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:SHISA9-CCL19 (FusionGDB2 ID:81134)

Fusion Gene Summary for SHISA9-CCL19

check button Fusion gene summary
Fusion gene informationFusion gene name: SHISA9-CCL19
Fusion gene ID: 81134
HgeneTgene
Gene symbol

SHISA9

CCL19

Gene ID

729993

6363

Gene nameshisa family member 9C-C motif chemokine ligand 19
SynonymsCKAMP44CKb11|ELC|MIP-3b|MIP3B|SCYA19
Cytomap

16p13.12

9p13.3

Type of geneprotein-codingprotein-coding
Descriptionprotein shisa-9cystine-knot AMPAR modulating proteinshisa homolog 9C-C motif chemokine 19CC chemokine ligand 19CK beta-11EBI1-ligand chemokineMIP-3-betabeta chemokine exodus-3chemokine (C-C motif) ligand 19epstein-Barr virus-induced molecule 1 ligand chemokineexodus-3macrophage inflammatory protein 3-betasmall
Modification date2020031320200315
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000424107, ENST00000558583, 
ENST00000558318, ENST00000423335, 
ENST00000482916, 		ENST00000311925, 
ENST00000485502, ENST00000378800, 
Fusion gene scores* DoF score6 X 6 X 3=1082 X 1 X 2=4
# samples 62
** MAII scorelog2(6/108*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(2/4*10)=2.32192809488736
Context

PubMed: SHISA9 [Title/Abstract] AND CCL19 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSHISA9(13297406)-CCL19(34690339), # 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
TgeneCCL19

GO:0001768

establishment of T cell polarity

12729902

TgeneCCL19

GO:0002407

dendritic cell chemotaxis

15778365

TgeneCCL19

GO:0002408

myeloid dendritic cell chemotaxis

14592837

TgeneCCL19

GO:0034695

response to prostaglandin E

14592837

TgeneCCL19

GO:0043123

positive regulation of I-kappaB kinase/NF-kappaB signaling

15059845

TgeneCCL19

GO:0043552

positive regulation of phosphatidylinositol 3-kinase activity

15059845|15778365

TgeneCCL19

GO:0045860

positive regulation of protein kinase activity

14592837|15059845

TgeneCCL19

GO:0046330

positive regulation of JNK cascade

15778365

TgeneCCL19

GO:0051209

release of sequestered calcium ion into cytosol

14592837

TgeneCCL19

GO:0051897

positive regulation of protein kinase B signaling

15059845|15778365

TgeneCCL19

GO:0070374

positive regulation of ERK1 and ERK2 cascade

15778365

TgeneCCL19

GO:0071731

response to nitric oxide

16249377

TgeneCCL19

GO:0090023

positive regulation of neutrophil chemotaxis

21051556

TgeneCCL19

GO:1901224

positive regulation of NIK/NF-kappaB signaling

15059845

TgeneCCL19

GO:2000147

positive regulation of cell motility

15778365

TgeneCCL19

GO:2000669

negative regulation of dendritic cell apoptotic process

15059845


check buttonFusion gene breakpoints across SHISA9 (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 CCL19 (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
ChimerDB4LGGTCGA-CS-5397-01ASHISA9chr16

13297406

+CCL19chr9

34690339

-


Top

Fusion Gene ORF analysis for SHISA9-CCL19

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-frameENST00000424107ENST00000311925SHISA9chr16

