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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:ATAD3C-SAMD11 (FusionGDB2 ID:HG219293TG148398)

Fusion Gene Summary for ATAD3C-SAMD11

check button Fusion gene summary
Fusion gene informationFusion gene name: ATAD3C-SAMD11
Fusion gene ID: hg219293tg148398
HgeneTgene
Gene symbol

ATAD3C

SAMD11

Gene ID

219293

148398

Gene nameATPase family AAA domain containing 3Csterile alpha motif domain containing 11
Synonyms-MRS
Cytomap('ATAD3C')('SAMD11')

1p36.33

1p36.33

Type of geneprotein-codingprotein-coding
DescriptionATPase family AAA domain-containing protein 3CATPase family, AAA domain containing 3Asterile alpha motif domain-containing protein 11SAM domain-containing protein 11
Modification date2020031320200313
UniProtAcc

Q5T2N8

.
Ensembl transtripts involved in fusion geneENST00000378785, 
Fusion gene scores* DoF score3 X 3 X 3=274 X 4 X 4=64
# samples 34
** MAII scorelog2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(4/64*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ATAD3C [Title/Abstract] AND SAMD11 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointATAD3C(1398088)-SAMD11(865535), # samples:1
Anticipated loss of major functional domain due to fusion event.ATAD3C-SAMD11 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
ATAD3C-SAMD11 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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 ATAD3C (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure
check buttonFusion gene breakpoints across SAMD11 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4UCECTCGA-EO-A1Y7-01AATAD3Cchr1

1398088

+SAMD11chr1

865535

+


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Fusion Gene ORF analysis for ATAD3C-SAMD11

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
5CDS-intronENST00000378785ENST00000478729ATAD3Cchr1

1398088

+SAMD11chr1

865535

+
In-frameENST00000378785ENST00000342066ATAD3Cchr1

1398088

+SAMD11chr1

865535

+

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)
ENST00000378785ATAD3Cchr11398088+ENST00000342066SAMD11chr1865535+4480208496540571030

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
ENST00000378785ENST00000342066ATAD3Cchr11398088+SAMD11chr1865535+0.0110490760.9889509

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Fusion Genomic Features for ATAD3C-SAMD11


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)
ATAD3Cchr11398088+SAMD11chr1865534+4.33E-050.9999566
ATAD3Cchr11398088+SAMD11chr1865534+4.33E-050.9999566

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.
genomic feature

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.
genomic feature of top 1%

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Fusion Protein Features for ATAD3C-SAMD11


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/chr1:1398088/chr1:865535)
- 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
ATAD3C

Q5T2N8

.
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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
HgeneATAD3Cchr1:1398088chr1:865535ENST00000378785+1112177_184363412.0Nucleotide bindingATP
TgeneSAMD11chr1:1398088chr1:865535ENST00000342066114543_60824682.0DomainSAM

