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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:CAP2-CCDC28B (FusionGDB2 ID:12827)

Fusion Gene Summary for CAP2-CCDC28B

check button Fusion gene summary
Fusion gene informationFusion gene name: CAP2-CCDC28B
Fusion gene ID: 12827
HgeneTgene
Gene symbol

CAP2

CCDC28B

Gene ID

10486

79140

Gene namecyclase associated actin cytoskeleton regulatory protein 2coiled-coil domain containing 28B
Synonyms--
Cytomap

6p22.3

1p35.2

Type of geneprotein-codingprotein-coding
Descriptionadenylyl cyclase-associated protein 22810452G09RikCAP 2CAP, adenylate cyclase-associated protein, 2coiled-coil domain-containing protein 28B
Modification date2020031320200313
UniProtAcc.

Q9BUN5

Ensembl transtripts involved in fusion geneENST00000229922, ENST00000378990, 
ENST00000465994, ENST00000489374, 
ENST00000493172, 		ENST00000373602, 
ENST00000421922, ENST00000483009, 
Fusion gene scores* DoF score4 X 4 X 2=325 X 4 X 3=60
# samples 45
** MAII scorelog2(4/32*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(5/60*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CAP2 [Title/Abstract] AND CCDC28B [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCAP2(17557021)-CCDC28B(32670811), # 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 CAP2 (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 CCDC28B (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
ChiTaRS5.0N/AF32490CAP2chr6

17557021

-CCDC28Bchr1

32670811

+


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Fusion Gene ORF analysis for CAP2-CCDC28B

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
3UTR-3CDSENST00000229922ENST00000373602CAP2chr6

17557021

-CCDC28Bchr1

32670811

+
3UTR-3UTRENST00000229922ENST00000421922CAP2chr6

17557021

-CCDC28Bchr1

32670811

+
3UTR-intronENST00000229922ENST00000483009CAP2chr6

17557021

-CCDC28Bchr1

32670811

+
5CDS-3UTRENST00000378990ENST00000421922CAP2chr6

17557021

-CCDC28Bchr1

32670811

+
5CDS-intronENST00000378990ENST00000483009CAP2chr6

17557021

-CCDC28Bchr1

32670811

+
In-frameENST00000378990ENST00000373602CAP2chr6

17557021

-CCDC28Bchr1

32670811

+
intron-3CDSENST00000465994ENST00000373602CAP2chr6

17557021

-CCDC28Bchr1

32670811

+
intron-3CDSENST00000489374ENST00000373602CAP2chr6

17557021

-CCDC28Bchr1

32670811

+
intron-3CDSENST00000493172ENST00000373602CAP2chr6

17557021

-CCDC28Bchr1

32670811

+
intron-3UTRENST00000465994ENST00000421922CAP2chr6

17557021

-CCDC28Bchr1

32670811

+
intron-3UTRENST00000489374ENST00000421922CAP2chr6

17557021

-CCDC28Bchr1

32670811

+
intron-3UTRENST00000493172ENST00000421922CAP2chr6

17557021

-CCDC28Bchr1

32670811

+
intron-intronENST00000465994ENST00000483009CAP2chr6

17557021

-CCDC28Bchr1

32670811

+
intron-intronENST00000489374ENST00000483009CAP2chr6

17557021

-CCDC28Bchr1

32670811

+
intron-intronENST00000493172ENST00000483009CAP2chr6

17557021

-CCDC28Bchr1

32670811

+

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)
ENST00000378990CAP2chr617557021-ENST00000373602CCDC28Bchr132670811+198918121031458451

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
ENST00000378990ENST00000373602CAP2chr617557021-CCDC28Bchr132670811+0.0006188390.9993812

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Fusion Genomic Features for CAP2-CCDC28B


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 CAP2-CCDC28B


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/chr6:17557021/chr1:32670811)
- 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
.CCDC28B

Q9BUN5

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: Involved in ciliogenesis. Regulates cilia length through its interaction with MAPKAP1/SIN1 but independently of mTORC2 complex. Modulates mTORC2 complex assembly and function, possibly enhances AKT1 phosphorylation. Does not seem to modulate assembly and function of mTORC1 complex. {ECO:0000269|PubMed:23015189, ECO:0000269|PubMed:23727834}.

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
TgeneCCDC28Bchr6:17557021chr1:32670811ENST0000037360206158_1830201.0Coiled coilOntology_term=ECO:0000255
TgeneCCDC28Bchr6:17557021chr1:32670811ENST0000042192205158_1830242.0Coiled coilOntology_term=ECO:0000255

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCAP2chr6:17557021chr1:32670811ENST00000229922-113232_2450478.0Compositional biasNote=Poly-Pro
HgeneCAP2chr6:17557021chr1:32670811ENST00000229922-113317_4550478.0DomainC-CAP/cofactor C-like


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Fusion Gene Sequence for CAP2-CCDC28B


