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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:RPL24-CNBD1 (FusionGDB2 ID:76263)

Fusion Gene Summary for RPL24-CNBD1

check button Fusion gene summary
Fusion gene informationFusion gene name: RPL24-CNBD1
Fusion gene ID: 76263
HgeneTgene
Gene symbol

RPL24

CNBD1

Gene ID

51187

168975

Gene nameribosomal L24 domain containing 1cyclic nucleotide binding domain containing 1
SynonymsC15orf15|HRP-L30-iso|L30|RLP24|RPL24|RPL24L|TVAS3-
Cytomap

15q21.3

8q21.3

Type of geneprotein-codingprotein-coding
Descriptionprobable ribosome biogenesis protein RLP2460S ribosomal protein L30 isologhomolog of yeast ribosomal like protein 24my024 proteinribosomal L24 domain-containing protein 1cyclic nucleotide-binding domain-containing protein 1
Modification date2020031320200313
UniProtAcc.

Q8NA66

Ensembl transtripts involved in fusion geneENST00000394077, ENST00000469605, 
ENST00000495401, 
ENST00000522427, 
ENST00000518476, 
Fusion gene scores* DoF score11 X 12 X 4=5287 X 7 X 3=147
# samples 147
** MAII scorelog2(14/528*10)=-1.91511110241349
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(7/147*10)=-1.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RPL24 [Title/Abstract] AND CNBD1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRPL24(101401614)-CNBD1(88218220), # 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 RPL24 (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 CNBD1 (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
ChimerDB4ESCATCGA-LN-A8I1RPL24chr3

101401614

-CNBD1chr8

88218220

+


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Fusion Gene ORF analysis for RPL24-CNBD1

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-3UTRENST00000394077ENST00000522427RPL24chr3

101401614

-CNBD1chr8

88218220

+
5CDS-3UTRENST00000469605ENST00000522427RPL24chr3

101401614

-CNBD1chr8

88218220

+
5CDS-3UTRENST00000495401ENST00000522427RPL24chr3

101401614

-CNBD1chr8

88218220

+
In-frameENST00000394077ENST00000518476RPL24chr3

101401614

-CNBD1chr8

88218220

+
In-frameENST00000469605ENST00000518476RPL24chr3

101401614

-CNBD1chr8

88218220

+
In-frameENST00000495401ENST00000518476RPL24chr3

101401614

-CNBD1chr8

88218220

+

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)
ENST00000394077RPL24chr3101401614-ENST00000518476CNBD1chr888218220+1547435821314410
ENST00000495401RPL24chr3101401614-ENST00000518476CNBD1chr888218220+147035851237410
ENST00000469605RPL24chr3101401614-ENST00000518476CNBD1chr888218220+1460348191227402

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
ENST00000394077ENST00000518476RPL24chr3101401614-CNBD1chr888218220+0.0008827170.9991173
ENST00000495401ENST00000518476RPL24chr3101401614-CNBD1chr888218220+0.0009985780.99900144
ENST00000469605ENST00000518476RPL24chr3101401614-CNBD1chr888218220+0.001076980.998923

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Fusion Genomic Features for RPL24-CNBD1


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)
RPL24chr3101401614-CNBD1chr888218220+6.53E-101
RPL24chr3101401614-CNBD1chr888218220+6.53E-101

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 RPL24-CNBD1


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/chr3:101401614/chr8:88218220)
- 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
.CNBD1

Q8NA66

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
TgeneCNBD1chr3:101401614chr8:88218220ENST00000518476311322_436143437.0Nucleotide bindingNote=cNMP

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneCNBD1chr3:101401614chr8:88218220ENST0000051847631121_24143437.0Compositional biasNote=Poly-Pro


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Fusion Gene Sequence for RPL24-CNBD1