- 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 ATAD3C-SAMD11


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.
>7371_7371_1_ATAD3C-SAMD11_ATAD3C_chr1_1398088_ENST00000378785_SAMD11_chr1_865535_ENST00000342066_length(transcript)=4480nt_BP=2084nt
CTTCATGATTAACTCCCCAAGGTCCTGCATATTTTCTCAATGGGCCACCGCGCCCGGCCAGAAGATTTTTATGGTAAAATTTTGTGATGG
GAAAACTCATCCCGGAAAATGTTGAGACCTGATGCTGAGTCCTCAGCAGCTCAGAGAATACGTACTTCTGTCCCAGGTCACCCAAACATT
GACCTGTGTCGGTTCCCCACTAGGAACAAAATGTAACTGAGGACGTTGTCAGATGCTTGTCCTCGTCACCCTGAGCTTGTTGGCTGCTAT
CTAATTCTTATTCTTTCATTTTCTTGCCCGCACGTTCTTGATAGCAGATCACTGACAACAGCCATTGGAAGCTTAGGAAAAGGGTATGTG
CCGGGCGCGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGC
TAACACGGTGAAACCGTCTCTACTAAAACTACAAAAATTAGCCGGGTGTGGTGGCGGTCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAG
GCAGGAGAGTGACGTGAACCCGAGAGGTAGAGCTTGCAGTAAGCAGAGATCATGCCACTGCACTCCAGCCTGGGCCAGAATGAGACTCCG
TCTCAAAAAAAAAAAAAAAAAAAGCATGTGTAACGTGAAAAAATGGACACTTTAGCCATCGCCTGACTTTCTGTTGAATTGGGAAAGAGC
CTCCTCCCGTCCACATGGGATGGCCTTCCTGATGTGGCTCTCCAAGACCATCCCTGGAGGGCATAAAACCTCACAAATGCATCAGGCCGT
GTGCTGGGGATGGGGCATCGTCACGCCAGGTCTGACTAGGAAGGAGGATGGGGAGGCAGGGCTGGGGGCTTTGAGGTCGAGGCGTGGCCG
TGGATTCCAGAAAGCCCCTTGGCTGGTGTGCGTGCCTGCCCAGCGGCATCCGTGTATCCTAACACCTGCCCTCCGTGTCCCTGCATCTGC
AGGCCATGTCAAAGGACGCCCTGAATCTGGCGCAGATGCAGGAGCAGACGCTGCAGTTGGAGCAACAGTCCAAGCTCAAACAACTTGTCA
ATGAGGATTTACGGAAGCAGGAGGAGTCCGTGCAGAAGCACCATCAGACCTTCTTGGAGTCCATCAGGGCGGCTGGCACCTTGTTTGGGG
AAGGATTCCGTGCCTTTGTGACAGACCGGGACAAAGTGACAGCCACGGTGGCTGGGCTGACGCTGCTGGCTGTCGGGGTCTACTCAGCCA
AGAATGCGACAGCCGTCACTGGCCGCTACATCGAGGCTCGGCTGGGGAAGCCGTCCCTAGTGAGGGAGACGTCCCGCATCACGGTGCTTG
AGGCGCTGCGGCACCCCATCCAGCAGGTCAGCCGGCGGCTCCTCAGTCGACCCCAGGACGTGCTGGAGGGTGTTGTGCTTAGTCCCAGCC
TGGAAGCACGGGTGCGCGACATCGCCATAATGACAAGGAACATCAAGAAGAACCGGGGCCTGTACAGGCACATCCTGCTGTACGGGCCAC
CAGGCACCGGGAAGACGCTGTTTGCCAAGAAACTCGCCCTGCACTCAGGCATGGACTACGCCATCATGACAGGCGGGGACGTGGCCCCCA
TGGGGCGGGAAGGCGTGACCGCCATGCACAAGCTCTTTGACTGGGCCAATACCAGCCGGCGCGGCCTCCTGCTCTTTGTGGATGAAGCGG
ACGCCTTCCTTCGGAAGCGAGCCACTGAGAAGATAAGCGAGGACCTCAGGGCCACACTGAACGCCTTCCTGTACCGCACGGGCCAGCACA
GCAACAAATTCATGCTGATCCTGGCCAGCTGCCACCCCGAGCAGTTCGACTGGGCCATCAATGCCTGCATCGACGTGATGGTCCACTTCG
ACCTGCCAGGGCAGGAGGAGCGGGCGCGCCTGGTGAGAATGTATCTTAACGAGTATGTTCTTAAGCCGGCCACAGAAGGAAAGCGGCGTC
TGAAGCTGGCCCAGTTTGACTACGGGAGGAAGTGCTTAGAGATCGCTCGGCTGACAGAGGGCATGTCATGCCGGAAGATCGCACAGCTGG