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.
>12827_12827_1_CAP2-CCDC28B_CAP2_chr6_17557021_ENST00000378990_CCDC28B_chr1_32670811_ENST00000373602_length(transcript)=1989nt_BP=1812nt
GGAGGGAGAGGGGAGGAGAAGGGGAGGGCCGCGGGAGGAGGGTACGAGTGGCCGACCACGGATTTGCATTGCCGAGGACGGGACCCCAGG
GCAGCGAAGCAGAATGGCCAACATGCAGGGACTGGTGGAAAGACTGGAACGAGCTGTCAGCCGCCTGGAGTCGCTGTCTGCAGAGTCCCA
CAGGCCCCCTGGGAACTGCGGGGAAGTCAATGGTGTCATTGCAGGTGTGGCACCCTCCGTGGAAGCCTTTGACAAGCTGATGGACAGTAT
GGTGGCCGAGTTTTTAAAGAACAGTAGGATCCTTGCTGGGGACGTGGAGACCCATAATGACGTGGCCGCACTTCTGAAACCCATATCGGA
AAAGATTCAGGAAATCCAAACTTTCAGAGAGAGAAACCGGGGGAGTAACATGTTTAATCATCTTTCGGCCGTCAGCGAAAGCATCCCTGC
CCTTGGATGGATAGCTGTGTCTCCCAAACCTGGTCCTTATGTCAAGGAGATGAATGACGCTGCCACCTTTTACACTAACAGGGTCTTAAA
GGACTACAAACACAGTGATTTGCGTCATGTGGATTGGGTGAAGTCATATTTGAACATTTGGAGTGAACTTCAAGCATACATCAAGGAACA
CCACACCACGGGCCTCACATGGAGCAAAACAGGTCCTGTAGCATCCACAGTATCAGCGTTTTCTGTCCTCTCCTCTGGGCCTGGCCTTCC
TCCACCCCCTCCTCCTCTGCCTCCTCCAGGGCCACCTCCACTTTTCGAGAATGAAGGCAAAAAAGAGGAATCTTCTCCTTCACGCTCAGC
TTTATTTGCCCAACTTAACCAGGGAGAAGCAATTACAAAAGGGCTCCGCCATGTCACAGATGACCAGAAGACATACAAAAATCCCAGCCT
GCGGGCTCAAGGAGGGCAAACTCAATCTCCCACCAAAAGTCACACTCCAAGTCCCACATCTCCTAAATCTTATCCTTCTCAAAAACATGC
CCCAGTGTTGGAGTTGGAAGGAAAGAAATGGAGAGTGGAGTACCAAGAGGACAGGAATGACCTTGTGATTTCAGAGACTGAGCTGAAACA
AGTGGCTTACATTTTCAAATGCGAAAAATCAACTATTCAGATAAAAGGGAAAGTAAACTCCATTATAATTGACAACTGTAAAAAACTCGG
CCTGGTGTTTGACAATGTGGTGGGCATTGTGGAAGTGATCAACTCCCAGGACATTCAAATCCAGGTAATGGGGAGAGTGCCAACAATTTC
CATTAATAAGACAGAAGGTTGCCACATATACCTCAGTGAAGATGCATTAGACTGTGAGATCGTGAGCGCCAAGTCATCTGAAATGAACAT
ACTTATCCCTCAGGATGGTGATTATAGAGAATTTCCCATTCCTGAACAGTTCAAGACAGCATGGGATGGATCCAAGTTAATCACTGAACC
TGCAGAAATTATGGCCTAACTTCCTGAGAGACCGAACCCCCTCACCTGAATCCCCCTCTATCAAACAAACAAAAAAGCAGCAGTAAAGAG
CTAGAAGTTGCAGTAGCCCCTACTGCTTTAGCTTTGGCCTCCAACGATTCTGTGCTATAGATACAGCACTGTTTCTGGCACGCCTCGTGG
GCATTTTGAAATATTTAACGTTTCCTCATGATTTGCCTTTGTGTGTGATTTTAGTTCCACATGATGACTTGTGAACATTAGGGATTTAAA
GGAAAAAAAAAAAGAATTCTGTTCCCCTCATATCATGAACACAGTAACTGATAGGTAAAAAGACTGCATGATTCACTTTTACACTTATAT
TTCATTGCTAGTCCGAGAACGCCGAGCCTGAGGAGCAGTCCGCTGCGTAGGCGTCCCACGCAGGCCCACACTGCCCCTCTCATTCTCTTC
AAACTGTGACTTTTTACAGACTCGGGCGGGTGTTCTGCGGCCCCCCAGGTGCTATGGGGGAGGGGGGCGTTGAATGGAATTAAACCAGAA

>12827_12827_1_CAP2-CCDC28B_CAP2_chr6_17557021_ENST00000378990_CCDC28B_chr1_32670811_ENST00000373602_length(amino acids)=451AA_BP=
MANMQGLVERLERAVSRLESLSAESHRPPGNCGEVNGVIAGVAPSVEAFDKLMDSMVAEFLKNSRILAGDVETHNDVAALLKPISEKIQE
IQTFRERNRGSNMFNHLSAVSESIPALGWIAVSPKPGPYVKEMNDAATFYTNRVLKDYKHSDLRHVDWVKSYLNIWSELQAYIKEHHTTG
LTWSKTGPVASTVSAFSVLSSGPGLPPPPPPLPPPGPPPLFENEGKKEESSPSRSALFAQLNQGEAITKGLRHVTDDQKTYKNPSLRAQG
GQTQSPTKSHTPSPTSPKSYPSQKHAPVLELEGKKWRVEYQEDRNDLVISETELKQVAYIFKCEKSTIQIKGKVNSIIIDNCKKLGLVFD
NVVGIVEVINSQDIQIQVMGRVPTISINKTEGCHIYLSEDALDCEIVSAKSSEMNILIPQDGDYREFPIPEQFKTAWDGSKLITEPAEIM

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

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Fusion Gene PPI Analysis for CAP2-CCDC28B


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 CAP2-CCDC28B


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 CAP2-CCDC28B


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