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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:ATP9A-SALL4 (FusionGDB2 ID:8366)

Fusion Gene Summary for ATP9A-SALL4

check button Fusion gene summary
Fusion gene informationFusion gene name: ATP9A-SALL4
Fusion gene ID: 8366
HgeneTgene
Gene symbol

ATP9A

SALL4

Gene ID

10079

57167

Gene nameATPase phospholipid transporting 9A (putative)spalt like transcription factor 4
SynonymsATPIIADRRS|HSAL4|ZNF797
Cytomap

20q13.2

20q13.2

Type of geneprotein-codingprotein-coding
Descriptionprobable phospholipid-transporting ATPase IIAATPase type IV, phospholipid-transporting (P-type),(putative)ATPase, class II, type 9Aphospholipid-transporting ATPase IIAsal-like protein 4zinc finger protein 797zinc finger protein SALL4
Modification date2020031320200322
UniProtAcc

O75110

.
Ensembl transtripts involved in fusion geneENST00000311637, ENST00000338821, 
ENST00000402822, ENST00000477492, 
ENST00000217086, ENST00000371539, 
ENST00000395997, ENST00000483130, 
Fusion gene scores* DoF score15 X 13 X 10=19503 X 3 X 3=27
# samples 163
** MAII scorelog2(16/1950*10)=-3.60733031374961
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: ATP9A [Title/Abstract] AND SALL4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointATP9A(50384841)-SALL4(50401223), # samples:1
Anticipated loss of major functional domain due to fusion event.ATP9A-SALL4 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
ATP9A-SALL4 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
ATP9A-SALL4 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
ATP9A-SALL4 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
ATP9A-SALL4 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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

check buttonFusion gene breakpoints across ATP9A (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 SALL4 (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-D8-A1XQ-01AATP9Achr20

50384841

-SALL4chr20

50401223

-


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Fusion Gene ORF analysis for ATP9A-SALL4

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
Frame-shiftENST00000311637ENST00000217086ATP9Achr20

