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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:PITPNB-RFPL3S (FusionGDB2 ID:65572)

Fusion Gene Summary for PITPNB-RFPL3S

check button Fusion gene summary
Fusion gene informationFusion gene name: PITPNB-RFPL3S
Fusion gene ID: 65572
HgeneTgene
Gene symbol

PITPNB

RFPL3S

Gene ID

23760

10737

Gene namephosphatidylinositol transfer protein betaRFPL3 antisense
SynonymsPI-TP-beta|PtdInsTP|VIB1BNCRNA00005|RFPL3-AS|RFPL3-AS1|RFPL3ANT|RFPL3AS
Cytomap

22q12.1

22q12.3

Type of geneprotein-codingncRNA
Descriptionphosphatidylinositol transfer protein beta isoformPtdIns transfer protein betaphosphotidylinositol transfer protein, betaRFPL3 antisense RNA 1 (non-protein coding)non-protein coding RNA 5ret finger protein-like 3 antisense
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000320996, ENST00000335272, 
ENST00000455418, 
ENST00000461833, 
ENST00000382086, ENST00000382084, 
ENST00000400234, 
Fusion gene scores* DoF score9 X 7 X 5=3152 X 2 X 2=8
# samples 92
** MAII scorelog2(9/315*10)=-1.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/8*10)=1.32192809488736
Context

PubMed: PITPNB [Title/Abstract] AND RFPL3S [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPITPNB(28292540)-RFPL3S(32756826), # samples:2
Anticipated loss of major functional domain due to fusion event.PITPNB-RFPL3S seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene 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
HgenePITPNB

GO:0015914

phospholipid transport

16274224


check buttonFusion gene breakpoints across PITPNB (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 RFPL3S (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
ChimerDB4BLCATCGA-XF-AAMW-01APITPNBchr22

28292540

-RFPL3Schr22

32756826

-
ChimerDB4BLCATCGA-XF-AAMWPITPNBchr22

28292540

-RFPL3Schr22

32756826

-


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Fusion Gene ORF analysis for PITPNB-RFPL3S

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-5UTRENST00000320996ENST00000461833PITPNBchr22

28292540

-RFPL3Schr22

32756826

-
5CDS-5UTRENST00000335272ENST00000461833PITPNBchr22

28292540

-RFPL3Schr22

32756826

-
5CDS-5UTRENST00000455418ENST00000461833PITPNBchr22

28292540

-RFPL3Schr22

32756826

-
5CDS-intronENST00000320996ENST00000382086PITPNBchr22

28292540

-RFPL3Schr22

32756826

-
5CDS-intronENST00000335272ENST00000382086PITPNBchr22

28292540

-RFPL3Schr22

32756826

-
5CDS-intronENST00000455418ENST00000382086PITPNBchr22

28292540

-RFPL3Schr22

32756826

-
Frame-shiftENST00000320996ENST00000382084PITPNBchr22

28292540

-RFPL3Schr22

32756826

-
Frame-shiftENST00000335272ENST00000382084PITPNBchr22

28292540

-RFPL3Schr22

32756826

-
Frame-shiftENST00000455418ENST00000382084PITPNBchr22

28292540

-RFPL3Schr22

32756826

-
In-frameENST00000320996ENST00000400234PITPNBchr22

28292540

-RFPL3Schr22

32756826

-
In-frameENST00000335272ENST00000400234PITPNBchr22

28292540

-RFPL3Schr22

32756826

-
In-frameENST00000455418ENST00000400234PITPNBchr22

28292540

-RFPL3Schr22

32756826

-

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)
ENST00000335272PITPNBchr2228292540-ENST00000400234RFPL3Schr2232756826-13834491163456235
ENST00000320996PITPNBchr2228292540-ENST00000400234RFPL3Schr2232756826-13704361150443235
ENST00000455418PITPNBchr2228292540-ENST00000400234RFPL3Schr2232756826-13123781092385235

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
ENST00000335272ENST00000400234PITPNBchr2228292540-RFPL3Schr2232756826-0.0043270310.9956729
ENST00000320996ENST00000400234PITPNBchr2228292540-RFPL3Schr2232756826-0.0031820130.99681795
ENST00000455418ENST00000400234PITPNBchr2228292540-RFPL3Schr2232756826-0.0112371360.9887629

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Fusion Genomic Features for PITPNB-RFPL3S


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.
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.

