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:SIPA1L3-RAB8A (FusionGDB2 ID:81400)

Fusion Gene Summary for SIPA1L3-RAB8A

check button Fusion gene summary
Fusion gene informationFusion gene name: SIPA1L3-RAB8A
Fusion gene ID: 81400
HgeneTgene
Gene symbol

SIPA1L3

RAB8A

Gene ID

23094

4218

Gene namesignal induced proliferation associated 1 like 3RAB8A, member RAS oncogene family
SynonymsCTRCT45|SPAL3|SPAR3MEL|RAB8
Cytomap

19q13.13-q13.2

19p13.11

Type of geneprotein-codingprotein-coding
Descriptionsignal-induced proliferation-associated 1-like protein 3SIPA1-like protein 3SPA-1-like protein 3spine-associated RapGAP 3ras-related protein Rab-8Amel transforming oncogene (RAB8 homolog)mel transforming oncogene (derived from cell line NK14)mel transforming oncogene (derived from cell line NK14)- RAB8 homologoncogene c-melras-associated protein RAB8
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000222345, ENST00000476317, 
ENST00000300935, ENST00000588105, 
ENST00000586682, 
Fusion gene scores* DoF score28 X 17 X 11=52363 X 3 X 3=27
# samples 354
** MAII scorelog2(35/5236*10)=-3.90303827011291
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/27*10)=0.567040592723894
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: SIPA1L3 [Title/Abstract] AND RAB8A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSIPA1L3(38397998)-RAB8A(16236280), # samples:3
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
HgeneSIPA1L3

GO:0003382

epithelial cell morphogenesis

26231217

HgeneSIPA1L3

GO:0090162

establishment of epithelial cell polarity

26231217

TgeneRAB8A

GO:0006904

vesicle docking involved in exocytosis

17574030

TgeneRAB8A

GO:0048210

Golgi vesicle fusion to target membrane

17574030

TgeneRAB8A

GO:0060271

cilium assembly

17574030


check buttonFusion gene breakpoints across SIPA1L3 (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 RAB8A (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
ChimerDB4UCECTCGA-PG-A914-01ASIPA1L3chr19

38397998

+RAB8Achr19

16236280

+
ChimerDB4UCECTCGA-PG-A914SIPA1L3chr19

38397998

+RAB8Achr19

16236279

+
ChimerDB4UCECTCGA-PG-A914SIPA1L3chr19

38397998

+RAB8Achr19

16236280

+
ChimerDB4UCECTCGA-PG-A914SIPA1L3chr19

38423332

+RAB8Achr19

16236280

+
ChimerDB4UCECTCGA-PG-A914-01ASIPA1L3chr19

38397998

-RAB8Achr19

16236280

+


Top

Fusion Gene ORF analysis for SIPA1L3-RAB8A

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
5UTR-3CDSENST00000222345ENST00000300935SIPA1L3chr19

38397998

+RAB8Achr19

16236280

+
5UTR-intronENST00000222345ENST00000588105SIPA1L3chr19

38397998

+RAB8Achr19

16236280

+
5UTR-intronENST00000222345ENST00000586682SIPA1L3chr19

38397998

+RAB8Achr19

16236280

+
intron-3CDSENST00000476317ENST00000300935SIPA1L3chr19

38397998

+RAB8Achr19

16236280

+
intron-intronENST00000476317ENST00000588105SIPA1L3chr19

38397998

+RAB8Achr19

16236280

+
intron-intronENST00000476317ENST00000586682SIPA1L3chr19

38397998

+RAB8Achr19

16236280

+
5UTR-3CDSENST00000222345ENST00000300935SIPA1L3chr19

38397998

+RAB8Achr19

16236279

+
5UTR-intronENST00000222345ENST00000588105SIPA1L3chr19

38397998

+RAB8Achr19

16236279

+
5UTR-intronENST00000222345ENST00000586682SIPA1L3chr19

38397998

+RAB8Achr19

16236279

+
intron-3CDSENST00000476317ENST00000300935SIPA1L3chr19

38397998

+RAB8Achr19

16236279

+
intron-intronENST00000476317ENST00000588105SIPA1L3chr19

38397998

+RAB8Achr19

16236279

+
intron-intronENST00000476317ENST00000586682SIPA1L3chr19

38397998

+RAB8Achr19

16236279

+
intron-3CDSENST00000222345ENST00000300935SIPA1L3chr19

38423332

+RAB8Achr19

16236280

+
intron-intronENST00000222345ENST00000588105SIPA1L3chr19

38423332

+RAB8Achr19

16236280

+
intron-intronENST00000222345ENST00000586682SIPA1L3chr19

38423332

+RAB8Achr19

16236280

+
3UTR-3CDSENST00000476317ENST00000300935SIPA1L3chr19

38423332

+RAB8Achr19

16236280

+
3UTR-intronENST00000476317ENST00000588105SIPA1L3chr19

38423332

+RAB8Achr19

16236280

+
3UTR-intronENST00000476317ENST00000586682SIPA1L3chr19

38423332

+RAB8Achr19

16236280

+

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)

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

Top

Fusion Genomic Features for SIPA1L3-RAB8A


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)
SIPA1L3chr1938423332+RAB8Achr1916236279+1.14E-070.9999999
SIPA1L3chr1938397998+RAB8Achr1916236279+1.65E-111
SIPA1L3chr1938397998+RAB8Achr1916236279+1.65E-111
SIPA1L3chr1938423332+RAB8Achr1916236279+1.14E-070.9999999
SIPA1L3chr1938397998+RAB8Achr1916236279+1.65E-111
SIPA1L3chr1938397998+RAB8Achr1916236279+1.65E-111

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 SIPA1L3-RAB8A


check button Go to

FGviewer for the breakpoints of :-:

.
- 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

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


Top

Fusion Gene Sequence for SIPA1L3-RAB8A


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.

Top

Fusion Gene PPI Analysis for SIPA1L3-RAB8A


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 SIPA1L3-RAB8A


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 SIPA1L3-RAB8A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSIPA1L3C0266539Congenital total cataract1ORPHANET
TgeneRAB8AC0003873Rheumatoid Arthritis1CTD_human