CCGTGTCCTGGCAGAACCGGGGGCGGCTGGCAGACAAGAGGACAGTCGCCCTGCCTGCCGCCCGGAACCTGAAGAAGGAGCGAACTCCCA
GCTTCTCTGCCAGCGATGGTGACAGCGACGGGAGTGGCCCCACCTGTGGGCGGCGGCCAGGCTTGAAGCAGGAGGATGGTCCGCACATCC
GTATCATGAAGAGAAGAGTCCACACCCACTGGGACGTGAACATCTCTTTCCGAGAGGCGTCCTGCAGCCAGGACGGCAACCTTCCCACCC
TCATATCCAGCGTCCACCGCAGCCGCCACCTCGTTATGCCCGAGCATCAGAGCCGCTGTGAATTCCAGAGAGGCAGCCTGGAGATTGGCC
TGCGACCCGCCGGTGACCTGTTGGGCAAGAGGCTGGGCCGCTCCCCCCGTATCAGCAGCGACTGCTTTTCAGAGAAGAGGGCACGAAGCG
AATCGCCTCAAGAGGCGCTGCTGCTGCCGCGGGAGCTGGGGCCCAGCATGGCCCCGGAGGACCATTACCGCCGGCTTGTGTCAGCACTGA
GCGAGGCCAGCACCTTTGAGGACCCTCAGCGCCTCTACCACCTGGGCCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTC
ATCACCTCCCCAGCCACGATCTCCTGAGGGTCCGGCAGGAGGTGGCGGCTGCAGCTCTGAGGGGCCCCAGTGGCCTGGAAGCCCACCTGC
CCTCCTCCACGGCAGGTCAGCGTCGGAAGCAGGGCCTGGCTCAGCACCGGGAGGGCGCCGCCCCAGCTGCCGCCCCGTCCTTCTCGGAGA
GGGAGCTGCCTCAGCCGCCCCCCTTGCTGTCGCCGCAGAATGCCCCTCACGTCGCCCTGGGCCCCCATCTCAGGCCCCCCTTCCTGGGGG
TGCCCTCGGCTCTGTGCCAGACCCCAGGCTACGGCTTCCTGCCCCCCGCGCAGGCGGAGATGTTCGCCTGGCAGCAGGAGCTCCTGCGGA
AGCAGAACCTGGCCCGGCTGGAGCTGCCCGCCGACCTCCTGCGGCAGAAGGAGCTGGAGAGCGCGCGCCCACAGCTGCTGGCGCCCGAGA
CCGCCCTGCGCCCCAACGACGGCGCCGAGGAGCTGCAGCGGCGCGGGGCCCTGCTGGTGCTGAACCACGGCGCGGCGCCACTGCTGGCCC
TGCCCCCCCAGGGGCCCCCGGGCTCCGGACCCCCCACCCCGTCCCGGGACTCTGCCCGGCGAGCCCCCCGGAAGGGGGGTCCCGGCCCTG
CCTCAGCGCGGCCCAGCGAGTCCAAGGAGATGACGGGGGCTAGGCTCTGGGCACAAGATGGCTCGGAAGACGAGCCCCCCAAAGACTCGG
ACGGAGAGGACCCCGAGACGGCAGCTGTTGGGTGCAGGGGGCCCACTCCGGGCCAAGCTCCAGCTGGAGGGGCCGGCGCCGAGGGGAAGG
GGCTTTTCCCAGGGTCCACACTGCCCCTGGGCTTCCCTTATGCCGTCAGCCCCTACTTCCACACAGGCGCGGTAGGGGGACTCTCCATGG
ATGGGGAGGAGGCCCCAGCCCCTGAGGACGTCACCAAGTGGACCGTGGATGACGTCTGCAGCTTCGTGGGGGGCCTGTCTGGCTGTGGAG
AGTACACTCGGGTCTTCAGGGAGCAGGGGATCGACGGGGAGACCCTGCCACTGCTGACGGAGGAGCACCTGCTGACCAACATGGGGCTGA
AGCTGGGGCCCGCCCTCAAGATCCGGGCCCAGGTGGCCAGGCGCCTGGGCCGAGTTTTCTACGTGGCCAGCTTCCCCGTGGCTCTGCCAC
TGCAGCCACCAACCCTGCGGGCCCCGGAGCGAGAACTCGGCACAGGAGAGCAGCCCTTGTCCCCCACGACGGCCACGTCCCCCTATGGAG
GGGGCCACGCCCTTGCCGGTCAAACTTCACCCAAGCAGGAGAATGGGACCTTGGCTCTACTTCCAGGGGCCCCCGACCCTTCCCAGCCTC
TGTGTTGAGGTTGCCGGGGGTAGGGGTGGGGCCACACAAATCTCCAGGAGCCACCACTCAACACAATGGCCCTGCCTCCCACCGCTTTAT
TTCTTTCGGTTTCGGATGCAAAACAAAAAATTTTAAAAGAAAATGTGACTTCAAAGGAAAGGAACAAATTTTCAAAGACTTGGGGGAGTG
AAGGCAGAGCCTGGTGCAGATGGACGAGGTCTGCAGACGGAGGGCAGAGGTGGTGGAAGGGGCCAGGGGCCTGCAGGCCTCCCCCTGGAA
CTGGGACTGGTCTCGGTCTGCTGACGTCAGGGTCAGCTCCCCCGCGGAGCTGACTTCAGCAGCCCACAGCTGTGGGGCTTCAGCAGCCAC