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Fusion Protein Features for PITPNB-RFPL3S


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/chr22:28292540/chr22:32756826)
- 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

- 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 PITPNB-RFPL3S


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.
>65572_65572_1_PITPNB-RFPL3S_PITPNB_chr22_28292540_ENST00000320996_RFPL3S_chr22_32756826_ENST00000400234_length(transcript)=1370nt_BP=436nt
TGAGAGGCGGTAGCGGCGGCGGCGGCGGTGGTATCGGCGGCAGCTGTGAGGGGGTTCCGGGAAGATGGTGCTGATCAAGGAATTCCGTGT
GGTTTTGCCATGTTCTGTTCAGGAGTATCAGGTTGGGCAGCTTTACTCTGTTGCAGAAGCTAGTAAGAATGAGACTGGTGGTGGAGAAGG
AATTGAAGTCTTAAAGAATGAACCTTATGAGAAGGATGGAGAAAAGGGACAGTATACGCACAAAATTTATCACCTAAAGAGCAAAGTGCC
TGCATTCGTGAGGATGATTGCTCCCGAGGGCTCCTTGGTGTTTCATGAGAAAGCCTGGAATGCGTACCCCTACTGTAGAACAATTGTAAC
GAATGAATATATGAAAGATGATTTCTTCATTAAAATCGAAACATGGCACAAACCAGACTTGGGAACATTAGAAAATTGGCGGCTTATTTG
GCCTCCCCAGGACGGACTGGAGCATCAGTAGTGCCTGAGTTCATCAAAGGACAGATGCTCAAGACACCTTGATCACCATTAGGTGGAATT
GAAGGAGCCAAAAATGGGCGCAGTGGCTCCTCAGCAGAGACGCTCCTGAATGTATAGACATGGGAACCACTTTCAGCATCAAAAAAGGAA
ACGTTCTGCATGCCCATATCCAGAAAAATCCCCACTCGCTGTAACTTGCGGTCTACTAAGAGGAAAGTCAGCGGCACCGTGCTGGCAGAG
AGGCGGCTTCCATCCCTCAAACTCACAGTCCAGAATCCAAGCTCTGTGGTCAGCTGGATCTTCCCTTTGCAGTGAACAGATTCTCTGCAG
ACTCCCAGGTCCCATTCTGTGCTTGTTCCCACGTCCACCTCCCAGTAGTGGCGGCCACAGGTAAAGCGAGGGGAGCCCAGGATGCAAACG
GACACGTCAAATCTCTCGGCAAGGTCTTGCCGATTCTGTGTGATGAGCCCACTTCGGACGCTCCTGAGGTCGTCAGAAATGAGGAGGAAG
TTGTTGGCTGTGTCGGCATCCAAGGTCATATCCACTGTGAAAAGGAAAACAAGTTGCTCAGCAAGTGGACAGAAGCCAACCCCATGCCTC
TCTTCTACTTCAAAGGCCCAAATATCTCCTGACTTTAGTTTCTTTAATTCTGTTTCTTCCTCCAAAATCAAAACTTTTCATGAGGAAACT
TCCCTATTTCAAATTTTCATAGGTATGCTTTGTGGCAATACGTGACTCTTATTCACAGTAGCAATTCTTATTTTACTTTACGTCACGTGT
TTGCTTCACTGAACTTTTCTTCATTTAGAGTGGAGGGTCTCTGAAGGCAGACACCATGCCCCCCTTTCTACCACCTTGATGTGTGAACAA

>65572_65572_1_PITPNB-RFPL3S_PITPNB_chr22_28292540_ENST00000320996_RFPL3S_chr22_32756826_ENST00000400234_length(amino acids)=235AA_BP=
MILEEETELKKLKSGDIWAFEVEERHGVGFCPLAEQLVFLFTVDMTLDADTANNFLLISDDLRSVRSGLITQNRQDLAERFDVSVCILGS
PRFTCGRHYWEVDVGTSTEWDLGVCRESVHCKGKIQLTTELGFWTVSLRDGSRLSASTVPLTFLLVDRKLQRVGIFLDMGMQNVSFFDAE

