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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:CCDC28A-CLEC16A (FusionGDB2 ID:HG25901TG23274)

Fusion Gene Summary for CCDC28A-CLEC16A

check button Fusion gene summary
Fusion gene informationFusion gene name: CCDC28A-CLEC16A
Fusion gene ID: hg25901tg23274
HgeneTgene
Gene symbol

CCDC28A

CLEC16A

Gene ID

25901

23274

Gene namecoiled-coil domain containing 28AC-type lectin domain containing 16A
SynonymsC6orf80|CCRL1APGop-1|KIAA0350
Cytomap('CCDC28A')('CLEC16A')

6q24.1

16p13.13

Type of geneprotein-codingprotein-coding
Descriptioncoiled-coil domain-containing protein 28Achemokine C-C motif receptor-like 1 adjacentprotein CLEC16AC-type lectin domain family 16 member A
Modification date2020032120200313
UniProtAcc

Q8IWP9

.
Ensembl transtripts involved in fusion geneENST00000332797, 
Fusion gene scores* DoF score4 X 5 X 4=8014 X 13 X 10=1820
# samples 617
** MAII scorelog2(6/80*10)=-0.415037499278844
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(17/1820*10)=-3.42033179894836
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CCDC28A [Title/Abstract] AND CLEC16A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCCDC28A(139101122)-CLEC16A(11260245), # samples:2
Anticipated loss of major functional domain due to fusion event.CCDC28A-CLEC16A 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.
CCDC28A-CLEC16A 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.
CCDC28A-CLEC16A 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.
CCDC28A-CLEC16A 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

check buttonFusion gene breakpoints across CCDC28A (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 CLEC16A (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
* 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
ChimerDB4LUADTCGA-50-5049-01ACCDC28Achr6

139101122

+CLEC16Achr16

11260245

+


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Fusion Gene ORF analysis for CCDC28A-CLEC16A

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-5UTRENST00000332797ENST00000381822CCDC28Achr6

139101122

+CLEC16Achr16

11260245

+
5CDS-intronENST00000332797ENST00000409552CCDC28Achr6

139101122

+CLEC16Achr16

11260245

+
5CDS-intronENST00000332797ENST00000465491CCDC28Achr6

139101122

+CLEC16Achr16

11260245

+
In-frameENST00000332797ENST00000409790CCDC28Achr6

139101122

+CLEC16Achr16

11260245

+

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)
ENST00000332797CCDC28Achr6139101122+ENST00000409790CLEC16Achr1611260245+47677471551267370

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
ENST00000332797ENST00000409790CCDC28Achr6139101122+CLEC16Achr1611260245+0.0371126120.96288735

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Fusion Genomic Features for CCDC28A-CLEC16A


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)
CCDC28Achr6139101122+CLEC16Achr1611260244+4.54E-070.9999995
CCDC28Achr6139101122+CLEC16Achr1611260244+4.54E-070.9999995

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 CCDC28A-CLEC16A


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/chr6:139101122/chr16:11260245)
- 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
CCDC28A

Q8IWP9

.
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
TgeneCLEC16Achr6:139101122chr16:11260245ENST0000038182204892_9330141.0Compositional biasNote=Ser-rich
TgeneCLEC16Achr6:139101122chr16:11260245ENST00000409552021892_9330907.0Compositional biasNote=Ser-rich
TgeneCLEC16Achr6:139101122chr16:11260245ENST000004097902124892_9338801054.0Compositional biasNote=Ser-rich
TgeneCLEC16Achr6:139101122chr16:11260245ENST000003818220451_1980141.0DomainFPL
TgeneCLEC16Achr6:139101122chr16:11260245ENST0000040955202151_1980907.0DomainFPL

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCCDC28Achr6:139101122chr16:11260245ENST00000332797+36234_263197275.0Coiled coilOntology_term=ECO:0000255
TgeneCLEC16Achr6:139101122chr16:11260245ENST00000409790212451_1988801054.0DomainFPL


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Fusion Gene Sequence for CCDC28A-CLEC16A


