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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:SIPA1L1-NF1 (FusionGDB2 ID:81363)

Fusion Gene Summary for SIPA1L1-NF1

check button Fusion gene summary
Fusion gene informationFusion gene name: SIPA1L1-NF1
Fusion gene ID: 81363
HgeneTgene
Gene symbol

SIPA1L1

NF1

Gene ID

26037

4763

Gene namesignal induced proliferation associated 1 like 1neurofibromin 1
SynonymsE6TP1|SPAR1NFNS|VRNF|WSS
Cytomap

14q24.2

17q11.2

Type of geneprotein-codingprotein-coding
Descriptionsignal-induced proliferation-associated 1-like protein 1SIPA1-like protein 1high-risk human papilloma viruses E6 oncoproteins targeted protein 1spine-associated RapGAP 1neurofibrominneurofibromatosis 1neurofibromatosis-related protein NF-1truncated neurofibromin 1
Modification date2020031320200322
UniProtAcc.

P21359

Ensembl transtripts involved in fusion geneENST00000381232, ENST00000555818, 
ENST00000358550, ENST00000537413, 
ENST00000554874, 		ENST00000356175, 
ENST00000358273, ENST00000431387, 
ENST00000581113, ENST00000417592, 
ENST00000444181, 
Fusion gene scores* DoF score13 X 9 X 5=58528 X 30 X 15=12600
# samples 1433
** MAII scorelog2(14/585*10)=-2.0630097975258
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(33/12600*10)=-5.25481389902883
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SIPA1L1 [Title/Abstract] AND NF1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSIPA1L1(71979562)-NF1(29652838), # 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
TgeneNF1

GO:0043547

positive regulation of GTPase activity

2121371


check buttonFusion gene breakpoints across SIPA1L1 (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 NF1 (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
ChimerDB4BRCATCGA-BH-A18V-06ASIPA1L1chr14

71979562

-NF1chr17

29652838

+


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Fusion Gene ORF analysis for SIPA1L1-NF1

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
intron-3CDSENST00000381232ENST00000356175SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-3CDSENST00000381232ENST00000358273SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-intronENST00000381232ENST00000431387SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-3UTRENST00000381232ENST00000581113SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-intronENST00000381232ENST00000417592SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-intronENST00000381232ENST00000444181SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-3CDSENST00000555818ENST00000356175SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-3CDSENST00000555818ENST00000358273SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-intronENST00000555818ENST00000431387SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-3UTRENST00000555818ENST00000581113SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-intronENST00000555818ENST00000417592SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-intronENST00000555818ENST00000444181SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-3CDSENST00000358550ENST00000356175SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-3CDSENST00000358550ENST00000358273SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-intronENST00000358550ENST00000431387SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-3UTRENST00000358550ENST00000581113SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-intronENST00000358550ENST00000417592SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-intronENST00000358550ENST00000444181SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-3CDSENST00000537413ENST00000356175SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-3CDSENST00000537413ENST00000358273SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-intronENST00000537413ENST00000431387SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-3UTRENST00000537413ENST00000581113SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-intronENST00000537413ENST00000417592SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-intronENST00000537413ENST00000444181SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-3CDSENST00000554874ENST00000356175SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-3CDSENST00000554874ENST00000358273SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-intronENST00000554874ENST00000431387SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-3UTRENST00000554874ENST00000581113SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-intronENST00000554874ENST00000417592SIPA1L1chr14

71979562

-NF1chr17

29652838

+
intron-intronENST00000554874ENST00000444181SIPA1L1chr14

71979562

-NF1chr17

29652838

+

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

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Fusion Genomic Features for SIPA1L1-NF1


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.

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Fusion Protein Features for SIPA1L1-NF1


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
.NF1

P21359

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: Stimulates the GTPase activity of Ras. NF1 shows greater affinity for Ras GAP, but lower specific activity. May be a regulator of Ras activity. {ECO:0000269|PubMed:2121371, ECO:0000269|PubMed:8417346}.

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


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Fusion Gene Sequence for SIPA1L1-NF1


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.

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Fusion Gene PPI Analysis for SIPA1L1-NF1