--------------------------------------------------------------
>65572_65572_2_PITPNB-RFPL3S_PITPNB_chr22_28292540_ENST00000335272_RFPL3S_chr22_32756826_ENST00000400234_length(transcript)=1383nt_BP=449nt
CGCGCAGGCGCTGTGAGAGGCGGTAGCGGCGGCGGCGGCGGTGGTATCGGCGGCAGCTGTGAGGGGGTTCCGGGAAGATGGTGCTGATCA
AGGAATTCCGTGTGGTTTTGCCATGTTCTGTTCAGGAGTATCAGGTTGGGCAGCTTTACTCTGTTGCAGAAGCTAGTAAGAATGAGACTG
GTGGTGGAGAAGGAATTGAAGTCTTAAAGAATGAACCTTATGAGAAGGATGGAGAAAAGGGACAGTATACGCACAAAATTTATCACCTAA
AGAGCAAAGTGCCTGCATTCGTGAGGATGATTGCTCCCGAGGGCTCCTTGGTGTTTCATGAGAAAGCCTGGAATGCGTACCCCTACTGTA
GAACAATTGTAACGAATGAATATATGAAAGATGATTTCTTCATTAAAATCGAAACATGGCACAAACCAGACTTGGGAACATTAGAAAATT
GGCGGCTTATTTGGCCTCCCCAGGACGGACTGGAGCATCAGTAGTGCCTGAGTTCATCAAAGGACAGATGCTCAAGACACCTTGATCACC
ATTAGGTGGAATTGAAGGAGCCAAAAATGGGCGCAGTGGCTCCTCAGCAGAGACGCTCCTGAATGTATAGACATGGGAACCACTTTCAGC
ATCAAAAAAGGAAACGTTCTGCATGCCCATATCCAGAAAAATCCCCACTCGCTGTAACTTGCGGTCTACTAAGAGGAAAGTCAGCGGCAC
CGTGCTGGCAGAGAGGCGGCTTCCATCCCTCAAACTCACAGTCCAGAATCCAAGCTCTGTGGTCAGCTGGATCTTCCCTTTGCAGTGAAC
AGATTCTCTGCAGACTCCCAGGTCCCATTCTGTGCTTGTTCCCACGTCCACCTCCCAGTAGTGGCGGCCACAGGTAAAGCGAGGGGAGCC
CAGGATGCAAACGGACACGTCAAATCTCTCGGCAAGGTCTTGCCGATTCTGTGTGATGAGCCCACTTCGGACGCTCCTGAGGTCGTCAGA
AATGAGGAGGAAGTTGTTGGCTGTGTCGGCATCCAAGGTCATATCCACTGTGAAAAGGAAAACAAGTTGCTCAGCAAGTGGACAGAAGCC
AACCCCATGCCTCTCTTCTACTTCAAAGGCCCAAATATCTCCTGACTTTAGTTTCTTTAATTCTGTTTCTTCCTCCAAAATCAAAACTTT
TCATGAGGAAACTTCCCTATTTCAAATTTTCATAGGTATGCTTTGTGGCAATACGTGACTCTTATTCACAGTAGCAATTCTTATTTTACT
TTACGTCACGTGTTTGCTTCACTGAACTTTTCTTCATTTAGAGTGGAGGGTCTCTGAAGGCAGACACCATGCCCCCCTTTCTACCACCTT

>65572_65572_2_PITPNB-RFPL3S_PITPNB_chr22_28292540_ENST00000335272_RFPL3S_chr22_32756826_ENST00000400234_length(amino acids)=235AA_BP=
MILEEETELKKLKSGDIWAFEVEERHGVGFCPLAEQLVFLFTVDMTLDADTANNFLLISDDLRSVRSGLITQNRQDLAERFDVSVCILGS
PRFTCGRHYWEVDVGTSTEWDLGVCRESVHCKGKIQLTTELGFWTVSLRDGSRLSASTVPLTFLLVDRKLQRVGIFLDMGMQNVSFFDAE