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.
>13766_13766_1_CCDC28A-CLEC16A_CCDC28A_chr6_139101122_ENST00000332797_CLEC16A_chr16_11260245_ENST00000409790_length(transcript)=4767nt_BP=747nt
GGCGGAGTAGCTTCCGGAAAGGGTACTGCATTTCCCGTTTCTACCTCCACTGCACCCGCTTATTGCGTCTTGCTCCTGGGTCACAGAGCC
TAAAACGACACACCCAACACGCCCGCCGGAGTTACAGCTAAAGGAAGGACAGGGGAAGCAATGAAATGCCGAGGGCGGAGCCAAGAGCGA
CACTGGGGGAGCAGGAAAAGGCGGGGCTTCCGCTTGGGGCATGGAGGCTGTACCTCTTACGTCACTTCCGTAAACAAACGGAGCTGCGGA
GGAGCGGGTCCCGGGATGTGACCGGGGCTCTGCTTGTGGCTGCGGCGGTGGCTTCTGAGGCTGTCGGGTCTTTGCGGGTTGCGGAAGGGG
GCCCCAATACCCTTCTTCTTCAGGTCTTAAGAAGCTGGCCGTGGTGCAATAAGGAACTTAAAACAATGGAAGAGCGGAAAGTGAAGAGGA
GGAGTCCTAAGTCTTTTAGTGCCCACTGTACTCAGGTTGTCAATGCCAAAAAAAATGCCATTCCAGTGAGTAAAAGCACAGGGTTTTCAA
ATCCTGCATCACAGTCAACTTCACAGCGACCAAAGTTAAAAAGAGTGATGAAAGAAAAGACCAAACCTCAGGGTGGAGAGGGCAAAGGCG
CTCAGTCAACTCCGATCCAGCACTCCTTCCTCACTGATGTCTCAGATGTTCAGGAGATGGAGAGAGGGCTGCTCAGTCTTTTGAATGATT
TCCACTCTGGAAAACTTCAAGCATTTGGCTTCGCCGTGGCCCAGTGCATAAACCAGCACAGCTCCCCGTCCCTGTCCTCACAGTCGCCAC
CCTCCGCCAGCGGGAGCCCCAGCGGCAGCGGGAGCACCAGCCACTGCGACTCTGGAGGCACCAGCTCGTCCTCCACCCCCTCCACAGCCC
AGAGTCCAGCAGATGCCCCCATGAGTCCAGAACTGCCTAAGCCTCACCTTCCTGACCAGTTGGTAATCGTCAACGAAACGGAAGCAGACT
CTAAGCCCAGCAAGAACGTGGCCAGGAGCGCAGCCGTGGAGACAGCCAGCCTGTCCCCCAGCCTCGTCCCTGCCCGGCAGCCCACCATTT
CCCTGCTCTGCGAGGACACGGCTGACACGCTGAGCGTCGAATCGCTGACCCTTGTCCCCCCAGTTGACCCCCACAGCCTCCGCAGCCTCA
CCGGCATGCCCCCGCTGTCCACGCCGGCTGCCGCCTGCACAGAGCCCGTGGGCGAAGAGGCTGCATGTGCTGAGCCTGTGGGCACCGCTG
AGGACTGAGTCAGTGCCGGGGCCTCCCTTTGTGTGTGTGGCCCCGCTGGTAGGGACCCCAGTGCCGCTGACTGGCAAGACACACTGGGAG
CACCCACCATTCTGTGCGGCCCCCAGCAGCCATCTCAACCACCTATCCCTGCGCTCCCTTGAATGGGAAGAAGCCCCACGTTGTCCTTGA
ATTCCTTTTTCACTTTGCATCTCTTCACGTGCAGGCTGGGACCAGCGGAGACACCGCGGCGAATGCAGATGACTGCACCGGCCACTCAGG
GAGCTGCCTGGGCTCCGTGTCTCTGAGCCCCGGGTGGCAGGACCCACCGGCACCTCTTTCTTCCTCTGTCATATGGCTCCTCTGTCACCA
GCCCCAGTGTGCACAGAAGAATTGGACCAGGTCACTGTACGTAGAAATTTGTAGAAAAGCAGACTTAGATAAACATCTCCTTTGGATATT
TATTTCCGCTTTTGGCAGCAGGTGAACATTTATTTTTAAAACTTCTATTTAAAAGAAGTCCAAAAACATCAACACTAAGGTTTGATGTCA
TGTGAAAAGTGTAATAATAACAGTTAAGATTTCATGATCATTTTCACTGGACCTTTCCTGATATTTTGTTTCAGAGTTCTTAGTGTGGCT
TTTTCCATTTATTTAAGTGATTCTTTGTTACTCACTAACTCTGCAAGCCTGTGGAATAATGAAGTACCTTCCTGGAAAGTTTGGATTATT
TTTTAAACAAAAACAAGGGAGATACATGTATTCTCAGGTACACACAGAGCTGAGAGGGCTGAATGGTTTTCTGCTATAGCAGCCGAGAGG
CCTCCCATCATGGAAAGATTTCTCCAGGAAAAGGAGGAATGTAGCCAGCTCCCCACTCAGGACGCTTCCTCATTTCTCTTCACCAAAACC
AAACAGAGACAGCTTCCAGCACCTTCTTCAGTGTTACCATCTCTAAGAAGGAACCAGTTGGGACCGTGAAGACTCCCGACCCTGTGGCCA