>7371_7371_1_ATAD3C-SAMD11_ATAD3C_chr1_1398088_ENST00000378785_SAMD11_chr1_865535_ENST00000342066_length(amino acids)=1030AA_BP=372
MPSVSLHLQAMSKDALNLAQMQEQTLQLEQQSKLKQLVNEDLRKQEESVQKHHQTFLESIRAAGTLFGEGFRAFVTDRDKVTATVAGLTL
LAVGVYSAKNATAVTGRYIEARLGKPSLVRETSRITVLEALRHPIQQVSRRLLSRPQDVLEGVVLSPSLEARVRDIAIMTRNIKKNRGLY
RHILLYGPPGTGKTLFAKKLALHSGMDYAIMTGGDVAPMGREGVTAMHKLFDWANTSRRGLLLFVDEADAFLRKRATEKISEDLRATLNA
FLYRTGQHSNKFMLILASCHPEQFDWAINACIDVMVHFDLPGQEERARLVRMYLNEYVLKPATEGKRRLKLAQFDYGRKCLEIARLTEGM
SCRKIAQLAVSWQNRGRLADKRTVALPAARNLKKERTPSFSASDGDSDGSGPTCGRRPGLKQEDGPHIRIMKRRVHTHWDVNISFREASC
SQDGNLPTLISSVHRSRHLVMPEHQSRCEFQRGSLEIGLRPAGDLLGKRLGRSPRISSDCFSEKRARSESPQEALLLPRELGPSMAPEDH
YRRLVSALSEASTFEDPQRLYHLGLPSHGEDPPWHDPPHHLPSHDLLRVRQEVAAAALRGPSGLEAHLPSSTAGQRRKQGLAQHREGAAP
AAAPSFSERELPQPPPLLSPQNAPHVALGPHLRPPFLGVPSALCQTPGYGFLPPAQAEMFAWQQELLRKQNLARLELPADLLRQKELESA
RPQLLAPETALRPNDGAEELQRRGALLVLNHGAAPLLALPPQGPPGSGPPTPSRDSARRAPRKGGPGPASARPSESKEMTGARLWAQDGS
EDEPPKDSDGEDPETAAVGCRGPTPGQAPAGGAGAEGKGLFPGSTLPLGFPYAVSPYFHTGAVGGLSMDGEEAPAPEDVTKWTVDDVCSF
VGGLSGCGEYTRVFREQGIDGETLPLLTEEHLLTNMGLKLGPALKIRAQVARRLGRVFYVASFPVALPLQPPTLRAPERELGTGEQPLSP

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Fusion Gene PPI Analysis for ATAD3C-SAMD11


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 ATAD3C-SAMD11


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 ATAD3C-SAMD11


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0023893Liver Cirrhosis, Experimental1CTD_human