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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:RIT1-NNMT (FusionGDB2 ID:74201)

Fusion Gene Summary for RIT1-NNMT

check button Fusion gene summary
Fusion gene informationFusion gene name: RIT1-NNMT
Fusion gene ID: 74201
HgeneTgene
Gene symbol

RIT1

NNMT

Gene ID

64919

4837

Gene nameBAF chromatin remodeling complex subunit BCL11Bnicotinamide N-methyltransferase
SynonymsATL1|ATL1-alpha|ATL1-beta|ATL1-delta|ATL1-gamma|CTIP-2|CTIP2|IDDFSTA|IMD49|RIT1|ZNF856B|hRIT1-alpha-
Cytomap

14q32.2

11q23.2

Type of geneprotein-codingprotein-coding
DescriptionB-cell lymphoma/leukemia 11BB cell CLL/lymphoma 11BB-cell CLL/lymphoma 11B (zinc finger protein)B-cell CLL/lymphoma 11B/T-cell receptor delta constant region fusion proteinB-cell lymphoma/leukaemia 11BBCL-11BBCL11B, BAF complex componentBCL11B/TRDCnicotinamide N-methyltransferase
Modification date2020031320200329
UniProtAcc.

P40261

Ensembl transtripts involved in fusion geneENST00000368322, ENST00000368323, 
ENST00000539040, 		ENST00000541754, 
ENST00000542647, ENST00000545255, 
ENST00000299964, ENST00000535185, 
ENST00000535401, 
Fusion gene scores* DoF score4 X 4 X 4=648 X 7 X 6=336
# samples 59
** MAII scorelog2(5/64*10)=-0.356143810225275
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/336*10)=-1.90046432644909
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RIT1 [Title/Abstract] AND NNMT [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRIT1(155874102)-NNMT(114182767), # samples:1
Anticipated loss of major functional domain due to fusion event.RIT1-NNMT seems lost the major protein functional domain in Tgene 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

check buttonFusion gene breakpoints across RIT1 (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 NNMT (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
ChimerDB4SARCTCGA-HB-A5W3-01ARIT1chr1

155874102

-NNMTchr11

114182767

+


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Fusion Gene ORF analysis for RIT1-NNMT

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-5UTRENST00000368322ENST00000541754RIT1chr1

155874102

-NNMTchr11

114182767

+
5CDS-5UTRENST00000368322ENST00000542647RIT1chr1

155874102

-NNMTchr11

114182767

+
5CDS-5UTRENST00000368322ENST00000545255RIT1chr1

155874102

-NNMTchr11

114182767

+
5CDS-5UTRENST00000368323ENST00000541754RIT1chr1

155874102

-NNMTchr11

114182767

+
5CDS-5UTRENST00000368323ENST00000542647RIT1chr1

155874102

-NNMTchr11

114182767

+
5CDS-5UTRENST00000368323ENST00000545255RIT1chr1

155874102

-NNMTchr11

114182767

+
5CDS-5UTRENST00000539040ENST00000541754RIT1chr1

155874102

-NNMTchr11

114182767

+
5CDS-5UTRENST00000539040ENST00000542647RIT1chr1

155874102

-NNMTchr11

114182767

+
5CDS-5UTRENST00000539040ENST00000545255RIT1chr1

155874102

-NNMTchr11

114182767

+
5CDS-intronENST00000368322ENST00000299964RIT1chr1

155874102

-NNMTchr11

114182767

+
5CDS-intronENST00000368322ENST00000535185RIT1chr1

155874102

-NNMTchr11

114182767

+
5CDS-intronENST00000368323ENST00000299964RIT1chr1

155874102

-NNMTchr11

114182767

+
5CDS-intronENST00000368323ENST00000535185RIT1chr1

155874102

-NNMTchr11

114182767

+
5CDS-intronENST00000539040ENST00000299964RIT1chr1

155874102

-NNMTchr11

114182767

+
5CDS-intronENST00000539040ENST00000535185RIT1chr1

155874102

-NNMTchr11

114182767

+
Frame-shiftENST00000368322ENST00000535401RIT1chr1

155874102

-NNMTchr11

114182767

+
Frame-shiftENST00000368323ENST00000535401RIT1chr1

155874102

-NNMTchr11

114182767

+
In-frameENST00000539040ENST00000535401RIT1chr1

155874102

-NNMTchr11

114182767

+

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)
ENST00000539040RIT1chr1155874102-ENST00000535401NNMTchr11114182767+1724483511915134

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
ENST00000539040ENST00000535401RIT1chr1155874102-NNMTchr11114182767+0.0071386820.99286133

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Fusion Genomic Features for RIT1-NNMT


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)
RIT1chr1155874101-NNMTchr11114182766+2.87E-121
RIT1chr1155874101-NNMTchr11114182766+2.87E-121

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 RIT1-NNMT


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/chr1:155874102/chr11:114182767)
- 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
.NNMT

P40261

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: Catalyzes the N-methylation of nicotinamide and other pyridines to form pyridinium ions. This activity is important for biotransformation of many drugs and xenobiotic compounds.

