Fusion Gene Studies
in Kim Lab

FusionBase FusionGDB FusionGDB2 FusionPDB FusionNeoAntigen FusionAI FusionNW FGviewer Publication Contact
FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:LRRFIP1-GNB1 (FusionGDB2 ID:HG9208TG2782)

Fusion Gene Summary for LRRFIP1-GNB1

check button Fusion gene summary
Fusion gene informationFusion gene name: LRRFIP1-GNB1
Fusion gene ID: hg9208tg2782
HgeneTgene
Gene symbol

LRRFIP1

GNB1

Gene ID

9208

2782

Gene nameLRR binding FLII interacting protein 1G protein subunit beta 1
SynonymsFLAP-1|FLAP1|FLIIAP1|GCF-2|GCF2|HUFI-1|TRIPMRD42
Cytomap('LRRFIP1')('GNB1')

2q37.3

1p36.33

Type of geneprotein-codingprotein-coding
Descriptionleucine-rich repeat flightless-interacting protein 1GC-binding factor 2LRR FLII-interacting protein 1NEDD8-conjugating enzymeTAR RNA-interacting proteinleucine rich repeat (in FLII) interacting protein 1guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1beta subunit, signal-transducing proteins GS/GIguanine nucleotide binding protein (G protein), beta polypeptide 1testicular tissue protein Li 72transducin beta chain 1
Modification date2020031320200321
UniProtAcc.

P62873

Ensembl transtripts involved in fusion geneENST00000308482, ENST00000244815, 
ENST00000289175, ENST00000392000, 
ENST00000468950, 
Fusion gene scores* DoF score16 X 12 X 9=172839 X 29 X 13=14703
# samples 2048
** MAII scorelog2(20/1728*10)=-3.11103131238874
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(48/14703*10)=-4.93693233652239
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LRRFIP1 [Title/Abstract] AND GNB1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLRRFIP1(238536383)-GNB1(1749314), # samples:1
Anticipated loss of major functional domain due to fusion event.LRRFIP1-GNB1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
LRRFIP1-GNB1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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
HgeneLRRFIP1

GO:0000122

negative regulation of transcription by RNA polymerase II

14522076


check buttonFusion gene breakpoints across LRRFIP1 (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 GNB1 (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
ChimerDB4STADTCGA-HU-A4GY-01ALRRFIP1chr2

238536383

+GNB1chr1

1749314

-


Top

Fusion Gene ORF analysis for LRRFIP1-GNB1

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-intronENST00000308482ENST00000472614LRRFIP1chr2

238536383

+GNB1chr1

1749314

-
In-frameENST00000308482ENST00000378609LRRFIP1chr2

238536383

+GNB1chr1

1749314

-
intron-3CDSENST00000244815ENST00000378609LRRFIP1chr2

238536383

+GNB1chr1

1749314

-
intron-3CDSENST00000289175ENST00000378609LRRFIP1chr2

238536383

+GNB1chr1

1749314

-
intron-3CDSENST00000392000ENST00000378609LRRFIP1chr2

238536383

+GNB1chr1

1749314

-
intron-3CDSENST00000468950ENST00000378609LRRFIP1chr2

238536383

+GNB1chr1

1749314

-
intron-intronENST00000244815ENST00000472614LRRFIP1chr2

238536383

+GNB1chr1

1749314

-
intron-intronENST00000289175ENST00000472614LRRFIP1chr2

238536383

+GNB1chr1

1749314

-
intron-intronENST00000392000ENST00000472614LRRFIP1chr2

238536383

+GNB1chr1

1749314

-
intron-intronENST00000468950ENST00000472614LRRFIP1chr2

238536383

+GNB1chr1

1749314

-

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)
ENST00000308482LRRFIP1chr2238536383+ENST00000378609GNB1chr11749314-2904165271130367

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
ENST00000308482ENST00000378609LRRFIP1chr2238536383+GNB1chr11749314-0.0013149390.99868506

Top

Fusion Genomic Features for LRRFIP1-GNB1


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

Top

Fusion Protein Features for LRRFIP1-GNB1


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/chr2:238536383/chr1:1749314)
- 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
.GNB1

P62873

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: Guanine nucleotide-binding proteins (G proteins) are involved as a modulator or transducer in various transmembrane signaling systems. The beta and gamma chains are required for the GTPase activity, for replacement of GDP by GTP, and for G protein-effector interaction.