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.
>76263_76263_1_RPL24-CNBD1_RPL24_chr3_101401614_ENST00000394077_CNBD1_chr8_88218220_ENST00000518476_length(transcript)=1547nt_BP=435nt
GGGGAGGAGATTTCCGGCCCCCATCCCCGCAGCGACCTTATAAGGTCTCTTCCCATGATTCTCTCTTTCTTTTCGCCATCTTTTGTCTTT
CCGTGGAGCTGTCGCCATGAAGGTCGAGCTGTGCAGTTTTAGCGGGTACAAGATCTACCCCGGACACGGGAGGCGCTACGCCAGGACCGA
CGGGAAGGTTTTCCAGTTTCTTAATGCGAAATGCGAGTCGGCTTTCCTTTCCAAGAGGAATCCTCGGCAGATAAACTGGACTGTCCTCTA
CAGAAGGAAGCACAAAAAGGGACAGTCGGAAGAAATTCAAAAGAAAAGAACCCGCCGAGCAGTCAAATTCCAGAGGGCCATTACTGGTGC
ATCTCTTGCTGATATAATGGCCAAGAGGAATCAGAAACCTGAAGTTAGAAAGGCTCAACGAGAACAAGCTATCAGGCCCATTCACAGGAC
GCCATATGAACACAAAACTGTGTGGAAGTTCCTGAAAACAATTCCAGATTTAACCTTTCAGCTAAATGATAAGCATCTGAAAACACTTAG
TAAGACTGTCTTTTCCGAAACCTGGTTGAAAGGCAGCACAGTGGTTGCAAATGATGGATTTTATGTAATACTGAAAGGCCTAGCTCGACC
TCAAACAAACGTGTATAAAAATCTGATTGAAGGAAGTGATTCACCAGACTCGTTCATATCTCAGAGTTTCCACAGCTTCATTTGGAGTGA
AGAATTCAAAAACTCTACACTTGCTGAGATGTACCTACCTTCATATGACTCAATGCTTAGCAAATGGAGTACCTTTGGGACTCTGGAAGT
TATGCCTCAGAATGAATCGGAAACACAGATGTTCTCGGTGGTGACAGAAGACGATTGTGAAATTCTTAAAATCCCAGCAAAGGGATATGC
AAAGATAAAGGAGGAAAAAATAAAACTTGAAAATATGCAAAAGTTGAAATTAATCCGTATGTGTCCTTATTATGAGGAATGGCCTACTTT
ATCCATATATGAGCTAATTGCACTCCTTAAATGGAAAAAATTTCCTCCAGGTCATGTGATAGTGGAAAGTGGAAATATAATTTCTTTTGT
GGGTTATATTAACTCTGGATGCTGTAACATTTATAGAAGTATTATAGGATTTGTGAAACTACGATCAAATAAAGTGAAAAGATCTCAAAA
ACTTGTTTATATGGGGAAACTTAAGGAGAAGGAGTCCTTTGGTGAGATTAGCGTCCTTCTTCAAGTTCCTTTCACGTGCACAATCATTAC
CAAAAAAGAAGTTGAGATGGCAATCATTGAAGATAAGGACCTATTTGTGGCCTAGATCTAGAAACAACCTCAGTGAACATTAATTAAGAA
AGTATTGACTAAATAATGGAATAATTGCATTCTGGAATACTATCAAACTACCAGCAATGAATTTGGTCTATTGTGACTACATATCCTGGA
TTCCCCAGGAAAGTCCCACTTTCGAATTGCCTTTCAAACACAGTTTTTATTAGCAGTCTTTCTTGGTTTGGATACTAAAATAAATATAGT

>76263_76263_1_RPL24-CNBD1_RPL24_chr3_101401614_ENST00000394077_CNBD1_chr8_88218220_ENST00000518476_length(amino acids)=410AA_BP=117
MSFRGAVAMKVELCSFSGYKIYPGHGRRYARTDGKVFQFLNAKCESAFLSKRNPRQINWTVLYRRKHKKGQSEEIQKKRTRRAVKFQRAI
TGASLADIMAKRNQKPEVRKAQREQAIRPIHRTPYEHKTVWKFLKTIPDLTFQLNDKHLKTLSKTVFSETWLKGSTVVANDGFYVILKGL
ARPQTNVYKNLIEGSDSPDSFISQSFHSFIWSEEFKNSTLAEMYLPSYDSMLSKWSTFGTLEVMPQNESETQMFSVVTEDDCEILKIPAK
GYAKIKEEKIKLENMQKLKLIRMCPYYEEWPTLSIYELIALLKWKKFPPGHVIVESGNIISFVGYINSGCCNIYRSIIGFVKLRSNKVKR