50384841

-SALL4chr20

50401223

-
In-frameENST00000311637ENST00000371539ATP9Achr20

50384841

-SALL4chr20

50401223

-
Frame-shiftENST00000311637ENST00000395997ATP9Achr20

50384841

-SALL4chr20

50401223

-
5CDS-intronENST00000311637ENST00000483130ATP9Achr20

50384841

-SALL4chr20

50401223

-
Frame-shiftENST00000338821ENST00000217086ATP9Achr20

50384841

-SALL4chr20

50401223

-
In-frameENST00000338821ENST00000371539ATP9Achr20

50384841

-SALL4chr20

50401223

-
Frame-shiftENST00000338821ENST00000395997ATP9Achr20

50384841

-SALL4chr20

50401223

-
5CDS-intronENST00000338821ENST00000483130ATP9Achr20

50384841

-SALL4chr20

50401223

-
Frame-shiftENST00000402822ENST00000217086ATP9Achr20

50384841

-SALL4chr20

50401223

-
In-frameENST00000402822ENST00000371539ATP9Achr20

50384841

-SALL4chr20

50401223

-
Frame-shiftENST00000402822ENST00000395997ATP9Achr20

50384841

-SALL4chr20

50401223

-
5CDS-intronENST00000402822ENST00000483130ATP9Achr20

50384841

-SALL4chr20

50401223

-
intron-3CDSENST00000477492ENST00000217086ATP9Achr20

50384841

-SALL4chr20

50401223

-
intron-3CDSENST00000477492ENST00000371539ATP9Achr20

50384841

-SALL4chr20

50401223

-
intron-3CDSENST00000477492ENST00000395997ATP9Achr20

50384841

-SALL4chr20

50401223

-
intron-intronENST00000477492ENST00000483130ATP9Achr20

50384841

-SALL4chr20

50401223

-

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 ATP9A-SALL4


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 ATP9A-SALL4


check button Go to

FGviewer for the breakpoints of chr20:50384841-chr20:50401223

.
- 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
ATP9A

O75110

.
FUNCTION: Plays a role in regulating membrane trafficking of cargo proteins, namely endosome to plasma membrane recycling and endosome to trans-Golgi network retrograde transport (PubMed:27733620, PubMed:30213940). In complex with MON2 and DOP1B, regulates SNX3 retromer-mediated endosomal sorting of WLS, a transporter of Wnt morphogens in developing tissues. Participates in the formation of endosomal carriers that direct WLS trafficking back to Golgi, away from lysosomal degradation (PubMed:30213940). Appears to be implicated in intercellular communication by negatively regulating the release of exosomes (PubMed:30947313). The flippase activity towards membrane lipids and its role in membrane asymmetry remains to be proved (PubMed:30947313). {ECO:0000269|PubMed:27733620, ECO:0000269|PubMed:30213940, ECO:0000269|PubMed:30947313}.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
TgeneSALL4chr20:50384841chr20:50401223ENST0000039599724566_588477.0617.0Zinc fingerC2H2-type 4
TgeneSALL4chr20:50384841chr20:50401223ENST0000039599724594_616477.0617.0Zinc fingerC2H2-type 5
TgeneSALL4chr20:50384841chr20:50401223ENST0000039599724626_648477.0617.0Zinc fingerC2H2-type 6
TgeneSALL4chr20:50384841chr20:50401223ENST0000039599724870_892477.0617.0Zinc fingerC2H2-type 7
TgeneSALL4chr20:50384841chr20:50401223ENST0000039599724898_920477.0617.0Zinc fingerC2H2-type 8

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneATP9Achr20:50384841chr20:50401223ENST00000338821-1281000_100622.6666666666666681048.0Topological domainExtracellular
HgeneATP9Achr20:50384841chr20:50401223ENST00000338821-1281031_104722.6666666666666681048.0Topological domainCytoplasmic
HgeneATP9Achr20:50384841chr20:50401223ENST00000338821-128120_30322.6666666666666681048.0Topological domainCytoplasmic
HgeneATP9Achr20:50384841chr20:50401223ENST00000338821-1282_6922.6666666666666681048.0Topological domainCytoplasmic
HgeneATP9Achr20:50384841chr20:50401223ENST00000338821-128326_33222.6666666666666681048.0Topological domainExtracellular
HgeneATP9Achr20:50384841chr20:50401223ENST00000338821-128355_84122.6666666666666681048.0Topological domainCytoplasmic
HgeneATP9Achr20:50384841chr20:50401223ENST00000338821-128863_87422.6666666666666681048.0Topological domainExtracellular
HgeneATP9Achr20:50384841chr20:50401223ENST00000338821-128894_92322.6666666666666681048.0Topological domainCytoplasmic
HgeneATP9Achr20:50384841chr20:50401223ENST00000338821-12892_9622.6666666666666681048.0Topological domainExtracellular
HgeneATP9Achr20:50384841chr20:50401223ENST00000338821-128943_94922.6666666666666681048.0Topological domainExtracellular
HgeneATP9Achr20:50384841chr20:50401223ENST00000338821-128973_97822.6666666666666681048.0Topological domainCytoplasmic
HgeneATP9Achr20:50384841chr20:50401223ENST00000402822-1231000_100622.666666666666668927.0Topological domainExtracellular
HgeneATP9Achr20:50384841chr20:50401223ENST00000402822-1231031_104722.666666666666668927.0Topological domainCytoplasmic
HgeneATP9Achr20:50384841chr20:50401223ENST00000402822-123120_30322.666666666666668927.0Topological domainCytoplasmic
HgeneATP9Achr20:50384841chr20:50401223ENST00000402822-1232_6922.666666666666668927.0Topological domainCytoplasmic
HgeneATP9Achr20:50384841chr20:50401223ENST00000402822-123326_33222.666666666666668927.0Topological domainExtracellular
