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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:RPS6-NCAPG (FusionGDB2 ID:77523)

Fusion Gene Summary for RPS6-NCAPG

check button Fusion gene summary
Fusion gene informationFusion gene name: RPS6-NCAPG
Fusion gene ID: 77523
HgeneTgene
Gene symbol

RPS6

NCAPG

Gene ID

6194

64151

Gene nameribosomal protein S6non-SMC condensin I complex subunit G
SynonymsS6CAPG|CHCG|NY-MEL-3|YCG1
Cytomap

9p22.1

4p15.31

Type of geneprotein-codingprotein-coding
Description40S ribosomal protein S6phosphoprotein NP33small ribosomal subunit protein eS6condensin complex subunit 3XCAP-G homologchromosome condensation protein Gchromosome-associated protein Gcondensin subunit CAP-Gmelanoma antigen NY-MEL-3
Modification date2020031320200313
UniProtAcc.

Q86XI2

Ensembl transtripts involved in fusion geneENST00000380394, ENST00000498815, 
ENST00000380384, ENST00000315377, 
ENST00000380381, 		ENST00000251496, 
Fusion gene scores* DoF score28 X 23 X 7=45084 X 4 X 2=32
# samples 324
** MAII scorelog2(32/4508*10)=-3.81634370528486
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/32*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: RPS6 [Title/Abstract] AND NCAPG [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRPS6(19380187)-NCAPG(17838781), # 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
HgeneRPS6

GO:0031929

TOR signaling

16428328

HgeneRPS6

GO:0043065

positive regulation of apoptotic process

18362888

TgeneNCAPG

GO:0007076

mitotic chromosome condensation

11136719


check buttonFusion gene breakpoints across RPS6 (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 NCAPG (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
ChimerDB4OVTCGA-13-0801RPS6chr9

19380187

-NCAPGchr4

17838781

+


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Fusion Gene ORF analysis for RPS6-NCAPG

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
In-frameENST00000380394ENST00000251496RPS6chr9

19380187

-NCAPGchr4

17838781

+
intron-3CDSENST00000498815ENST00000251496RPS6chr9

19380187

-NCAPGchr4

17838781

+
intron-3CDSENST00000380384ENST00000251496RPS6chr9

19380187

-NCAPGchr4

17838781

+
intron-3CDSENST00000315377ENST00000251496RPS6chr9

19380187

-NCAPGchr4

17838781

+
In-frameENST00000380381ENST00000251496RPS6chr9

19380187

-NCAPGchr4

17838781

+

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)
ENST00000380394RPS6chr919380187-ENST00000251496NCAPGchr417838781+244165591003314
ENST00000380381RPS6chr919380187-ENST00000251496NCAPGchr417838781+24234741985314

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
ENST00000380394ENST00000251496RPS6chr919380187-NCAPGchr417838781+0.0008641960.9991358
ENST00000380381ENST00000251496RPS6chr919380187-NCAPGchr417838781+0.0008757740.9991242

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Fusion Genomic Features for RPS6-NCAPG


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)
RPS6chr919380187-NCAPGchr417838781+0.68202520.31797478
RPS6chr919380187-NCAPGchr417838781+0.68202520.31797478

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 RPS6-NCAPG


check button Go to

FGviewer for the breakpoints of chr9:19380187-chr4:17838781

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.NCAPG

Q86XI2

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Regulatory subunit of the condensin-2 complex, a complex which establishes mitotic chromosome architecture and is involved in physical rigidity of the chromatid axis. {ECO:0000269|PubMed:14532007, ECO:0000269|PubMed:30609410}.

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
TgeneNCAPGchr9:19380187chr4:17838781ENST000002514961321912_917703.01016.0Compositional biasNote=Poly-Thr
TgeneNCAPGchr9:19380187chr4:17838781ENST000002514961321865_907703.01016.0RepeatNote=HEAT 10

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneNCAPGchr9:19380187chr4:17838781ENST00000251496132188_91703.01016.0Compositional biasNote=Poly-Glu
TgeneNCAPGchr9:19380187chr4:17838781ENST000002514961321138_173703.01016.0RepeatNote=HEAT 2
TgeneNCAPGchr9:19380187chr4:17838781ENST000002514961321174_212703.01016.0RepeatNote=HEAT 3
TgeneNCAPGchr9:19380187chr4:17838781ENST000002514961321238_275703.01016.0RepeatNote=HEAT 4
TgeneNCAPGchr9:19380187chr4:17838781ENST000002514961321276_313703.01016.0RepeatNote=HEAT 5
TgeneNCAPGchr9:19380187chr4:17838781ENST000002514961321399_436703.01016.0RepeatNote=HEAT 6
TgeneNCAPGchr9:19380187chr4:17838781ENST000002514961321439_478703.01016.0RepeatNote=HEAT 7
TgeneNCAPGchr9:19380187chr4:17838781ENST000002514961321617_654703.01016.0RepeatNote=HEAT 8
TgeneNCAPGchr9:19380187chr4:17838781ENST000002514961321687_724703.01016.0RepeatNote=HEAT 9
TgeneNCAPGchr9:19380187chr4:17838781ENST00000251496132194_131703.01016.0RepeatNote=HEAT 1