13297406

+CCL19chr9

34690339

-
5CDS-intronENST00000424107ENST00000485502SHISA9chr16

13297406

+CCL19chr9

34690339

-
5CDS-intronENST00000424107ENST00000378800SHISA9chr16

13297406

+CCL19chr9

34690339

-
In-frameENST00000558583ENST00000311925SHISA9chr16

13297406

+CCL19chr9

34690339

-
5CDS-intronENST00000558583ENST00000485502SHISA9chr16

13297406

+CCL19chr9

34690339

-
5CDS-intronENST00000558583ENST00000378800SHISA9chr16

13297406

+CCL19chr9

34690339

-
intron-3CDSENST00000558318ENST00000311925SHISA9chr16

13297406

+CCL19chr9

34690339

-
intron-intronENST00000558318ENST00000485502SHISA9chr16

13297406

+CCL19chr9

34690339

-
intron-intronENST00000558318ENST00000378800SHISA9chr16

13297406

+CCL19chr9

34690339

-
intron-3CDSENST00000423335ENST00000311925SHISA9chr16

13297406

+CCL19chr9

34690339

-
intron-intronENST00000423335ENST00000485502SHISA9chr16

13297406

+CCL19chr9

34690339

-
intron-intronENST00000423335ENST00000378800SHISA9chr16

13297406

+CCL19chr9

34690339

-
intron-3CDSENST00000482916ENST00000311925SHISA9chr16

13297406

+CCL19chr9

34690339

-
intron-intronENST00000482916ENST00000485502SHISA9chr16

13297406

+CCL19chr9

34690339

-
intron-intronENST00000482916ENST00000378800SHISA9chr16

13297406

+CCL19chr9

34690339

-

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)
ENST00000424107SHISA9chr1613297406+ENST00000311925CCL19chr934690339-17921292731539488
ENST00000558583SHISA9chr1613297406+ENST00000311925CCL19chr934690339-17921292731539488

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
ENST00000424107ENST00000311925SHISA9chr1613297406+CCL19chr934690339-0.178740470.8212595
ENST00000558583ENST00000311925SHISA9chr1613297406+CCL19chr934690339-0.178740470.8212595

Top

Fusion Genomic Features for SHISA9-CCL19


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.

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.

Top

Fusion Protein Features for SHISA9-CCL19


check button Go to

FGviewer for the breakpoints of chr16:13297406-chr9:34690339

.
- 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
..
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: 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.

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
HgeneSHISA9chr16:13297406chr9:34690339ENST00000424107+3524_149282.3333333333333425.0Topological domainExtracellular
HgeneSHISA9chr16:13297406chr9:34690339ENST00000424107+35150_170282.3333333333333425.0TransmembraneHelical

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSHISA9chr16:13297406chr9:34690339ENST00000423335+12171_4240222.0Topological domainCytoplasmic
HgeneSHISA9chr16:13297406chr9:34690339ENST00000423335+1224_1490222.0Topological domainExtracellular
HgeneSHISA9chr16:13297406chr9:34690339ENST00000424107+35171_424282.3333333333333425.0Topological domainCytoplasmic
HgeneSHISA9chr16:13297406chr9:34690339ENST00000423335+12150_1700222.0TransmembraneHelical


Top

Fusion Gene Sequence for SHISA9-CCL19


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_ENST00000424107_ENST00000311925_TCGA-CS-5397-01A_SHISA9_chr16_13297406_+_CCL19_chr9_34690339_length(transcript)=1792nt_BP=1292nt
CTCTTCAGCGCACTTGGCGAGCTGGTGAGGTGAGAGGGATACTGCGAGAGGGCTAGGGGCGGCCAGTCCGGGGCTGCCGGCCAAGGCTAG
GCGCTGCCAGCCCGATTCTCCTCTGCTCTCCACCCCCGCCTCACCCAGTGGCCGGCCGGACCTGCACCCCGCGCTTGACCCCGCTCATCC
TCCCCCCGCCCGGCCGGGCGCGCTCCTCCCCGGCCGGCCCCTCGGCGCGCGGCGCGCTGGAGGCGAACGCGGGCTGAGGCGAACGCGGGC
TGAGCCGAGCGCAGTGGCCGCCGACCACCGAGCGCCCCGCGCCGCTCCCTGCATGTGCGGCCCGCGGCGGCTCGCAGCTCCCGGCAGCAG
CCTCGGCAGCTTCGGCCGCGCCTCGAGAGGCGGCCGCAGAGGCTCCAGCGGCGGCCGAGCGGCCGAGCCCGGGCTGGGAGACACCATGCG
CCGCGTCCTTCGGCTGCTCCTCGGTTGCTTCCTCACCGAGCTGTGCGCCCGCGTGTGCCGGGCGCAGGAGCGAGCGGGACACGGGCAGCT
GGCGCAACTGGGCGGCGTGTTGCTGCTGGCGGGGGGCAACCGCTCCGGGGCCGCCTCCGGAGAGGCCAGCGAGGGCGCTGAGGCATCGGA
CGCGCCCCCGACCCGGGCGCCCACGCCGGACTTCTGCCGGGGCTACTTCGATGTCATGGGCCAGTGGGACCCGCCGTTCAACTGCAGCTC
GGGCGACTTCATCTTCTGCTGCGGGACTTGTGGCTTCCGGTTCTGCTGCACGTTTAAGAAGCGGCGACTGAACCAAAGCACCTGCACCAA
CTACGACACGCCGCTCTGGCTCAACACCGGCAAGCCCCCCGCCCGCAAGGACGACCCCTTGCACGACCCCACCAAGGACAAGACCAACCT
GATCGTCTACATCATCTGCGGGGTGGTGGCCGTCATGGTGCTCGTGGGCATCTTCACCAAGCTGGGGCTGGAGAAAGCGCACCGGCCCCA
AAGGGAGCACATGTCCAGGGCCCTTGCGGATGTCATGAGACCACAGGGCCACTGCAACACTGATCACATGGAGAGAGACCTAAACATCGT
TGTCCACGTCCAGCATTATGAGAACATGGACACGAGAACCCCCATAAATAATCTTCATGCCACCCAGATGAACAACGCAGTGCCCACCTC
TCCTCTGCTCCAGCAGATGGGCCATCCACATTCGTACCCGAACCTGGGCCAGATCTCCAACCCCTATGAACAGCAGCCACCAGGAAAAGA
GCTCAACAAGTACGCCTCCTTAAAGGCAGTCGCCCCAACTCTGAGTGGCACCAATGATGCTGAAGACTGCTGCCTGTCTGTGACCCAGAA
ACCCATCCCTGGGTACATCGTGAGGAACTTCCACTACCTTCTCATCAAGGATGGCTGCAGGGTGCCTGCTGTAGTGTTCACCACACTGAG
GGGCCGCCAGCTCTGTGCACCCCCAGACCAGCCCTGGGTAGAACGCATCATCCAGAGACTGCAGAGGACCTCAGCCAAGATGAAGCGCCG
CAGCAGTTAACCTATGACCGTGCAGAGGGAGCCCGGAGTCCGAGTCAAGCATTGTGAATTATTACCTAACCTGGGGAACCGAGGACCAGA
AGGAAGGACCAGGCTTCCAGCTCCTCTGCACCAGACCTGACCAGCCAGGACAGGGCCTGGGGTGTGTGTGAGTGTGAGTGTGAGCGAGAG