--------------------------------------------------------------
>76263_76263_2_RPL24-CNBD1_RPL24_chr3_101401614_ENST00000469605_CNBD1_chr8_88218220_ENST00000518476_length(transcript)=1460nt_BP=348nt
TTTCCGTGGAGCTGTCGCCATGAAGGTCGAGCTGTGCAGTTTTAGCGGGTACAAGATCTACCCCGGACACGGGAGGCGCTACGCCAGGAC
CGACGGGAAGGTTTTCCAGTTTCTTAATGCGAAATGCGAGTCGGCTTTCCTTTCCAAGAGGAATCCTCGGCAGATAAACTGGACTGTCCT
CTACAGAAGGAAGCACAAAAAGGGACAGTCGGAAGAAATTCAAAAGAAAAGAACCCGCCGAGCAGTCAAATTCCAGAGGGCCATTACTGG
TGCATCTCTTGCTGATATAATGGCCAAGAGGAATCAGAAACCTGAAGTTAGAAAGGCTCAACGAGAACAAGCTATCAGGCCCATTCACAG
GACGCCATATGAACACAAAACTGTGTGGAAGTTCCTGAAAACAATTCCAGATTTAACCTTTCAGCTAAATGATAAGCATCTGAAAACACT
TAGTAAGACTGTCTTTTCCGAAACCTGGTTGAAAGGCAGCACAGTGGTTGCAAATGATGGATTTTATGTAATACTGAAAGGCCTAGCTCG
ACCTCAAACAAACGTGTATAAAAATCTGATTGAAGGAAGTGATTCACCAGACTCGTTCATATCTCAGAGTTTCCACAGCTTCATTTGGAG
TGAAGAATTCAAAAACTCTACACTTGCTGAGATGTACCTACCTTCATATGACTCAATGCTTAGCAAATGGAGTACCTTTGGGACTCTGGA
AGTTATGCCTCAGAATGAATCGGAAACACAGATGTTCTCGGTGGTGACAGAAGACGATTGTGAAATTCTTAAAATCCCAGCAAAGGGATA
TGCAAAGATAAAGGAGGAAAAAATAAAACTTGAAAATATGCAAAAGTTGAAATTAATCCGTATGTGTCCTTATTATGAGGAATGGCCTAC
TTTATCCATATATGAGCTAATTGCACTCCTTAAATGGAAAAAATTTCCTCCAGGTCATGTGATAGTGGAAAGTGGAAATATAATTTCTTT
TGTGGGTTATATTAACTCTGGATGCTGTAACATTTATAGAAGTATTATAGGATTTGTGAAACTACGATCAAATAAAGTGAAAAGATCTCA
AAAACTTGTTTATATGGGGAAACTTAAGGAGAAGGAGTCCTTTGGTGAGATTAGCGTCCTTCTTCAAGTTCCTTTCACGTGCACAATCAT
TACCAAAAAAGAAGTTGAGATGGCAATCATTGAAGATAAGGACCTATTTGTGGCCTAGATCTAGAAACAACCTCAGTGAACATTAATTAA
GAAAGTATTGACTAAATAATGGAATAATTGCATTCTGGAATACTATCAAACTACCAGCAATGAATTTGGTCTATTGTGACTACATATCCT
GGATTCCCCAGGAAAGTCCCACTTTCGAATTGCCTTTCAAACACAGTTTTTATTAGCAGTCTTTCTTGGTTTGGATACTAAAATAAATAT

>76263_76263_2_RPL24-CNBD1_RPL24_chr3_101401614_ENST00000469605_CNBD1_chr8_88218220_ENST00000518476_length(amino acids)=402AA_BP=109
MKVELCSFSGYKIYPGHGRRYARTDGKVFQFLNAKCESAFLSKRNPRQINWTVLYRRKHKKGQSEEIQKKRTRRAVKFQRAITGASLADI
MAKRNQKPEVRKAQREQAIRPIHRTPYEHKTVWKFLKTIPDLTFQLNDKHLKTLSKTVFSETWLKGSTVVANDGFYVILKGLARPQTNVY
KNLIEGSDSPDSFISQSFHSFIWSEEFKNSTLAEMYLPSYDSMLSKWSTFGTLEVMPQNESETQMFSVVTEDDCEILKIPAKGYAKIKEE
KIKLENMQKLKLIRMCPYYEEWPTLSIYELIALLKWKKFPPGHVIVESGNIISFVGYINSGCCNIYRSIIGFVKLRSNKVKRSQKLVYMG

