Fusion Gene Studies
in Kim Lab

FusionBase FusionGDB FusionGDB2 FusionPDB FusionNeoAntigen FusionAI FusionNW FGviewer Publication Contact
FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact

Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:ARL16-CSNK1D (FusionGDB2 ID:HG339231TG1453)

Fusion Gene Summary for ARL16-CSNK1D

check button Fusion gene summary
Fusion gene informationFusion gene name: ARL16-CSNK1D
Fusion gene ID: hg339231tg1453
HgeneTgene
Gene symbol

ARL16

CSNK1D

Gene ID

339231

1453

Gene nameADP ribosylation factor like GTPase 16casein kinase 1 delta
Synonyms-ASPS|CKI-delta|CKId|CKIdelta|FASPS2|HCKID
Cytomap('ARL16')('CSNK1D')

17q25.3

17q25.3

Type of geneprotein-codingprotein-coding
DescriptionADP-ribosylation factor-like protein 16casein kinase I isoform deltacasein kinase Itau-protein kinase CSNK1D
Modification date2020032020200313
UniProtAcc

Q0P5N6

.
Ensembl transtripts involved in fusion geneENST00000397498, ENST00000570561, 
ENST00000574938, ENST00000573392, 
ENST00000576135, 
Fusion gene scores* DoF score5 X 3 X 4=6020 X 19 X 9=3420
# samples 522
** MAII scorelog2(5/60*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(22/3420*10)=-3.9584208962486
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ARL16 [Title/Abstract] AND CSNK1D [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointARL16(79650566)-CSNK1D(80223672), # samples:1
Anticipated loss of major functional domain due to fusion event.ARL16-CSNK1D 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.
ARL16-CSNK1D 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.
ARL16-CSNK1D 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.
ARL16-CSNK1D 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.
ARL16-CSNK1D seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
ARL16-CSNK1D seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
ARL16-CSNK1D seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
ARL16-CSNK1D seems lost the major protein functional domain in Tgene partner, which is a kinase 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
TgeneCSNK1D

GO:0006468

protein phosphorylation

16618118

TgeneCSNK1D

GO:0018105

peptidyl-serine phosphorylation

25500533

TgeneCSNK1D

GO:0051225

spindle assembly

10826492


check buttonFusion gene breakpoints across ARL16 (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 CSNK1D (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
ChimerDB4BLCATCGA-BL-A0C8-01AARL16chr17

79650566

-CSNK1Dchr17

80223672

-


Top

Fusion Gene ORF analysis for ARL16-CSNK1D

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-intronENST00000397498ENST00000578904ARL16chr17