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Fusion Gene Sequence for RPS6-NCAPG


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.
>In-frame_ENST00000380394_ENST00000251496_TCGA-13-0801_RPS6_chr9_19380187_-_NCAPG_chr4_17838781_length(transcript)=2441nt_BP=65nt
GCTAAGCGGAAGTTGGCCCTCTTTTCCGTGGCGCCTCGGAGGCGTTCAGCTGCTTCAAGATGAAGGTATCTGAACTTAGGACTGGAGCTG
CAGAAGGACTAGCCAAGCTGATGTTCTCTGGGCTTTTGGTCAGCAGCAGGATTCTTTCTCGTCTTATTTTGTTATGGTACAATCCTGTGA
CTGAAGAGGATGTTCAACTTCGACATTGCCTAGGCGTGTTCTTCCCCGTGTTTGCTTATGCAAGCAGGACTAATCAGGAATGCTTTGAAG
AAGCTTTTCTTCCAACCCTGCAAACACTGGCCAATGCCCCTGCATCTTCTCCTTTAGCTGAAATTGATATCACAAATGTTGCTGAGTTAC
TTGTAGATTTGACAAGACCAAGTGGATTAAATCCTCAGGCCAAGACTTCCCAAGATTATCAGGCCTTAACAGTACATGACAATTTGGCTA
TGAAAATTTGCAATGAGATCTTAACAAGTCCGTGCTCGCCAGAAATTCGAGTCTATACAAAAGCCTTGAGTTCTTTAGAACTCAGTAGCC
ATCTTGCAAAAGATCTTCTGGTTCTATTGAATGAGATTCTGGAGCAAGTAAAAGATAGGACATGTCTGAGAGCTTTGGAGAAAATCAAGA
TTCAGTTAGAAAAAGGAAATAAAGAATTTGGTGACCAAGCTGAAGCAGCACAGGATGCCACCTTGACTACAACTACTTTCCAAAATGAAG
ATGAAAAGAATAAAGAAGTATATATGACTCCACTCAGGGGTGTAAAAGCAACCCAAGCATCAAAGTCTACTCAGCTAAAGACTAACAGAG
GACAGAGAAAAGTGACAGTTTCAGCTAGGACGAACAGGAGGTGTCAGACTGCTGAAGCCGACTCTGAAAGTGATCATGAAGTTCCAGAAC
CAGAATCAGAAATGAAGATGAGACTACCAAGACGAGCCAAAACCGCAGCACTAGAAAAAAGTAAACTTAACCTTGCCCAATTTCTCAATG
AAGATCTAAGTTAGGAAAGACGATGGAGGTGGAATCCTTTAAGATTATGTCCAGTTATTTGCTTTAATAAAGAAGAAGTTACCCTTGTCA
AAATCAGAACAAACCTGATGTCTTTCTGAAGATTTTCTGCTGTGCGCTTCCACGTTACTTTGGCCTGTATTAAAGCAGTAGAGCAGCATC
AGTTATTATAGTCCAGAAAAAGTGTGCATCAGTCAGTCACACAGATTTATCACAATCTGAGGTGGGCCTAGGAATCTCATTTTTAAATAG
TCTCTCCAAGTGATTCTTATGAACTCTTTATGTTTAAAATCATGTCATTATGGAAAACTTACAAGTGTAACTAGCTAGTAGCTTGCATTT
GAGAAGCTTATGACTTAGATGGGCAGAATCAACAAAGATGAAACCGCCTGAGGACACATTTAACAAGTAACATTTCTAGGGAAAATGAAG
GAAGTACCACAAACTGGCTAGAAAGGAGCTTATCAATCACCAGTGAGGAAGACCAGTATAACGTTCAACAACAGTTATTTTGACAAAAAC
TTATTTTGTGATTCCTACAGTGAAAACATTTTTGGTGATATCTGCCTGGGAAATCTCTCTTCCTAAAGTATTTGTATATGGGAGTCCTTG
TTTGTGAATGTTTCCTGGATTAGGGAGGTGTCAACATAAATGTATTATTAACCATGAAGCTGCTCGCTATATTTTTGGCATAACAAAATA
ATATTTATTTACTGTGGATAATAATTCTAGTGGGAATATAATGTGACAGGAACTTCTCTTTATATACGCTACCAATTTATGAGCACTATT
CACTGTCAATTTCATTTCTTGTCTTTTGAAATTGACACTTGGCCTGACTTACGAAACTTGTACTATATGAAATTGGTCCTCTTTTCTGCA
ATACCCAACGAAACACCTTTTCTCTTTATTATTCAGAAATGTCCTAACATGGATCTGTTTGTTTTAATAATTGTGCTTTTTTTAGGCTTA
TCATCTACTAGAGGCCATTTACTTAAGGTGAAATTTTAAGATGGAGCTAAAGTAAGATCACTGGTTTTTAGAACCAAATTGCTATACATA
TGTGCCTCATAGAACTTATAAAAGGAGTCAAAGTTTCAAAGCAAGATAGTTATTAAGCAAAAGGAAAAATGGTAATGATAGAAAGTCAGT
TAAAAATAGATGATTGTTCTTCATTCTGTTTGTTGGCTCTGTGTTCTCCTGTGCTTCAGATTCCTTATGTGTTGTTGTTTTAAAGACAAT
TTGCAGGGGGTTGGGAGAAGGACTGAAAAGGTACATTAAGTGTGCTGTAAGGAAAAGTCTTAGAAACATAATAAGCTAAAATCCCATTCA
CACATGGCCAGGCTATCCAAAAAGAAAGGAGCCATGTTCTCATGTGGTTTACCATACCAAAGCTTGCTTTCTCTGGCATGGGAAAAATAA