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
HgeneRIT1chr1:155874102chr11:114182767ENST00000368322-56134_137160237.0Nucleotide bindingGTP
HgeneRIT1chr1:155874102chr11:114182767ENST00000368322-5628_35160237.0Nucleotide bindingGTP
HgeneRIT1chr1:155874102chr11:114182767ENST00000368322-5675_79160237.0Nucleotide bindingGTP
HgeneRIT1chr1:155874102chr11:114182767ENST00000368323-56134_137143220.0Nucleotide bindingGTP
HgeneRIT1chr1:155874102chr11:114182767ENST00000368323-5628_35143220.0Nucleotide bindingGTP
HgeneRIT1chr1:155874102chr11:114182767ENST00000368323-5675_79143220.0Nucleotide bindingGTP
HgeneRIT1chr1:155874102chr11:114182767ENST00000539040-4528_35107184.0Nucleotide bindingGTP
HgeneRIT1chr1:155874102chr11:114182767ENST00000539040-4575_79107184.0Nucleotide bindingGTP
TgeneNNMTchr1:155874102chr11:114182767ENST0000029996413142_143120265.0RegionS-adenosyl-L-methionine binding
TgeneNNMTchr1:155874102chr11:114182767ENST0000053540135142_143120265.0RegionS-adenosyl-L-methionine binding

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneRIT1chr1:155874102chr11:114182767ENST00000539040-45134_137107184.0Nucleotide bindingGTP
TgeneNNMTchr1:155874102chr11:114182767ENST000002999641363_64120265.0RegionS-adenosyl-L-methionine binding
TgeneNNMTchr1:155874102chr11:114182767ENST000005354013563_64120265.0RegionS-adenosyl-L-methionine binding


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Fusion Gene Sequence for RIT1-NNMT


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.
>74201_74201_1_RIT1-NNMT_RIT1_chr1_155874102_ENST00000539040_NNMT_chr11_114182767_ENST00000535401_length(transcript)=1724nt_BP=483nt
GACTCGGGCGCCGGTGGCGCCATCTTACTCGGTTGCGGGAGGGGTCACAGGTCAGTGCCGGAGCCTCCGCGAGTGAAGGAAGACGAAGTG
CGTGACCCGACCGGCTGTGGTGTTCCAGTCCCCACTGACCAGTAGGAGCAGCAGGGCGTCGGCTTGTGAGCCATGACCATGCAGTTCATC
AGCCACCGATTCCCAGAAGATCATGATCCCACCATTGAAGATGCTTATAAGATCAGGATCCGTATTGATGATGAGCCTGCCAATCTGGAC
ATTTTGGATACAGCTGGACAGGCAGAGTTTACAGCCATGCGGGACCAGTATATGAGGGCAGGAGAAGGGTTTATCATCTGTTACTCTATC
ACGGATCGTCGAAGTTTCCATGAAGTTCGTGAGTTTAAACAGCTTATTTATCGAGTCCGACGTACTGACGATACACCTGTGGTTCTTGTG
GGAAACAAGTCAGACCTCAAACAGCTAAGACAGAGTCAAGGGTCCAGAGAAGGAGGAGAAGTTGAGACAGGCGGTCAAGCAGGTGCTGAA
GTGTGATGTGACTCAGAGCCAGCCACTGGGGGCCGTCCCCTTACCCCCGGCTGACTGCGTGCTCAGCACACTGTGTCTGGATGCCGCCTG
CCCAGACCTCCCCACCTACTGCAGGGCGCTCAGGAACCTCGGCAGCCTACTGAAGCCAGGGGGCTTCCTGGTGATCATGGATGCGCTCAA
GAGCAGCTACTACATGATTGGTGAGCAGAAGTTCTCCAGCCTCCCCCTGGGCCGGGAGGCAGTAGAGGCTGCTGTGAAAGAGGCTGGCTA
CACAATCGAATGGTTTGAGGTGATCTCGCAAAGTTATTCTTCCACCATGGCCAACAACGAAGGACTTTTCTCCCTGGTGGCGAGGAAGCT
GAGCAGACCCCTGTGATGCCTGTGACCTCAATTAAAGCAATTCCTTTGACCTGTCCAGTTGACTTTAGTCCTTGTTTCTAACTGCCAAGT
CATGTGCTGAGTAGAGGCTCAGTGGTTGGGGCCCAATGGTTCATCTAGGACGGGACTAGAGAGGTCAGTCTACAAGCAATCCATTGACCA
CTTACTTGGTGCTGCACACAAATGTTGGTGCTATGGGACCCAAAGATGAGCAATTAGTATTCCAGTCTTCATTGCCTGTGCTTACAAAAG
AAGACCTCACTTCCCTAAACATCTAGTTATGGCGGCTCAAGCCCGTACCTGCCTACAGAGAAGTGTCTGCAGTTACTCACTATTAGTTTC
CTAAGGGGGCACTGCTGGCTCCTTCTCTCCCAGGAATGGGCTTCTCCTATTCTTTAACTCTTGCCTTCTCCCTGGAGAGGCTACCAAACC
CTGGCCTCTGCCGCTGTTCAGGCTGCCATGTGGGTATAGCTGTTTGCTAGACTCCACTCTGGCCTCAGGGGCCAGAGAACAGCTGTCCAG
CATTTCTGTTCATCCCAGCAATCCAAAAAAAAATTTTTTTAAGCTACAAAGATCACTCCATTTTCAAATTCAGACTCTGCCACTTATTAG
CTGTTTCTCATTAGGCAAGTTATATAACCTTGCAGTGCCTCACTTTCCTCATCTATAAAATGAGATTAAAATAGTCTTTTTATTAAGAGA
ATTAAAGTGAATTGTGGCCAGGCACTGTGGCTCATGCCTGTAATCCCAGCGCTTTGGGAGGCTGAGGCAGACAGATTGCTTGAGCTCAGA

>74201_74201_1_RIT1-NNMT_RIT1_chr1_155874102_ENST00000539040_NNMT_chr11_114182767_ENST00000535401_length(amino acids)=134AA_BP=
MRQAVKQVLKCDVTQSQPLGAVPLPPADCVLSTLCLDAACPDLPTYCRALRNLGSLLKPGGFLVIMDALKSSYYMIGEQKFSSLPLGREA

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

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Fusion Gene PPI Analysis for RIT1-NNMT


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 RIT1-NNMT


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 RIT1-NNMT


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