TGATGGAAATCAAAGGAAGACACCCTCTACGTCACCTGCCCTCGACTGTGTGTGCCCACATGTGCCGAGAGATGGCCCAGAGCCAGTTCC
CCTCCAGCTGCAAGGGCATGGTGTCCCCAGAGCTCTGAGTCTGTCACTCTCCCTCTGCTACTGCTGCTGATCTGAATATGGAAACCCCAT
GGTTCCCTTCCCCATTCGGACTGGGTGTGTACAAGCAAGGACCCAGATGCATCAGACACAGCCCCCAAGATGTTCCTTTCTACTCGGCCA
GCTCGGGAGCCAGACACAGCACTCACAGCCCAGGCCGTGATCCACCCTCCCCAAGTCCACCAGGGCCAGCGGCCCCTCACCTCTCTGGTC
ACTGGTGAGACCTTCCACAACTTTCCTCCAGACCTGCCAGCAGATGTGCCCACCAGGGGCATTAGGTATCCGCCGGAGCCTGGCCATAGG
GTAGTCTCGGGAGCCGCGCTGAGATCTTTTGCCACCTGCATTTTAGAAGAACATGGTCTCTGTCTCCTCGGCCCAGCCAGCTGTCCCGGC
AAGGCCTGCCGAGGGCAGTTTTCAACCTCATGAAGGAAACACAGTCCTGCCAAGGAGGGGGAGTGGCGCCCATGGGGACAGGCCTCAGTC
CTTAGAAGCCCTCTGGGTAGCTGTGCCCACCCAGCCTTCATGGCTGCAGGTACAAGGACCTTTGCTTCCATAGAGAAAACGCACAGCTCA
GAAAGGGGGCCACATGGGCAGAAACCCAAAGGAAGGACAAACCACGACCACCGTGGCCATCTGCAGAATCCCTGGAAGAGAAGGAAGGCA
GGGTGGAGCGGGGGGAAGACCATCATGGAGAGAAGGACCACAGCATCAGGAGACGGGACACGCCACACCCAGCAGGCAGCCTGTGTGTTG
CTTAATTTTTTAAGAGCAAGAGGGGTAGAGAGGATCAAGCTGGCCCTGGCTGGAGATGGCTAGCCCCTGAGACATGCACTTCTGGTTTTG
AAATGACTCTGTCTGTGGGGCAGCAGAAACTAGAGAAGGCAAGTGGCTGCCCCACCCCAAGGCGTGACCAGGAGGAACAGCCTGCAGCTC
ACTCCATGCCACACGGGTGGGCCACCAGCCTGCTGTCAGAAGTCTCTGGGCTCCAACTGGTCTTGTAACCACTGAGCACTGAAGGAGAGA
GGTCTTGGTCAGGGCTGGACAGCATGCCCGGGAGGACCAGCAGAGGATTAAAGGTGACTGGGAGGACCAGCGGAGGATAAAAGACACTGC
TCAGGGCAGGGCTTCTACCCTGCATCCCTGGCCAAGAAAAGGGCAGTCCCCATGTGGGCTTGCAGGGTCACTCTCAGGGGCCTCTTTCAG
CTGGGGCTGGCAACTTGCGTCTGGGGGACACCTCCAGGTGTGTGGGGTGAGGATTTCCTATAACCAGGGCTCCCAGAAGCTTTGCTTATG
TAAGGAGGTCTGGGAGCCAGCCCATTGGAGGCCACCAGCCATTTTGGCTTCAAAGGACCCCACCTCACCCAGGTCTCAGCGGCAGTGGGC
ACAGCTATGTCTTCAGGAGCTCCCGTCAAACCTCATAGCTGGGGCGCTCCCAGACAGGCCAGTCCAGACAGGACACGCTGGGCCCCTGGC
ATCCAGAGGAAGAGCCAGGAGTGTGGGAAGGCCCACAGTGGGGGCTGTGGCTTCTGACACTCAGGTCATAGCCTCAGAGGTCTGAGGTCA
GCCCCCACAGACCCATCCGGCCCGCCCCCCAAGTCCCTGCAGAGAGCACTTAGAGTTATGGCCCAGGCCCTGGTCCACCCTTCCCCTGTG
CACCTCCGGCTGGGTTTGCCAAGTCAGGGAGCAGGGCTGGCCGCAGGAACTCCCAAACCTTGGCTTTGAATATTGTTGTGGAGGTGTGCT
CGTCCCTTTCTGGACGTGCAAGGTACCTGTCCCAGCAGGTCAGATGGGGCCAGCTGAGGCGCTCCCCCAGGCAGGAAGGGCCAGCCTTCA
CCATCGCGTGGGATTGGGAGGAGGGGCCTCCGTGAGCAGCCCCTCCTCTGCCGCTGTCCCAGCCCAGTCCCTCTCCCGGAGCCTTGGCAG
CCTCCCACAACCCAGACACTTGCGTTCACAAGCAACCTAAGGGGCAGGTGAAGAAGCGCAGCCCTGCCAGACGCGCTAGATTCCTCTAAG
GTCTCTGAGATGCACCGTTTTTTAAAAAGGCGTGGGGTGAACTGATTTTGATCTTCTTGTCTAGATGCAATAAATAAATCTGAAGCATTT
AATGTAGTCATCTTGACATTGGGCCTACACTGTACGAGTTCCTTATGTTTCCTTGAGCTAAAAATATGTAAATAATTTTTGTCCCAGTGA
GAACCGAGGGTTAGAAAACCTCGATGCCTCTGAGCCTCGGGACCGCTCTAGGGAAGTACCTGCTTTCGCCAGCATGACTCATGCTTCGTG