79650566

-CSNK1Dchr17

80223672

-
5UTR-3CDSENST00000570561ENST00000314028ARL16chr17

79650566

-CSNK1Dchr17

80223672

-
5UTR-3CDSENST00000570561ENST00000392334ARL16chr17

79650566

-CSNK1Dchr17

80223672

-
5UTR-3CDSENST00000570561ENST00000398519ARL16chr17

79650566

-CSNK1Dchr17

80223672

-
5UTR-3CDSENST00000574938ENST00000314028ARL16chr17

79650566

-CSNK1Dchr17

80223672

-
5UTR-3CDSENST00000574938ENST00000392334ARL16chr17

79650566

-CSNK1Dchr17

80223672

-
5UTR-3CDSENST00000574938ENST00000398519ARL16chr17

79650566

-CSNK1Dchr17

80223672

-
5UTR-intronENST00000570561ENST00000578904ARL16chr17

79650566

-CSNK1Dchr17

80223672

-
5UTR-intronENST00000574938ENST00000578904ARL16chr17

79650566

-CSNK1Dchr17

80223672

-
Frame-shiftENST00000397498ENST00000314028ARL16chr17

79650566

-CSNK1Dchr17

80223672

-
Frame-shiftENST00000397498ENST00000398519ARL16chr17

79650566

-CSNK1Dchr17

80223672

-
In-frameENST00000397498ENST00000392334ARL16chr17

79650566

-CSNK1Dchr17

80223672

-
intron-3CDSENST00000573392ENST00000314028ARL16chr17

79650566

-CSNK1Dchr17

80223672

-
intron-3CDSENST00000573392ENST00000392334ARL16chr17

79650566

-CSNK1Dchr17

80223672

-
intron-3CDSENST00000573392ENST00000398519ARL16chr17

79650566

-CSNK1Dchr17

80223672

-
intron-3CDSENST00000576135ENST00000314028ARL16chr17

79650566

-CSNK1Dchr17

80223672

-
intron-3CDSENST00000576135ENST00000392334ARL16chr17

79650566

-CSNK1Dchr17

80223672

-
intron-3CDSENST00000576135ENST00000398519ARL16chr17

79650566

-CSNK1Dchr17

80223672

-
intron-intronENST00000573392ENST00000578904ARL16chr17

79650566

-CSNK1Dchr17

80223672

-
intron-intronENST00000576135ENST00000578904ARL16chr17

79650566

-CSNK1Dchr17

80223672

-

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)
ENST00000397498ARL16chr1779650566-ENST00000392334CSNK1Dchr1780223672-19462913861444352

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
ENST00000397498ENST00000392334ARL16chr1779650566-CSNK1Dchr1780223672-0.0299682730.9700317

Top

Fusion Genomic Features for ARL16-CSNK1D


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

Top

Fusion Protein Features for ARL16-CSNK1D


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/chr17:79650566/chr17:80223672)
- 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
ARL16

Q0P5N6

.
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
HgeneARL16chr17:79650566chr17:80223672ENST00000397498-2530_3764198.0Nucleotide bindingGTP
TgeneCSNK1Dchr17:79650566chr17:80223672ENST0000031402809278_36425416.0RegionNote=Centrosomal localization signal (CLS)
TgeneCSNK1Dchr17:79650566chr17:80223672ENST0000031402809317_34225416.0RegionAutoinhibitory
TgeneCSNK1Dchr17:79650566chr17:80223672ENST00000392334010278_36425420.3333333333333RegionNote=Centrosomal localization signal (CLS)
TgeneCSNK1Dchr17:79650566chr17:80223672ENST00000392334010317_34225420.3333333333333RegionAutoinhibitory

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneARL16chr17:79650566chr17:80223672ENST00000397498-25139_14264198.0Nucleotide bindingGTP
HgeneARL16chr17:79650566chr17:80223672ENST00000397498-2582_8664198.0Nucleotide bindingGTP
TgeneCSNK1Dchr17:79650566chr17:80223672ENST00000314028099_27725416.0DomainProtein kinase
TgeneCSNK1Dchr17:79650566chr17:80223672ENST000003923340109_27725420.3333333333333DomainProtein kinase
TgeneCSNK1Dchr17:79650566chr17:80223672ENST000003140280915_2325416.0Nucleotide bindingATP
TgeneCSNK1Dchr17:79650566chr17:80223672ENST0000039233401015_2325420.3333333333333Nucleotide bindingATP