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
TgeneGNB1chr2:238536383chr1:1749314ENST00000378609212141_17019872.3333333333334RepeatNote=WD 3
TgeneGNB1chr2:238536383chr1:1749314ENST00000378609212182_21219872.3333333333334RepeatNote=WD 4
TgeneGNB1chr2:238536383chr1:1749314ENST00000378609212224_25419872.3333333333334RepeatNote=WD 5
TgeneGNB1chr2:238536383chr1:1749314ENST00000378609212268_29819872.3333333333334RepeatNote=WD 6
TgeneGNB1chr2:238536383chr1:1749314ENST00000378609212310_34019872.3333333333334RepeatNote=WD 7
TgeneGNB1chr2:238536383chr1:1749314ENST0000037860921253_8319872.3333333333334RepeatNote=WD 1
TgeneGNB1chr2:238536383chr1:1749314ENST0000037860921295_12519872.3333333333334RepeatNote=WD 2

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneLRRFIP1chr2:238536383chr1:1749314ENST00000244815+110128_2500785.0Coiled coilOntology_term=ECO:0000269
HgeneLRRFIP1chr2:238536383chr1:1749314ENST00000289175+18128_2500753.0Coiled coilOntology_term=ECO:0000269
HgeneLRRFIP1chr2:238536383chr1:1749314ENST00000308482+124128_25032641.0Coiled coilOntology_term=ECO:0000269
HgeneLRRFIP1chr2:238536383chr1:1749314ENST00000392000+111128_2500809.0Coiled coilOntology_term=ECO:0000269
HgeneLRRFIP1chr2:238536383chr1:1749314ENST00000244815+110567_5930785.0Compositional biasNote=Lys-rich
HgeneLRRFIP1chr2:238536383chr1:1749314ENST00000289175+18567_5930753.0Compositional biasNote=Lys-rich
HgeneLRRFIP1chr2:238536383chr1:1749314ENST00000308482+124567_59332641.0Compositional biasNote=Lys-rich
HgeneLRRFIP1chr2:238536383chr1:1749314ENST00000392000+111567_5930809.0Compositional biasNote=Lys-rich
HgeneLRRFIP1chr2:238536383chr1:1749314ENST00000244815+110485_5840785.0RegionNote=DNA-binding
HgeneLRRFIP1chr2:238536383chr1:1749314ENST00000289175+18485_5840753.0RegionNote=DNA-binding
HgeneLRRFIP1chr2:238536383chr1:1749314ENST00000308482+124485_58432641.0RegionNote=DNA-binding
HgeneLRRFIP1chr2:238536383chr1:1749314ENST00000392000+111485_5840809.0RegionNote=DNA-binding