--------------------------------------------------------------
>65572_65572_3_PITPNB-RFPL3S_PITPNB_chr22_28292540_ENST00000455418_RFPL3S_chr22_32756826_ENST00000400234_length(transcript)=1312nt_BP=378nt
ATGGGAGATTTGTTGATGGAGAAGTGCCGTGTGGTTTTGCCATGTTCTGTTCAGGAGTATCAGGTTGGGCAGCTTTACTCTGTTGCAGAA
GCTAGTAAGAATGAGACTGGTGGTGGAGAAGGAATTGAAGTCTTAAAGAATGAACCTTATGAGAAGGATGGAGAAAAGGGACAGTATACG
CACAAAATTTATCACCTAAAGAGCAAAGTGCCTGCATTCGTGAGGATGATTGCTCCCGAGGGCTCCTTGGTGTTTCATGAGAAAGCCTGG
AATGCGTACCCCTACTGTAGAACAATTGTAACGAATGAATATATGAAAGATGATTTCTTCATTAAAATCGAAACATGGCACAAACCAGAC
TTGGGAACATTAGAAAATTGGCGGCTTATTTGGCCTCCCCAGGACGGACTGGAGCATCAGTAGTGCCTGAGTTCATCAAAGGACAGATGC
TCAAGACACCTTGATCACCATTAGGTGGAATTGAAGGAGCCAAAAATGGGCGCAGTGGCTCCTCAGCAGAGACGCTCCTGAATGTATAGA
CATGGGAACCACTTTCAGCATCAAAAAAGGAAACGTTCTGCATGCCCATATCCAGAAAAATCCCCACTCGCTGTAACTTGCGGTCTACTA
AGAGGAAAGTCAGCGGCACCGTGCTGGCAGAGAGGCGGCTTCCATCCCTCAAACTCACAGTCCAGAATCCAAGCTCTGTGGTCAGCTGGA
TCTTCCCTTTGCAGTGAACAGATTCTCTGCAGACTCCCAGGTCCCATTCTGTGCTTGTTCCCACGTCCACCTCCCAGTAGTGGCGGCCAC
AGGTAAAGCGAGGGGAGCCCAGGATGCAAACGGACACGTCAAATCTCTCGGCAAGGTCTTGCCGATTCTGTGTGATGAGCCCACTTCGGA
CGCTCCTGAGGTCGTCAGAAATGAGGAGGAAGTTGTTGGCTGTGTCGGCATCCAAGGTCATATCCACTGTGAAAAGGAAAACAAGTTGCT
CAGCAAGTGGACAGAAGCCAACCCCATGCCTCTCTTCTACTTCAAAGGCCCAAATATCTCCTGACTTTAGTTTCTTTAATTCTGTTTCTT
CCTCCAAAATCAAAACTTTTCATGAGGAAACTTCCCTATTTCAAATTTTCATAGGTATGCTTTGTGGCAATACGTGACTCTTATTCACAG
TAGCAATTCTTATTTTACTTTACGTCACGTGTTTGCTTCACTGAACTTTTCTTCATTTAGAGTGGAGGGTCTCTGAAGGCAGACACCATG

>65572_65572_3_PITPNB-RFPL3S_PITPNB_chr22_28292540_ENST00000455418_RFPL3S_chr22_32756826_ENST00000400234_length(amino acids)=235AA_BP=
MILEEETELKKLKSGDIWAFEVEERHGVGFCPLAEQLVFLFTVDMTLDADTANNFLLISDDLRSVRSGLITQNRQDLAERFDVSVCILGS
PRFTCGRHYWEVDVGTSTEWDLGVCRESVHCKGKIQLTTELGFWTVSLRDGSRLSASTVPLTFLLVDRKLQRVGIFLDMGMQNVSFFDAE

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

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Fusion Gene PPI Analysis for PITPNB-RFPL3S


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 PITPNB-RFPL3S


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 PITPNB-RFPL3S


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