>13766_13766_1_CCDC28A-CLEC16A_CCDC28A_chr6_139101122_ENST00000332797_CLEC16A_chr16_11260245_ENST00000409790_length(amino acids)=370AA_BP=197
MPRAEPRATLGEQEKAGLPLGAWRLYLLRHFRKQTELRRSGSRDVTGALLVAAAVASEAVGSLRVAEGGPNTLLLQVLRSWPWCNKELKT
MEERKVKRRSPKSFSAHCTQVVNAKKNAIPVSKSTGFSNPASQSTSQRPKLKRVMKEKTKPQGGEGKGAQSTPIQHSFLTDVSDVQEMER
GLLSLLNDFHSGKLQAFGFAVAQCINQHSSPSLSSQSPPSASGSPSGSGSTSHCDSGGTSSSSTPSTAQSPADAPMSPELPKPHLPDQLV
IVNETEADSKPSKNVARSAAVETASLSPSLVPARQPTISLLCEDTADTLSVESLTLVPPVDPHSLRSLTGMPPLSTPAAACTEPVGEEAA

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

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Fusion Gene PPI Analysis for CCDC28A-CLEC16A


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 CCDC28A-CLEC16A


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 CCDC28A-CLEC16A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0011854Diabetes Mellitus, Insulin-Dependent2CTD_human
TgeneC0026769Multiple Sclerosis2CTD_human
TgeneC0162538Immunoglobulin A deficiency (disorder)2CTD_human
TgeneC0205734Diabetes, Autoimmune2CTD_human
TgeneC0342302Brittle diabetes2CTD_human
TgeneC0751324Multiple Sclerosis, Acute Fulminating2CTD_human
TgeneC3837958Diabetes Mellitus, Ketosis-Prone2CTD_human
TgeneC4554117Diabetes Mellitus, Sudden-Onset2CTD_human
TgeneC0001403Addison Disease1CTD_human
TgeneC0008312Primary biliary cirrhosis1CTD_human
TgeneC0023892Biliary cirrhosis1CTD_human
TgeneC0024141Lupus Erythematosus, Systemic1CTD_human
TgeneC0238065Secondary Biliary Cholangitis1CTD_human
TgeneC0242380Libman-Sacks Disease1CTD_human
TgeneC4551595Biliary Cirrhosis, Primary, 11CTD_human