>In-frame_ENST00000380394_ENST00000251496_TCGA-13-0801_RPS6_chr9_19380187_-_NCAPG_chr4_17838781_length(amino acids)=314AA_start in transcript=59_stop in transcript=1003
MKVSELRTGAAEGLAKLMFSGLLVSSRILSRLILLWYNPVTEEDVQLRHCLGVFFPVFAYASRTNQECFEEAFLPTLQTLANAPASSPLA
EIDITNVAELLVDLTRPSGLNPQAKTSQDYQALTVHDNLAMKICNEILTSPCSPEIRVYTKALSSLELSSHLAKDLLVLLNEILEQVKDR
TCLRALEKIKIQLEKGNKEFGDQAEAAQDATLTTTTFQNEDEKNKEVYMTPLRGVKATQASKSTQLKTNRGQRKVTVSARTNRRCQTAEA

--------------------------------------------------------------
>In-frame_ENST00000380381_ENST00000251496_TCGA-13-0801_RPS6_chr9_19380187_-_NCAPG_chr4_17838781_length(transcript)=2423nt_BP=47nt
CTCTTTTCCGTGGCGCCTCGGAGGCGTTCAGCTGCTTCAAGATGAAGGTATCTGAACTTAGGACTGGAGCTGCAGAAGGACTAGCCAAGC
TGATGTTCTCTGGGCTTTTGGTCAGCAGCAGGATTCTTTCTCGTCTTATTTTGTTATGGTACAATCCTGTGACTGAAGAGGATGTTCAAC
TTCGACATTGCCTAGGCGTGTTCTTCCCCGTGTTTGCTTATGCAAGCAGGACTAATCAGGAATGCTTTGAAGAAGCTTTTCTTCCAACCC
TGCAAACACTGGCCAATGCCCCTGCATCTTCTCCTTTAGCTGAAATTGATATCACAAATGTTGCTGAGTTACTTGTAGATTTGACAAGAC
CAAGTGGATTAAATCCTCAGGCCAAGACTTCCCAAGATTATCAGGCCTTAACAGTACATGACAATTTGGCTATGAAAATTTGCAATGAGA
TCTTAACAAGTCCGTGCTCGCCAGAAATTCGAGTCTATACAAAAGCCTTGAGTTCTTTAGAACTCAGTAGCCATCTTGCAAAAGATCTTC
TGGTTCTATTGAATGAGATTCTGGAGCAAGTAAAAGATAGGACATGTCTGAGAGCTTTGGAGAAAATCAAGATTCAGTTAGAAAAAGGAA
ATAAAGAATTTGGTGACCAAGCTGAAGCAGCACAGGATGCCACCTTGACTACAACTACTTTCCAAAATGAAGATGAAAAGAATAAAGAAG
TATATATGACTCCACTCAGGGGTGTAAAAGCAACCCAAGCATCAAAGTCTACTCAGCTAAAGACTAACAGAGGACAGAGAAAAGTGACAG
TTTCAGCTAGGACGAACAGGAGGTGTCAGACTGCTGAAGCCGACTCTGAAAGTGATCATGAAGTTCCAGAACCAGAATCAGAAATGAAGA
TGAGACTACCAAGACGAGCCAAAACCGCAGCACTAGAAAAAAGTAAACTTAACCTTGCCCAATTTCTCAATGAAGATCTAAGTTAGGAAA
GACGATGGAGGTGGAATCCTTTAAGATTATGTCCAGTTATTTGCTTTAATAAAGAAGAAGTTACCCTTGTCAAAATCAGAACAAACCTGA
TGTCTTTCTGAAGATTTTCTGCTGTGCGCTTCCACGTTACTTTGGCCTGTATTAAAGCAGTAGAGCAGCATCAGTTATTATAGTCCAGAA
AAAGTGTGCATCAGTCAGTCACACAGATTTATCACAATCTGAGGTGGGCCTAGGAATCTCATTTTTAAATAGTCTCTCCAAGTGATTCTT
ATGAACTCTTTATGTTTAAAATCATGTCATTATGGAAAACTTACAAGTGTAACTAGCTAGTAGCTTGCATTTGAGAAGCTTATGACTTAG
ATGGGCAGAATCAACAAAGATGAAACCGCCTGAGGACACATTTAACAAGTAACATTTCTAGGGAAAATGAAGGAAGTACCACAAACTGGC
