchr12:21790005chr3:25637911ENST00000396076-7831_53279335.0Nucleotide bindingNAD

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneRARBchr12:21790005chr3:25637911ENST000003306886888_153383449.0DNA bindingNuclear receptor
TgeneRARBchr12:21790005chr3:25637911ENST000004049696888_153390456.0DNA bindingNuclear receptor
TgeneRARBchr12:21790005chr3:25637911ENST000004370426888_153271337.0DNA bindingNuclear receptor
TgeneRARBchr12:21790005chr3:25637911ENST000004586466888_153271337.0DNA bindingNuclear receptor
TgeneRARBchr12:21790005chr3:25637911ENST0000033068868183_417383449.0DomainNR LBD
TgeneRARBchr12:21790005chr3:25637911ENST0000040496968183_417390456.0DomainNR LBD
TgeneRARBchr12:21790005chr3:25637911ENST0000043704268183_417271337.0DomainNR LBD
TgeneRARBchr12:21790005chr3:25637911ENST0000045864668183_417271337.0DomainNR LBD
TgeneRARBchr12:21790005chr3:25637911ENST0000033068868154_182383449.0RegionNote=Hinge
TgeneRARBchr12:21790005chr3:25637911ENST00000330688681_87383449.0RegionNote=Modulating
TgeneRARBchr12:21790005chr3:25637911ENST0000040496968154_182390456.0RegionNote=Hinge
TgeneRARBchr12:21790005chr3:25637911ENST00000404969681_87390456.0RegionNote=Modulating
TgeneRARBchr12:21790005chr3:25637911ENST0000043704268154_182271337.0RegionNote=Hinge
TgeneRARBchr12:21790005chr3:25637911ENST00000437042681_87271337.0RegionNote=Modulating
TgeneRARBchr12:21790005chr3:25637911ENST0000045864668154_182271337.0RegionNote=Hinge
TgeneRARBchr12:21790005chr3:25637911ENST00000458646681_87271337.0RegionNote=Modulating
TgeneRARBchr12:21790005chr3:25637911ENST0000033068868124_148383449.0Zinc fingerNR C4-type
TgeneRARBchr12:21790005chr3:25637911ENST000003306886888_108383449.0Zinc fingerNR C4-type
TgeneRARBchr12:21790005chr3:25637911ENST0000040496968124_148390456.0Zinc fingerNR C4-type
TgeneRARBchr12:21790005chr3:25637911ENST000004049696888_108390456.0Zinc fingerNR C4-type
TgeneRARBchr12:21790005chr3:25637911ENST0000043704268124_148271337.0Zinc fingerNR C4-type
TgeneRARBchr12:21790005chr3:25637911ENST000004370426888_108271337.0Zinc fingerNR C4-type
TgeneRARBchr12:21790005chr3:25637911ENST0000045864668124_148271337.0Zinc fingerNR C4-type
TgeneRARBchr12:21790005chr3:25637911ENST000004586466888_108271337.0Zinc fingerNR C4-type


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Fusion Gene Sequence for LDHB-RARB


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.
>44346_44346_1_LDHB-RARB_LDHB_chr12_21790005_ENST00000396076_RARB_chr3_25637911_ENST00000404969_length(transcript)=1367nt_BP=1170nt
TCCGCACGACTGTTACAGAGGTCTCCAGAGCCTTCTCTCTCCTGGTAGGTTTCGGCTCAGGACCCTGAATCCTGGCCCACAGGCAAGCCT
GATGGGACGTGCGGGGTAGTACTTGTATGGGGAGACGCGGGAAGGAGGAAGAAGCACATCTGTCCTCCGCGGCCTTTAGCTCTGAGCATC
CGGCCGCGGGCCCTGACTTTGCCGCTCAGTTTGGGGCGCAGGGGGGGCCGTGCCCTGGCGGAGGAGCAGAAGGCAGAGGGTAGCAGCTGC
GGCTCAGCGGAGAGACTTGTTGCATTTGCAGCTAAAACCAGGCCCTACTTGTCCTTGTGCAAAATGGCAACTCTTAAGGAAAAACTCATT
GCACCAGTTGCGGAAGAAGAGGCAACAGTTCCAAACAATAAGATCACTGTAGTGGGTGTTGGACAAGTTGGTATGGCGTGTGCTATCAGC
ATTCTGGGAAAGTCTCTGGCTGATGAACTTGCTCTTGTGGATGTTTTGGAAGATAAGCTTAAAGGAGAAATGATGGATCTGCAGCATGGG
AGCTTATTTCTTCAGACACCTAAAATTGTGGCAGATAAAGATTATTCTGTGACTGCCAATTCTAAGATTGTAGTGGTAACTGCAGGAGTC
CGTCAGCAAGAAGGGGAGAGTCGGCTCAATCTGGTGCAGAGAAATGTTAATGTCTTCAAATTCATTATTCCTCAGATCGTCAAGTACAGT
CCTGATTGCATCATAATTGTGGTTTCCAACCCAGTGGACATTCTTACGTATGTTACCTGGAAACTAAGTGGATTACCCAAACACCGCGTG
ATTGGAAGTGGATGTAATCTGGATTCTGCTAGATTTCGCTACCTTATGGCTGAAAAACTTGGCATTCATCCCAGCAGCTGCCATGGATGG
ATTTTGGGGGAACATGGCGACTCAAGTGTGGCTGTGTGGAGTGGTGTGAATGTGGCAGGTGTTTCTCTCCAGGAATTGAATCCAGAAATG
GGAACTGACAATGATAGTGAAAATTGGAAGGAAGTGCATAAGATGGTGGTTGAAAGTGCCTATGAAGTCATCAAGCTAAAAGGATATACC
AACTGGGCTATTGGATTAAGTGTGGCTGATCTTATTGAATCCATGTTGAAAAATCTATCCAGGATTCATCCCGTGTCAACAATGGTAAAG
GTGCAGAGCGTGTAATTACCTTGAAAATGGAAATTCCTGGATCAATGCCACCTCTCATTCAAGAAATGCTGGAGAATTCTGAAGGACATG
AACCCTTGACCCCAAGTTCAAGTGGGAACACAGCAGAGCACAGTCCTAGCATCTCACCCAGCTCAGTGGAAAACAGTGGGGTCAGTCAGT

>44346_44346_1_LDHB-RARB_LDHB_chr12_21790005_ENST00000396076_RARB_chr3_25637911_ENST00000404969_length(amino acids)=337AA_BP=
MSIRPRALTLPLSLGRRGGRALAEEQKAEGSSCGSAERLVAFAAKTRPYLSLCKMATLKEKLIAPVAEEEATVPNNKITVVGVGQVGMAC
AISILGKSLADELALVDVLEDKLKGEMMDLQHGSLFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIV
KYSPDCIIIVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVAGVSLQELN

--------------------------------------------------------------

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Fusion Gene PPI Analysis for LDHB-RARB


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 LDHB-RARB


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 LDHB-RARB


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