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:ABCA6-LIG3 (FusionGDB2 ID:HG23460TG3980)

Fusion Gene Summary for ABCA6-LIG3

check button Fusion gene summary
Fusion gene informationFusion gene name: ABCA6-LIG3
Fusion gene ID: hg23460tg3980
HgeneTgene
Gene symbol

ABCA6

LIG3

Gene ID

23460

3980

Gene nameATP binding cassette subfamily A member 6DNA ligase 3
SynonymsEST155051LIG2|LIG3alpha
Cytomap('ABCA6')('LIG3')

17q24.2-q24.3

17q12

Type of geneprotein-codingprotein-coding
DescriptionATP-binding cassette sub-family A member 6ABC transporter ABCA6ATP-binding cassette A6ATP-binding cassette, sub-family A (ABC1), member 6DNA ligase 3ligase II, DNA, ATP-dependentligase III, DNA, ATP-dependentpolydeoxyribonucleotide synthase [ATP] 3
Modification date2020031320200313
UniProtAcc

Q8N139

P49916

Ensembl transtripts involved in fusion geneENST00000284425, ENST00000446604, 
ENST00000590645, 
Fusion gene scores* DoF score2 X 2 X 2=86 X 6 X 4=144
# samples 26
** MAII scorelog2(2/8*10)=1.32192809488736log2(6/144*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ABCA6 [Title/Abstract] AND LIG3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointABCA6(67102264)-LIG3(33323083), # samples:2
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
TgeneLIG3

GO:0006288

base-excision repair, DNA ligation

19589734

TgeneLIG3

GO:0006302

double-strand break repair

19589734

TgeneLIG3

GO:0033151

V(D)J recombination

9809069



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
ChimerDB4BRCATCGA-A2-A0T1-01AABCA6chr17

67102264

-LIG3chr17

33323083

+


Top

Fusion Gene ORF analysis for ABCA6-LIG3

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-3CDSENST00000284425ENST00000262327ABCA6chr17

67102264

-LIG3chr17

33323083

+
intron-3CDSENST00000284425ENST00000378526ABCA6chr17

67102264

-LIG3chr17

33323083

+
intron-3CDSENST00000446604ENST00000262327ABCA6chr17

67102264

-LIG3chr17

33323083

+
intron-3CDSENST00000446604ENST00000378526ABCA6chr17

67102264

-LIG3chr17

33323083

+
intron-3CDSENST00000590645ENST00000262327ABCA6chr17

67102264

-LIG3chr17

33323083

+
intron-3CDSENST00000590645ENST00000378526ABCA6chr17

67102264

-LIG3chr17

33323083

+
intron-intronENST00000284425ENST00000586407ABCA6chr17

67102264

-LIG3chr17

33323083

+
intron-intronENST00000446604ENST00000586407ABCA6chr17

67102264

-LIG3chr17

33323083

+
intron-intronENST00000590645ENST00000586407ABCA6chr17

67102264

-LIG3chr17

33323083

+

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 ABCA6-LIG3


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)


Top

Fusion Protein Features for ABCA6-LIG3


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/:67102264/:33323083)
- 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
ABCA6

Q8N139

LIG3

P49916

FUNCTION: Probable transporter which may play a role in macrophage lipid transport and homeostasis. {ECO:0000305|PubMed:10639163}.FUNCTION: Isoform 3 functions as heterodimer with DNA-repair protein XRCC1 in the nucleus and can correct defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents. Isoform 1 is targeted to mitochondria, where it functions as DNA ligase in mitochondrial base-excision DNA repair (PubMed:10207110, PubMed:24674627). {ECO:0000269|PubMed:10207110, ECO:0000269|PubMed:24674627}.

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 ABCA6-LIG3


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 ABCA6-LIG3


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 ABCA6-LIG3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneLIG3P49916DB00290BleomycinInhibitorSmall moleculeApproved|Investigational

Top

Related Diseases for ABCA6-LIG3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneABCA6C0009402Colorectal Carcinoma1CTD_human
HgeneABCA6C0009404Colorectal Neoplasms1CTD_human
HgeneABCA6C0162820Dermatitis, Allergic Contact1CTD_human