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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:INTU-LARP1B (FusionGDB2 ID:40001)

Fusion Gene Summary for INTU-LARP1B

check button Fusion gene summary
Fusion gene informationFusion gene name: INTU-LARP1B
Fusion gene ID: 40001
HgeneTgene
Gene symbol

INTU

LARP1B

Gene ID

27152

55132

Gene nameinturned planar cell polarity proteinLa ribonucleoprotein 1B
SynonymsCPLANE4|INT|OFD17|PDZD6|PDZK6|SRTD20LARP2
Cytomap

4q28.1

4q28.2

Type of geneprotein-codingprotein-coding
Descriptionprotein inturnedPDZ domain containing 6PDZ domain-containing protein 6ciliogenesis and planar polarity effector 4homolog of inturnedinturned planar cell polarity effector homologla-related protein 1BLa ribonucleoprotein domain family member 1BLa ribonucleoprotein domain family, member 2la-related protein 2
Modification date2020032720200313
UniProtAcc

Q9ULD6

Q659C4

Ensembl transtripts involved in fusion geneENST00000335251, ENST00000296461, 
ENST00000512995, 		ENST00000264584, 
ENST00000326639, ENST00000354456, 
ENST00000394288, ENST00000427266, 
ENST00000432347, ENST00000441387, 
ENST00000506199, ENST00000512292, 
Fusion gene scores* DoF score1 X 1 X 1=112 X 15 X 3=540
# samples 114
** MAII scorelog2(1/1*10)=3.32192809488736log2(14/540*10)=-1.94753258010586
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

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

Most frequent breakpointINTU(128627992)-LARP1B(129011057), # samples:1
LARP1B(129017950)-INTU(128619391), # 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 INTU (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 LARP1B (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/AEC564330INTUchr4

128627992

+LARP1Bchr4

129011057

+


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Fusion Gene ORF analysis for INTU-LARP1B

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-intronENST00000335251ENST00000264584INTUchr4

128627992

+LARP1Bchr4

129011057

+
5CDS-intronENST00000335251ENST00000326639INTUchr4

128627992

+LARP1Bchr4

129011057

+
5CDS-intronENST00000335251ENST00000354456INTUchr4

128627992

+LARP1Bchr4

129011057

+
5CDS-intronENST00000335251ENST00000394288INTUchr4

128627992

+LARP1Bchr4

129011057

+
5CDS-intronENST00000335251ENST00000427266INTUchr4

128627992

+LARP1Bchr4

129011057

+
5CDS-intronENST00000335251ENST00000432347INTUchr4

128627992

+LARP1Bchr4

129011057

+
5CDS-intronENST00000335251ENST00000441387INTUchr4

128627992

+LARP1Bchr4

129011057

+
5CDS-intronENST00000335251ENST00000506199INTUchr4

128627992

+LARP1Bchr4

129011057

+
5CDS-intronENST00000335251ENST00000512292INTUchr4

128627992

+LARP1Bchr4

129011057

+
intron-intronENST00000296461ENST00000264584INTUchr4

128627992

+LARP1Bchr4

129011057

+
intron-intronENST00000296461ENST00000326639INTUchr4

128627992

+LARP1Bchr4

129011057

+
intron-intronENST00000296461ENST00000354456INTUchr4

128627992

+LARP1Bchr4

129011057

+
intron-intronENST00000296461ENST00000394288INTUchr4

128627992

+LARP1Bchr4

129011057

+
intron-intronENST00000296461ENST00000427266INTUchr4

128627992

+LARP1Bchr4

129011057

+
intron-intronENST00000296461ENST00000432347INTUchr4

128627992

+LARP1Bchr4

129011057

+
intron-intronENST00000296461ENST00000441387INTUchr4

128627992

+LARP1Bchr4

129011057

+
intron-intronENST00000296461ENST00000506199INTUchr4

128627992

+LARP1Bchr4

129011057

+
intron-intronENST00000296461ENST00000512292INTUchr4

128627992

+LARP1Bchr4

129011057

+
intron-intronENST00000512995ENST00000264584INTUchr4

128627992

+LARP1Bchr4

129011057

+
intron-intronENST00000512995ENST00000326639INTUchr4

128627992

+LARP1Bchr4

129011057

+
intron-intronENST00000512995ENST00000354456INTUchr4

128627992

+LARP1Bchr4

129011057

+
intron-intronENST00000512995ENST00000394288INTUchr4

128627992

+LARP1Bchr4

129011057

+
intron-intronENST00000512995ENST00000427266INTUchr4

128627992

+LARP1Bchr4

129011057

+
intron-intronENST00000512995ENST00000432347INTUchr4

128627992

+LARP1Bchr4

129011057

+
intron-intronENST00000512995ENST00000441387INTUchr4

128627992

+LARP1Bchr4

129011057

+
intron-intronENST00000512995ENST00000506199INTUchr4

128627992

+LARP1Bchr4

129011057

+
intron-intronENST00000512995ENST00000512292INTUchr4

128627992

+LARP1Bchr4

129011057

+

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 INTU-LARP1B


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 INTU-LARP1B


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/:128627992/:129011057)
- 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
INTU

Q9ULD6

LARP1B

Q659C4

FUNCTION: Plays a key role in ciliogenesis and embryonic development. Regulator of cilia formation by controlling the organization of the apical actin cytoskeleton and the positioning of the basal bodies at the apical cell surface, which in turn is essential for the normal orientation of elongating ciliary microtubules. Plays a key role in definition of cell polarity via its role in ciliogenesis but not via conversion extension. Has an indirect effect on hedgehog signaling (By similarity). Proposed to function as core component of the CPLANE (ciliogenesis and planar polarity effectors) complex involved in the recruitment of peripheral IFT-A proteins to basal bodies (PubMed:27158779). {ECO:0000250|UniProtKB:Q059U7, ECO:0000250|UniProtKB:Q2I0E5, ECO:0000305|PubMed:27158779}.

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 INTU-LARP1B


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 INTU-LARP1B


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 INTU-LARP1B


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 INTU-LARP1B


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