Top

Fusion Gene Sequence for ARL16-CSNK1D


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.
>6580_6580_1_ARL16-CSNK1D_ARL16_chr17_79650566_ENST00000397498_CSNK1D_chr17_80223672_ENST00000392334_length(transcript)=1946nt_BP=291nt
GTCTTCCGCTCTCCCGCTAACGCTGCGCGCTAATTGGACGCGCCCTTGGAACAATGAGCCCTAAGAACCAATGAGAAGTCCGAAGGTGAG
AACTATCCAATGAGAGTGGCCGGTGGGCGGGCCTTGAGCCGCGGCGCCGAGCTACGGGTGCCGGGTGGAGCGAAGCACGGAATGTGTCTC
CTGCTGGGGGCCACGGGCGTCGGGAAGACGCTGCTGGTGAAACGGCTGCAGGAGGTGAGCTCCCGGGATGGGAAAGGCGACCTGGGGGAG
CCGCCCCCGACACGGCCCACGGTACGGACATTGCTGCAGGAGAAGAGGTTGCCATCAAGCTTGAATGTGTCAAAACCAAACACCCTCAGC
TCCACATTGAGAGCAAAATCTACAAGATGATGCAGGGAGGAGTGGGCATCCCCACCATCAGATGGTGCGGGGCAGAGGGGGACTACAACG
TCATGGTGATGGAGCTGCTGGGGCCAAGCCTGGAGGACCTCTTCAACTTCTGCTCCAGGAAATTCAGCCTCAAAACCGTCCTGCTGCTTG
CTGACCAAATGATCAGTCGCATCGAATACATTCATTCAAAGAACTTCATCCACCGGGATGTGAAGCCAGACAACTTCCTCATGGGCCTGG
GGAAGAAGGGCAACCTGGTGTACATCATCGACTTCGGGCTGGCCAAGAAGTACCGGGATGCACGCACCCACCAGCACATCCCCTATCGTG
AGAACAAGAACCTCACGGGGACGGCGCGGTACGCCTCCATCAACACGCACCTTGGAATTGAACAATCCCGAAGAGATGACTTGGAGTCTC
TGGGCTACGTGCTAATGTACTTCAACCTGGGCTCTCTCCCCTGGCAGGGGCTGAAGGCTGCCACCAAGAGACAGAAATACGAAAGGATTA
GCGAGAAGAAAATGTCCACCCCCATCGAAGTGTTGTGTAAAGGCTACCCTTCCGAATTTGCCACATACCTGAATTTCTGCCGTTCCTTGC
GTTTTGACGACAAGCCTGACTACTCGTACCTGCGGCAGCTTTTCCGGAATCTGTTCCATCGCCAGGGCTTCTCCTATGACTACGTGTTCG
ACTGGAACATGCTCAAATTTGGTGCCAGCCGGGCCGCCGATGACGCCGAGCGGGAGCGCAGGGACCGAGAGGAGCGGCTGAGACACTCGC
GGAACCCGGCTACCCGCGGCCTCCCTTCCACAGCCTCCGGCCGCCTGCGGGGGACGCAGGAAGTGGCTCCCCCCACACCCCTCACCCCTA
CCTCACACACGGCTAACACCTCCCCCCGGCCCGTCTCCGGCATGGAGAGAGAGCGGAAAGTGAGTATGCGGCTGCACCGCGGGGCCCCCG
TCAACATCTCCTCGTCCGACCTCACAGGCCGACAAGATACCTCTCGCATGTCCACCTCACAGAATAGCATTCCTTTCGAACACCACGGCA
AGTAGCTGCTCGTCTCCCATCGGAAGGCAGCACTGGATTCCTGGTCGGGTGGCTTCCAGTGGTCTTCAGTCTGTCGTGCACCGATGAGAA
CTCTCCTTATTGCTGTGAAGGGCAGACAATGCATGGCTGATCTACTCTGTTACCAATGGCTTTACTAGTGACACGTCCCCCGGTCTAGGA
TCGAAATGTTAACACCGGGAGCTCTCCAGGCCACTCACCCAGCGACGCTCGTGGGGGAAACATACTAAACGGACAGACTCCAAGAGCTGC
CACCGCTGGGGCTGCACTGCGGCCCCCCACGTGAACTCGGTTGTAACGGGGCTGGGAAGAAAAGCAGAGAGAGAATTGCAGAGAATCAGA
CTCCTTTTCCAGGGCCTCAGCTCCCTCCAGTGGTGGCCGCCCTGTACTCCCTGACGATTCCACTGTAACTACCAATCTTCTACTTGGTTA

>6580_6580_1_ARL16-CSNK1D_ARL16_chr17_79650566_ENST00000397498_CSNK1D_chr17_80223672_ENST00000392334_length(amino acids)=352AA_BP=
MMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYI
IDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPI
EVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLKFGASRAADDAERERRDREERLRHSRNPATRGLP

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

Top

Fusion Gene PPI Analysis for ARL16-CSNK1D


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


Top

Related Drugs for ARL16-CSNK1D


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for ARL16-CSNK1D


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC3808874ADVANCED SLEEP PHASE SYNDROME, FAMILIAL, 23GENOMICS_ENGLAND;UNIPROT
TgeneC1858496Advanced Sleep-Phase Syndrome, Familial1CTD_human;ORPHANET