Top

Fusion Gene Sequence for LRRFIP1-GNB1


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.
>50077_50077_1_LRRFIP1-GNB1_LRRFIP1_chr2_238536383_ENST00000308482_GNB1_chr1_1749314_ENST00000378609_length(transcript)=2904nt_BP=165nt
GGGGCCGGGCCGGGGCGGCGCGAGCGGCTGGAGCAACGGGCCCCGCGGCAGCTGCGGGCGACGCGGTCGATGGACATGGGCACCCAGGGA
TCGGGGCGCAAGCGGCTCCCCAACCGGGAGCGGCTCACGGCGGAGGACGACGCGCTCAACCAGATCGCGCGGGAGGACGCCAGGAAAGCA
TGTGCAGATGCAACTCTCTCTCAGATCACAAACAACATCGACCCAGTGGGAAGAATCCAAATGCGCACGAGGAGGACACTGCGGGGGCAC
CTGGCCAAGATCTACGCCATGCACTGGGGCACAGACTCCAGGCTTCTCGTCAGTGCCTCGCAGGATGGTAAACTTATCATCTGGGACAGC
TACACCACCAACAAGGTCCACGCCATCCCTCTGCGCTCCTCCTGGGTCATGACCTGTGCATATGCCCCTTCTGGGAACTATGTGGCCTGC
GGTGGCCTGGATAACATTTGCTCCATTTACAATCTGAAAACTCGTGAGGGGAACGTGCGCGTGAGTCGTGAGCTGGCAGGACACACAGGT
TACCTGTCCTGCTGCCGATTCCTGGATGACAATCAGATCGTCACCAGCTCTGGAGACACCACGTGTGCCCTGTGGGACATCGAGACCGGC
CAGCAGACGACCACGTTTACCGGACACACTGGAGATGTCATGAGCCTTTCTCTTGCTCCTGACACCAGACTGTTCGTCTCTGGTGCTTGT
GATGCTTCAGCCAAACTCTGGGATGTGCGAGAAGGCATGTGCCGGCAGACCTTCACTGGCCACGAGTCTGACATCAATGCCATTTGCTTC
TTTCCAAATGGCAATGCATTTGCCACTGGCTCAGACGACGCCACCTGCAGGCTGTTTGACCTTCGTGCTGACCAGGAGCTCATGACTTAC
TCCCATGACAACATCATCTGCGGGATCACCTCTGTCTCCTTCTCCAAGAGCGGGCGCCTCCTCCTTGCTGGGTACGACGACTTCAACTGC
AACGTCTGGGATGCACTCAAAGCCGACCGGGCAGGTGTCTTGGCTGGGCATGACAACCGCGTCAGCTGCCTGGGCGTGACTGACGATGGC
ATGGCTGTGGCGACAGGGTCCTGGGATAGCTTCCTCAAGATCTGGAACTAACGCCAGTAGCATGTGGATGCCATGGAGACTGGAAGACCA
TTCCAACTTGGACGCGTTACCATGAGAGCATATCCTATCCAACCGTACTAACGTGGACACCCTACACCTCCCCTCAGAACTTCAAAAGGG
CAAGATCTTTTTTCCTTCACTTATTGCTGAAACCAAGAGCACAATTCCCATTGAGAGAAAGATCTCTGTGCTGTAAACTAAAACAAATTG
TGCATTCCTTCCGGGGCCATCGTCTTTGTTTTCTTTTTTGTCTTGAATGAATTTTAAAAGGAAATATATAATAAAAATGTTAACCAGAAG
GTAAACTTGAGTGTAATTGTCAGACAGACACACTTTTCCACCAGTGTATTTGAATTTTAGACCAGTGACCCTGTTTTGTGGCATTCATGC
AAAACATGCTGAGGGCTTTGTTCATCTGGTCATCGTGTCCAAATTTCAGTCATGTTTGTAGCAAGATTTTGGAAGCATTCATATTTCCTT
TTTAAAATGTATTCCTTTGTGTTCAACAGTTAATCAAAACCAGAGAGTCTAGGGCAGCCTCTCTGATGTTGTCAATGATGTAAATTCAGT
CCCTGGTTTTTAATTTTCTGTCTGATGTCACAGATCATTGTTGCACACAAACGTGGCATAGAAAAGAACATGTTCAGAAGCCATGGGGCC
AAGCACATGCGGGGACGGTCTCAAATGCGTGATCAGAGAATCCTTCACCTTTGCTGAAAAGTGAGCTCAGATCCAGCACCATGTTCCTCC
TGACCCATCCTGTCTATCTTCTCAGTTGAGTTTTTAATCTCACTTTGGGTTTCCTTGTGAAGTTGGAGGGAAGTTTATAATAGCCTAACA
CTACCCCACCCCCAACTAGGAGGAACCTCTGTTTTCAAGAGAGATGCCTGTCCTGTGCTTGGATAGTCAGTCAATTATTTGTGTATGAAA
CAATGTACAAATCAATGTTTTGAAAATAATGATCTCAGACTTTCTAAGTTAAATTTTAAAAATTTTGATTGTTTGCCATATTGGGTGGGT
TTACTCTTAGAATCGCATGCTGTAGAAATGCTCAAAAGTGCATATGGGACTCAGTCCTTAGGTGTTCTTTTTCTTTTAAGAAATAACCTC
TTACAGTTGTAACCATTGCGGCTCTGTCCACTTCTCGTTGCTGCTCTGTGGCACATATCGGAAGCAGTACAGCGCGCGGCTCTACACGCT
TGGGTAGCGGGATAAGTCACTGTTTTCTTTATTTCTTTAAAAAAAAAAAAGTTCTGTTGCAAACGACTGCTGTTGGATTCTGAGGGTGGG
GAGGGAGAGAGAGGGAGGGAGAGGGAGTGAAGAGCCTGCCCTCCTATATGGATTCTTCAGGGCCCTCCACATCTGAGGTGGCTCATTCCC
ATCACACACAGATTGTCCTGGTGTTCATTTCAAGGCCAGTGTTCAGCAGCAGCGTTTGGAAAGCAGGTTCTGTGGGACCCCCCGCCCCGC
CCCCCGCACTCCTTCATAGCAGCAGTAGTGGCTTCTCCATCCTGTTTTCTGCAACATTCTATACAAAACTGTGCTGTGACCTTGCGGTAG
GCCTGGATCTGGCAAAGAGAATACAAATGAAACCCCTTCTTTCTCTTTCCGTCCAACAACTCTGTAGAGCTCTCTGCACCCTTACCCCTT
TCCACCTTTTGTATTTAATTTTAAAGTCAGTGTACTGCAAGGAAGCTGGATGCAAGATAGATACTATATTAAACTGTACTGTTATTTAAG

>50077_50077_1_LRRFIP1-GNB1_LRRFIP1_chr2_238536383_ENST00000308482_GNB1_chr1_1749314_ENST00000378609_length(amino acids)=367AA_BP=46
MEQRAPRQLRATRSMDMGTQGSGRKRLPNRERLTAEDDALNQIAREDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHW
GTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLD
DNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFAT
GSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWD

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

Top

Fusion Gene PPI Analysis for LRRFIP1-GNB1


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


Top

Related Drugs for LRRFIP1-GNB1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for LRRFIP1-GNB1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneLRRFIP1C0023893Liver Cirrhosis, Experimental1CTD_human
TgeneC4310774MENTAL RETARDATION, AUTOSOMAL DOMINANT 425CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0003469Anxiety Disorders1CTD_human
TgeneC0011573Endogenous depression1CTD_human
TgeneC0011581Depressive disorder1CTD_human
TgeneC0025193Melancholia1CTD_human
TgeneC0036572Seizures1GENOMICS_ENGLAND
TgeneC0041696Unipolar Depression1CTD_human
TgeneC0086133Depressive Syndrome1CTD_human
TgeneC0282126Depression, Neurotic1CTD_human
TgeneC0376280Anxiety States, Neurotic1CTD_human
TgeneC0424605Developmental delay (disorder)1GENOMICS_ENGLAND
TgeneC0557874Global developmental delay1GENOMICS_ENGLAND
TgeneC1279420Anxiety neurosis (finding)1CTD_human
TgeneC3714756Intellectual Disability1GENOMICS_ENGLAND