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 SIPA1L1-NF1


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 SIPA1L1-NF1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSIPA1L1C0043094Weight Gain1CTD_human
HgeneSIPA1L1C0087031Juvenile-Onset Still Disease1CTD_human
HgeneSIPA1L1C1135196Heart Failure, Diastolic1CTD_human
HgeneSIPA1L1C3495559Juvenile arthritis1CTD_human
HgeneSIPA1L1C3714758Juvenile psoriatic arthritis1CTD_human
HgeneSIPA1L1C4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative1CTD_human
HgeneSIPA1L1C4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive1CTD_human
TgeneNF1C0027831Neurofibromatosis 144CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneNF1C1708353Hereditary Paraganglioma-Pheochromocytoma Syndrome10CLINGEN
TgeneNF1C0349639Juvenile Myelomonocytic Leukemia7CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneNF1C2931482Neurofibromatosis-Noonan syndrome6CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneNF1C0553586Cafe-au-lait macules with pulmonary stenosis5CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneNF1C0162678Neurofibromatoses3CGI;CTD_human;GENOMICS_ENGLAND
TgeneNF1C0004114Astrocytoma2CTD_human
TgeneNF1C0023467Leukemia, Myelocytic, Acute2CTD_human
TgeneNF1C0025202melanoma2CGI;CTD_human
TgeneNF1C0026998Acute Myeloid Leukemia, M12CTD_human
TgeneNF1C0205768Subependymal Giant Cell Astrocytoma2CTD_human
TgeneNF1C0206727Nerve Sheath Tumors2CTD_human
TgeneNF1C0280783Juvenile Pilocytic Astrocytoma2CTD_human
TgeneNF1C0280785Diffuse Astrocytoma2CTD_human
TgeneNF1C0334579Anaplastic astrocytoma2CTD_human
TgeneNF1C0334580Protoplasmic astrocytoma2CTD_human
TgeneNF1C0334581Gemistocytic astrocytoma2CTD_human
TgeneNF1C0334582Fibrillary Astrocytoma2CTD_human
TgeneNF1C0334583Pilocytic Astrocytoma2CTD_human
TgeneNF1C0338070Childhood Cerebral Astrocytoma2CTD_human
TgeneNF1C0547065Mixed oligoastrocytoma2CTD_human
TgeneNF1C0750935Cerebral Astrocytoma2CTD_human
TgeneNF1C0750936Intracranial Astrocytoma2CTD_human
TgeneNF1C0751689Peripheral Nerve Sheath Neoplasm2CTD_human
TgeneNF1C0751691Perineurioma2CTD_human
TgeneNF1C1704230Grade I Astrocytoma2CTD_human
TgeneNF1C1834235NEUROFIBROMATOSIS, FAMILIAL SPINAL2CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneNF1C1879321Acute Myeloid Leukemia (AML-M2)2CTD_human
TgeneNF1C0001430Adenoma1CTD_human
TgeneNF1C0004352Autistic Disorder1CTD_human
TgeneNF1C0016057Fibrosarcoma1CTD_human
TgeneNF1C0017636Glioblastoma1CTD_human
TgeneNF1C0017638Glioma1CGI;CTD_human
TgeneNF1C0020796Profound Mental Retardation1CTD_human
TgeneNF1C0023186Learning Disorders1CTD_human
TgeneNF1C0023827liposarcoma1CTD_human
TgeneNF1C0025363Mental Retardation, Psychosocial1CTD_human
TgeneNF1C0026654Moyamoya Disease1GENOMICS_ENGLAND
TgeneNF1C0027809Neurilemmoma1CTD_human
TgeneNF1C0027830neurofibroma1CTD_human
TgeneNF1C0027962Melanocytic nevus1CTD_human
TgeneNF1C0028326Noonan Syndrome1GENOMICS_ENGLAND
TgeneNF1C0031511Pheochromocytoma1CTD_human
TgeneNF1C0035320Retinal Neovascularization1CTD_human
TgeneNF1C0205646Adenoma, Basal Cell1CTD_human
TgeneNF1C0205647Follicular adenoma1CTD_human
TgeneNF1C0205648Adenoma, Microcystic1CTD_human
TgeneNF1C0205649Adenoma, Monomorphic1CTD_human
TgeneNF1C0205650Papillary adenoma1CTD_human
TgeneNF1C0205651Adenoma, Trabecular1CTD_human
TgeneNF1C0205824Liposarcoma, Dedifferentiated1CTD_human
TgeneNF1C0205825Liposarcoma, Pleomorphic1CTD_human
TgeneNF1C0205944Sarcoma, Epithelioid1CTD_human
TgeneNF1C0205945Sarcoma, Spindle Cell1CTD_human
TgeneNF1C0259783mixed gliomas1CTD_human
TgeneNF1C0334588Giant Cell Glioblastoma1CTD_human
TgeneNF1C0555198Malignant Glioma1CTD_human
TgeneNF1C0751262Adult Learning Disorders1CTD_human
TgeneNF1C0751263Learning Disturbance1CTD_human
TgeneNF1C0751265Learning Disabilities1CTD_human
TgeneNF1C0751374Schwannomatosis, Plexiform1CTD_human
TgeneNF1C0917816Mental deficiency1CTD_human
TgeneNF1C0917817Neurofibromatosis 31CTD_human
TgeneNF1C1257877Pheochromocytoma, Extra-Adrenal1CTD_human
TgeneNF1C1261473Sarcoma1CTD_human
TgeneNF1C1330966Developmental Academic Disorder1CTD_human
TgeneNF1C1370889Liposarcoma, well differentiated1CTD_human
TgeneNF1C1621958Glioblastoma Multiforme1CTD_human
TgeneNF1C3150928NF1 Microdeletion Syndrome1ORPHANET
TgeneNF1C3714756Intellectual Disability1CTD_human