>In-frame_ENST00000424107_ENST00000311925_TCGA-CS-5397-01A_SHISA9_chr16_13297406_+_CCL19_chr9_34690339_length(amino acids)=488AA_start in transcript=73_stop in transcript=1539
MPAKARRCQPDSPLLSTPASPSGRPDLHPALDPAHPPPARPGALLPGRPLGARRAGGERGLRRTRAEPSAVAADHRAPRAAPCMCGPRRL
AAPGSSLGSFGRASRGGRRGSSGGRAAEPGLGDTMRRVLRLLLGCFLTELCARVCRAQERAGHGQLAQLGGVLLLAGGNRSGAASGEASE
GAEASDAPPTRAPTPDFCRGYFDVMGQWDPPFNCSSGDFIFCCGTCGFRFCCTFKKRRLNQSTCTNYDTPLWLNTGKPPARKDDPLHDPT
KDKTNLIVYIICGVVAVMVLVGIFTKLGLEKAHRPQREHMSRALADVMRPQGHCNTDHMERDLNIVVHVQHYENMDTRTPINNLHATQMN
NAVPTSPLLQQMGHPHSYPNLGQISNPYEQQPPGKELNKYASLKAVAPTLSGTNDAEDCCLSVTQKPIPGYIVRNFHYLLIKDGCRVPAV