--------------------------------------------------------------
>76263_76263_3_RPL24-CNBD1_RPL24_chr3_101401614_ENST00000495401_CNBD1_chr8_88218220_ENST00000518476_length(transcript)=1470nt_BP=358nt
ATCTTTTGTCTTTCCGTGGAGCTGTCGCCATGAAGGTCGAGCTGTGCAGTTTTAGCGGGTACAAGATCTACCCCGGACACGGGAGGCGCT
ACGCCAGGACCGACGGGAAGGTTTTCCAGTTTCTTAATGCGAAATGCGAGTCGGCTTTCCTTTCCAAGAGGAATCCTCGGCAGATAAACT
GGACTGTCCTCTACAGAAGGAAGCACAAAAAGGGACAGTCGGAAGAAATTCAAAAGAAAAGAACCCGCCGAGCAGTCAAATTCCAGAGGG
CCATTACTGGTGCATCTCTTGCTGATATAATGGCCAAGAGGAATCAGAAACCTGAAGTTAGAAAGGCTCAACGAGAACAAGCTATCAGGC
CCATTCACAGGACGCCATATGAACACAAAACTGTGTGGAAGTTCCTGAAAACAATTCCAGATTTAACCTTTCAGCTAAATGATAAGCATC
TGAAAACACTTAGTAAGACTGTCTTTTCCGAAACCTGGTTGAAAGGCAGCACAGTGGTTGCAAATGATGGATTTTATGTAATACTGAAAG
GCCTAGCTCGACCTCAAACAAACGTGTATAAAAATCTGATTGAAGGAAGTGATTCACCAGACTCGTTCATATCTCAGAGTTTCCACAGCT
TCATTTGGAGTGAAGAATTCAAAAACTCTACACTTGCTGAGATGTACCTACCTTCATATGACTCAATGCTTAGCAAATGGAGTACCTTTG
GGACTCTGGAAGTTATGCCTCAGAATGAATCGGAAACACAGATGTTCTCGGTGGTGACAGAAGACGATTGTGAAATTCTTAAAATCCCAG
CAAAGGGATATGCAAAGATAAAGGAGGAAAAAATAAAACTTGAAAATATGCAAAAGTTGAAATTAATCCGTATGTGTCCTTATTATGAGG
AATGGCCTACTTTATCCATATATGAGCTAATTGCACTCCTTAAATGGAAAAAATTTCCTCCAGGTCATGTGATAGTGGAAAGTGGAAATA
TAATTTCTTTTGTGGGTTATATTAACTCTGGATGCTGTAACATTTATAGAAGTATTATAGGATTTGTGAAACTACGATCAAATAAAGTGA
AAAGATCTCAAAAACTTGTTTATATGGGGAAACTTAAGGAGAAGGAGTCCTTTGGTGAGATTAGCGTCCTTCTTCAAGTTCCTTTCACGT
GCACAATCATTACCAAAAAAGAAGTTGAGATGGCAATCATTGAAGATAAGGACCTATTTGTGGCCTAGATCTAGAAACAACCTCAGTGAA
CATTAATTAAGAAAGTATTGACTAAATAATGGAATAATTGCATTCTGGAATACTATCAAACTACCAGCAATGAATTTGGTCTATTGTGAC
TACATATCCTGGATTCCCCAGGAAAGTCCCACTTTCGAATTGCCTTTCAAACACAGTTTTTATTAGCAGTCTTTCTTGGTTTGGATACTA

>76263_76263_3_RPL24-CNBD1_RPL24_chr3_101401614_ENST00000495401_CNBD1_chr8_88218220_ENST00000518476_length(amino acids)=410AA_BP=117
MSFRGAVAMKVELCSFSGYKIYPGHGRRYARTDGKVFQFLNAKCESAFLSKRNPRQINWTVLYRRKHKKGQSEEIQKKRTRRAVKFQRAI
TGASLADIMAKRNQKPEVRKAQREQAIRPIHRTPYEHKTVWKFLKTIPDLTFQLNDKHLKTLSKTVFSETWLKGSTVVANDGFYVILKGL
ARPQTNVYKNLIEGSDSPDSFISQSFHSFIWSEEFKNSTLAEMYLPSYDSMLSKWSTFGTLEVMPQNESETQMFSVVTEDDCEILKIPAK
GYAKIKEEKIKLENMQKLKLIRMCPYYEEWPTLSIYELIALLKWKKFPPGHVIVESGNIISFVGYINSGCCNIYRSIIGFVKLRSNKVKR

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

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Fusion Gene PPI Analysis for RPL24-CNBD1


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 RPL24-CNBD1


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 RPL24-CNBD1


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