TAGAAAGGAGCTTATCAATCACCAGTGAGGAAGACCAGTATAACGTTCAACAACAGTTATTTTGACAAAAACTTATTTTGTGATTCCTAC
AGTGAAAACATTTTTGGTGATATCTGCCTGGGAAATCTCTCTTCCTAAAGTATTTGTATATGGGAGTCCTTGTTTGTGAATGTTTCCTGG
ATTAGGGAGGTGTCAACATAAATGTATTATTAACCATGAAGCTGCTCGCTATATTTTTGGCATAACAAAATAATATTTATTTACTGTGGA
TAATAATTCTAGTGGGAATATAATGTGACAGGAACTTCTCTTTATATACGCTACCAATTTATGAGCACTATTCACTGTCAATTTCATTTC
TTGTCTTTTGAAATTGACACTTGGCCTGACTTACGAAACTTGTACTATATGAAATTGGTCCTCTTTTCTGCAATACCCAACGAAACACCT
TTTCTCTTTATTATTCAGAAATGTCCTAACATGGATCTGTTTGTTTTAATAATTGTGCTTTTTTTAGGCTTATCATCTACTAGAGGCCAT
TTACTTAAGGTGAAATTTTAAGATGGAGCTAAAGTAAGATCACTGGTTTTTAGAACCAAATTGCTATACATATGTGCCTCATAGAACTTA
TAAAAGGAGTCAAAGTTTCAAAGCAAGATAGTTATTAAGCAAAAGGAAAAATGGTAATGATAGAAAGTCAGTTAAAAATAGATGATTGTT
CTTCATTCTGTTTGTTGGCTCTGTGTTCTCCTGTGCTTCAGATTCCTTATGTGTTGTTGTTTTAAAGACAATTTGCAGGGGGTTGGGAGA
AGGACTGAAAAGGTACATTAAGTGTGCTGTAAGGAAAAGTCTTAGAAACATAATAAGCTAAAATCCCATTCACACATGGCCAGGCTATCC

>In-frame_ENST00000380381_ENST00000251496_TCGA-13-0801_RPS6_chr9_19380187_-_NCAPG_chr4_17838781_length(amino acids)=314AA_start in transcript=41_stop in transcript=985
MKVSELRTGAAEGLAKLMFSGLLVSSRILSRLILLWYNPVTEEDVQLRHCLGVFFPVFAYASRTNQECFEEAFLPTLQTLANAPASSPLA
EIDITNVAELLVDLTRPSGLNPQAKTSQDYQALTVHDNLAMKICNEILTSPCSPEIRVYTKALSSLELSSHLAKDLLVLLNEILEQVKDR
TCLRALEKIKIQLEKGNKEFGDQAEAAQDATLTTTTFQNEDEKNKEVYMTPLRGVKATQASKSTQLKTNRGQRKVTVSARTNRRCQTAEA

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Fusion Gene PPI Analysis for RPS6-NCAPG


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 RPS6-NCAPG


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 RPS6-NCAPG


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRPS6C0006142Malignant neoplasm of breast1CTD_human
HgeneRPS6C0024623Malignant neoplasm of stomach1CTD_human
HgeneRPS6C0038356Stomach Neoplasms1CTD_human
HgeneRPS6C0235874Disease Exacerbation1CTD_human
HgeneRPS6C0678222Breast Carcinoma1CTD_human
HgeneRPS6C1257931Mammary Neoplasms, Human1CTD_human
HgeneRPS6C1458155Mammary Neoplasms1CTD_human
HgeneRPS6C1708349Hereditary Diffuse Gastric Cancer1CTD_human
HgeneRPS6C2239176Liver carcinoma1CTD_human
HgeneRPS6C4704874Mammary Carcinoma, Human1CTD_human
TgeneNCAPGC2239176Liver carcinoma1CTD_human