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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:LARP1B-C4orf29 (FusionGDB2 ID:44113)

Fusion Gene Summary for LARP1B-C4orf29

check button Fusion gene summary
Fusion gene informationFusion gene name: LARP1B-C4orf29
Fusion gene ID: 44113
HgeneTgene
Gene symbol

LARP1B

C4orf29

Gene ID

55132

80167

Gene nameLa ribonucleoprotein 1Babhydrolase domain containing 18
SynonymsLARP2C4orf29
Cytomap

4q28.2

4q28.2

Type of geneprotein-codingprotein-coding
Descriptionla-related protein 1BLa ribonucleoprotein domain family member 1BLa ribonucleoprotein domain family, member 2la-related protein 2protein ABHD18abhydrolase domain-containing protein 18alpha/beta hydrolase domain-containing protein 18
Modification date2020031320200313
UniProtAcc

Q659C4

.
Ensembl transtripts involved in fusion geneENST00000264584, ENST00000326639, 
ENST00000394288, ENST00000427266, 
ENST00000432347, ENST00000441387, 
ENST00000512292, ENST00000354456, 
ENST00000506199, 		ENST00000388795, 
ENST00000398965, ENST00000444616, 
Fusion gene scores* DoF score10 X 10 X 4=4002 X 2 X 2=8
# samples 112
** MAII scorelog2(11/400*10)=-1.86249647625006
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(2/8*10)=1.32192809488736
Context

PubMed: LARP1B [Title/Abstract] AND C4orf29 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLARP1B(129012667)-C4orf29(128956917), # 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

check buttonFusion gene breakpoints across LARP1B (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 C4orf29 (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
ChimerDB4BLCATCGA-XF-A9SP-01ALARP1Bchr4

129012667

-C4orf29chr4

128956917

+


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Fusion Gene ORF analysis for LARP1B-C4orf29

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-intronENST00000264584ENST00000388795LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5CDS-intronENST00000264584ENST00000398965LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5CDS-intronENST00000264584ENST00000444616LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5CDS-intronENST00000326639ENST00000388795LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5CDS-intronENST00000326639ENST00000398965LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5CDS-intronENST00000326639ENST00000444616LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5CDS-intronENST00000394288ENST00000388795LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5CDS-intronENST00000394288ENST00000398965LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5CDS-intronENST00000394288ENST00000444616LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5CDS-intronENST00000427266ENST00000388795LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5CDS-intronENST00000427266ENST00000398965LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5CDS-intronENST00000427266ENST00000444616LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5CDS-intronENST00000432347ENST00000388795LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5CDS-intronENST00000432347ENST00000398965LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5CDS-intronENST00000432347ENST00000444616LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5CDS-intronENST00000441387ENST00000388795LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5CDS-intronENST00000441387ENST00000398965LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5CDS-intronENST00000441387ENST00000444616LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5CDS-intronENST00000512292ENST00000388795LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5CDS-intronENST00000512292ENST00000398965LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5CDS-intronENST00000512292ENST00000444616LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5UTR-intronENST00000354456ENST00000388795LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5UTR-intronENST00000354456ENST00000398965LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
5UTR-intronENST00000354456ENST00000444616LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
intron-intronENST00000506199ENST00000388795LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
intron-intronENST00000506199ENST00000398965LARP1Bchr4

129012667

-C4orf29chr4

128956917

+
intron-intronENST00000506199ENST00000444616LARP1Bchr4

129012667

-C4orf29chr4

128956917

+

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 LARP1B-C4orf29


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 LARP1B-C4orf29


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/:129012667/:128956917)
- 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
LARP1B

Q659C4

.
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 LARP1B-C4orf29


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 LARP1B-C4orf29


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 LARP1B-C4orf29


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 LARP1B-C4orf29


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