--------------------------------------------------------------
>In-frame_ENST00000558583_ENST00000311925_TCGA-CS-5397-01A_SHISA9_chr16_13297406_+_CCL19_chr9_34690339_length(transcript)=1792nt_BP=1292nt
CTCTTCAGCGCACTTGGCGAGCTGGTGAGGTGAGAGGGATACTGCGAGAGGGCTAGGGGCGGCCAGTCCGGGGCTGCCGGCCAAGGCTAG
GCGCTGCCAGCCCGATTCTCCTCTGCTCTCCACCCCCGCCTCACCCAGTGGCCGGCCGGACCTGCACCCCGCGCTTGACCCCGCTCATCC
TCCCCCCGCCCGGCCGGGCGCGCTCCTCCCCGGCCGGCCCCTCGGCGCGCGGCGCGCTGGAGGCGAACGCGGGCTGAGGCGAACGCGGGC
TGAGCCGAGCGCAGTGGCCGCCGACCACCGAGCGCCCCGCGCCGCTCCCTGCATGTGCGGCCCGCGGCGGCTCGCAGCTCCCGGCAGCAG
CCTCGGCAGCTTCGGCCGCGCCTCGAGAGGCGGCCGCAGAGGCTCCAGCGGCGGCCGAGCGGCCGAGCCCGGGCTGGGAGACACCATGCG
CCGCGTCCTTCGGCTGCTCCTCGGTTGCTTCCTCACCGAGCTGTGCGCCCGCGTGTGCCGGGCGCAGGAGCGAGCGGGACACGGGCAGCT
GGCGCAACTGGGCGGCGTGTTGCTGCTGGCGGGGGGCAACCGCTCCGGGGCCGCCTCCGGAGAGGCCAGCGAGGGCGCTGAGGCATCGGA
CGCGCCCCCGACCCGGGCGCCCACGCCGGACTTCTGCCGGGGCTACTTCGATGTCATGGGCCAGTGGGACCCGCCGTTCAACTGCAGCTC
GGGCGACTTCATCTTCTGCTGCGGGACTTGTGGCTTCCGGTTCTGCTGCACGTTTAAGAAGCGGCGACTGAACCAAAGCACCTGCACCAA
CTACGACACGCCGCTCTGGCTCAACACCGGCAAGCCCCCCGCCCGCAAGGACGACCCCTTGCACGACCCCACCAAGGACAAGACCAACCT
GATCGTCTACATCATCTGCGGGGTGGTGGCCGTCATGGTGCTCGTGGGCATCTTCACCAAGCTGGGGCTGGAGAAAGCGCACCGGCCCCA
AAGGGAGCACATGTCCAGGGCCCTTGCGGATGTCATGAGACCACAGGGCCACTGCAACACTGATCACATGGAGAGAGACCTAAACATCGT
TGTCCACGTCCAGCATTATGAGAACATGGACACGAGAACCCCCATAAATAATCTTCATGCCACCCAGATGAACAACGCAGTGCCCACCTC
TCCTCTGCTCCAGCAGATGGGCCATCCACATTCGTACCCGAACCTGGGCCAGATCTCCAACCCCTATGAACAGCAGCCACCAGGAAAAGA
GCTCAACAAGTACGCCTCCTTAAAGGCAGTCGCCCCAACTCTGAGTGGCACCAATGATGCTGAAGACTGCTGCCTGTCTGTGACCCAGAA
ACCCATCCCTGGGTACATCGTGAGGAACTTCCACTACCTTCTCATCAAGGATGGCTGCAGGGTGCCTGCTGTAGTGTTCACCACACTGAG
GGGCCGCCAGCTCTGTGCACCCCCAGACCAGCCCTGGGTAGAACGCATCATCCAGAGACTGCAGAGGACCTCAGCCAAGATGAAGCGCCG
CAGCAGTTAACCTATGACCGTGCAGAGGGAGCCCGGAGTCCGAGTCAAGCATTGTGAATTATTACCTAACCTGGGGAACCGAGGACCAGA
AGGAAGGACCAGGCTTCCAGCTCCTCTGCACCAGACCTGACCAGCCAGGACAGGGCCTGGGGTGTGTGTGAGTGTGAGTGTGAGCGAGAG

>In-frame_ENST00000558583_ENST00000311925_TCGA-CS-5397-01A_SHISA9_chr16_13297406_+_CCL19_chr9_34690339_length(amino acids)=488AA_start in transcript=73_stop in transcript=1539
MPAKARRCQPDSPLLSTPASPSGRPDLHPALDPAHPPPARPGALLPGRPLGARRAGGERGLRRTRAEPSAVAADHRAPRAAPCMCGPRRL
AAPGSSLGSFGRASRGGRRGSSGGRAAEPGLGDTMRRVLRLLLGCFLTELCARVCRAQERAGHGQLAQLGGVLLLAGGNRSGAASGEASE
GAEASDAPPTRAPTPDFCRGYFDVMGQWDPPFNCSSGDFIFCCGTCGFRFCCTFKKRRLNQSTCTNYDTPLWLNTGKPPARKDDPLHDPT
KDKTNLIVYIICGVVAVMVLVGIFTKLGLEKAHRPQREHMSRALADVMRPQGHCNTDHMERDLNIVVHVQHYENMDTRTPINNLHATQMN
NAVPTSPLLQQMGHPHSYPNLGQISNPYEQQPPGKELNKYASLKAVAPTLSGTNDAEDCCLSVTQKPIPGYIVRNFHYLLIKDGCRVPAV

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

Top

Fusion Gene PPI Analysis for SHISA9-CCL19


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 SHISA9-CCL19


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 SHISA9-CCL19


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneCCL19C0020517Hypersensitivity1CTD_human
TgeneCCL19C0032285Pneumonia1CTD_human
TgeneCCL19C0032300Lobar Pneumonia1CTD_human
TgeneCCL19C0162820Dermatitis, Allergic Contact1CTD_human
TgeneCCL19C0887898Experimental Lung Inflammation1CTD_human
TgeneCCL19C1527304Allergic Reaction1CTD_human
TgeneCCL19C3714636Pneumonitis1CTD_human