HgeneATP9Achr20:50384841chr20:50401223ENST00000402822-123355_84122.666666666666668927.0Topological domainCytoplasmic
HgeneATP9Achr20:50384841chr20:50401223ENST00000402822-123863_87422.666666666666668927.0Topological domainExtracellular
HgeneATP9Achr20:50384841chr20:50401223ENST00000402822-123894_92322.666666666666668927.0Topological domainCytoplasmic
HgeneATP9Achr20:50384841chr20:50401223ENST00000402822-12392_9622.666666666666668927.0Topological domainExtracellular
HgeneATP9Achr20:50384841chr20:50401223ENST00000402822-123943_94922.666666666666668927.0Topological domainExtracellular
HgeneATP9Achr20:50384841chr20:50401223ENST00000402822-123973_97822.666666666666668927.0Topological domainCytoplasmic
HgeneATP9Achr20:50384841chr20:50401223ENST00000338821-1281007_103022.6666666666666681048.0TransmembraneHelical
HgeneATP9Achr20:50384841chr20:50401223ENST00000338821-128304_32522.6666666666666681048.0TransmembraneHelical
HgeneATP9Achr20:50384841chr20:50401223ENST00000338821-128333_35422.6666666666666681048.0TransmembraneHelical
HgeneATP9Achr20:50384841chr20:50401223ENST00000338821-12870_9122.6666666666666681048.0TransmembraneHelical
HgeneATP9Achr20:50384841chr20:50401223ENST00000338821-128842_86222.6666666666666681048.0TransmembraneHelical
HgeneATP9Achr20:50384841chr20:50401223ENST00000338821-128875_89322.6666666666666681048.0TransmembraneHelical
HgeneATP9Achr20:50384841chr20:50401223ENST00000338821-128924_94222.6666666666666681048.0TransmembraneHelical
HgeneATP9Achr20:50384841chr20:50401223ENST00000338821-128950_97222.6666666666666681048.0TransmembraneHelical
HgeneATP9Achr20:50384841chr20:50401223ENST00000338821-128979_99922.6666666666666681048.0TransmembraneHelical
HgeneATP9Achr20:50384841chr20:50401223ENST00000338821-12897_11922.6666666666666681048.0TransmembraneHelical
HgeneATP9Achr20:50384841chr20:50401223ENST00000402822-1231007_103022.666666666666668927.0TransmembraneHelical
HgeneATP9Achr20:50384841chr20:50401223ENST00000402822-123304_32522.666666666666668927.0TransmembraneHelical
HgeneATP9Achr20:50384841chr20:50401223ENST00000402822-123333_35422.666666666666668927.0TransmembraneHelical
HgeneATP9Achr20:50384841chr20:50401223ENST00000402822-12370_9122.666666666666668927.0TransmembraneHelical
HgeneATP9Achr20:50384841chr20:50401223ENST00000402822-123842_86222.666666666666668927.0TransmembraneHelical
HgeneATP9Achr20:50384841chr20:50401223ENST00000402822-123875_89322.666666666666668927.0TransmembraneHelical
HgeneATP9Achr20:50384841chr20:50401223ENST00000402822-123924_94222.666666666666668927.0TransmembraneHelical
HgeneATP9Achr20:50384841chr20:50401223ENST00000402822-123950_97222.666666666666668927.0TransmembraneHelical
HgeneATP9Achr20:50384841chr20:50401223ENST00000402822-123979_99922.666666666666668927.0TransmembraneHelical
HgeneATP9Achr20:50384841chr20:50401223ENST00000402822-12397_11922.666666666666668927.0TransmembraneHelical
TgeneSALL4chr20:50384841chr20:50401223ENST0000021708624382_404914.01054.0Zinc fingerC2H2-type 2
TgeneSALL4chr20:50384841chr20:50401223ENST0000021708624410_432914.01054.0Zinc fingerC2H2-type 3
TgeneSALL4chr20:50384841chr20:50401223ENST0000021708624566_588914.01054.0Zinc fingerC2H2-type 4
TgeneSALL4chr20:50384841chr20:50401223ENST0000021708624594_616914.01054.0Zinc fingerC2H2-type 5
TgeneSALL4chr20:50384841chr20:50401223ENST0000021708624626_648914.01054.0Zinc fingerC2H2-type 6
TgeneSALL4chr20:50384841chr20:50401223ENST000002170862472_94914.01054.0Zinc fingerC2H2-type 1%3B atypical
TgeneSALL4chr20:50384841chr20:50401223ENST0000021708624870_892914.01054.0Zinc fingerC2H2-type 7
TgeneSALL4chr20:50384841chr20:50401223ENST0000021708624898_920914.01054.0Zinc fingerC2H2-type 8
TgeneSALL4chr20:50384841chr20:50401223ENST0000039599724382_404477.0617.0Zinc fingerC2H2-type 2
TgeneSALL4chr20:50384841chr20:50401223ENST0000039599724410_432477.0617.0Zinc fingerC2H2-type 3
TgeneSALL4chr20:50384841chr20:50401223ENST000003959972472_94477.0617.0Zinc fingerC2H2-type 1%3B atypical


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Fusion Gene Sequence for ATP9A-SALL4


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 ATP9A-SALL4


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 ATP9A-SALL4


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 ATP9A-SALL4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneSALL4C1623209Okihiro Syndrome7CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneSALL4C0013261Duane Retraction Syndrome2CTD_human
TgeneSALL4C0751083Duane Retraction Syndrome, Type 22CTD_human
TgeneSALL4C0751084Duane Retraction Syndrome, Type 32CTD_human
TgeneSALL4C0994516Type 1 Duane Retraction Syndrome2CTD_human
TgeneSALL4C0018818Ventricular Septal Defects1CTD_human
TgeneSALL4C0206762Limb Deformities, Congenital1CTD_human
TgeneSALL4C0265239Wildervanck's syndrome1CTD_human
TgeneSALL4C0265264Holt-Oram syndrome1CTD_human
TgeneSALL4C0279626Squamous cell carcinoma of esophagus1CTD_human
TgeneSALL4C0376634Craniofacial Abnormalities1CTD_human
TgeneSALL4C1327918Oculootoradial syndrome1CTD_human;GENOMICS_ENGLAND;ORPHANET