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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:A2M-SERPINA1 (FusionGDB2 ID:30)

Fusion Gene Summary for A2M-SERPINA1

check button Fusion gene summary
Fusion gene informationFusion gene name: A2M-SERPINA1
Fusion gene ID: 30
HgeneTgene
Gene symbol

A2M

SERPINA1

Gene ID

2

5265

Gene namealpha-2-macroglobulinserpin family A member 1
SynonymsA2MD|CPAMD5|FWP007|S863-7A1A|A1AT|AAT|PI|PI1|PRO2275|alpha1AT|nNIF
Cytomap

12p13.31

14q32.13

Type of geneprotein-codingprotein-coding
Descriptionalpha-2-macroglobulinC3 and PZP-like alpha-2-macroglobulin domain-containing protein 5alpha-2-Malpha-1-antitrypsinalpha-1 antitrypsinalpha-1 protease inhibitoralpha-1-antiproteinasealpha-1-antitrypsin nullalpha-1-antitrypsin short transcript variant 1C4alpha-1-antitrypsin short transcript variant 1C5epididymis secretory sperm binding protein
Modification date2020032820200327
UniProtAcc

P01023

.
Ensembl transtripts involved in fusion geneENST00000318602, ENST00000542567, 
ENST00000402629, ENST00000555289, 
ENST00000355814, ENST00000393087, 
ENST00000393088, ENST00000404814, 
ENST00000437397, ENST00000440909, 
ENST00000448921, ENST00000449399, 
Fusion gene scores* DoF score15 X 18 X 6=162016 X 17 X 6=1632
# samples 2018
** MAII scorelog2(20/1620*10)=-3.01792190799726
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(18/1632*10)=-3.18057224564182
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: A2M [Title/Abstract] AND SERPINA1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointA2M(9232690)-SERPINA1(94844977), # samples:2
Anticipated loss of major functional domain due to fusion event.A2M-SERPINA1 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene 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
HgeneA2M

GO:0001869

negative regulation of complement activation, lectin pathway

12538697


check buttonFusion gene breakpoints across A2M (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 SERPINA1 (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 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
ChimerDB4LIHCTCGA-DD-A3A3-01AA2Mchr12

9232690

-SERPINA1chr14

94844977

-


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Fusion Gene ORF analysis for A2M-SERPINA1

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-intronENST00000318602ENST00000402629A2Mchr12

9232690

-SERPINA1chr14

94844977

-
5CDS-intronENST00000318602ENST00000555289A2Mchr12

9232690

-SERPINA1chr14

94844977

-
5UTR-3CDSENST00000542567ENST00000355814A2Mchr12

9232690

-SERPINA1chr14

94844977

-
5UTR-3CDSENST00000542567ENST00000393087A2Mchr12

9232690

-SERPINA1chr14

94844977

-
5UTR-3CDSENST00000542567ENST00000393088A2Mchr12

9232690

-SERPINA1chr14

94844977

-
5UTR-3CDSENST00000542567ENST00000404814A2Mchr12

9232690

-SERPINA1chr14

94844977

-
5UTR-3CDSENST00000542567ENST00000437397A2Mchr12

9232690

-SERPINA1chr14

94844977

-
5UTR-3CDSENST00000542567ENST00000440909A2Mchr12

9232690

-SERPINA1chr14

94844977

-
5UTR-3CDSENST00000542567ENST00000448921A2Mchr12

9232690

-SERPINA1chr14

94844977

-
5UTR-3CDSENST00000542567ENST00000449399A2Mchr12

9232690

-SERPINA1chr14

94844977

-
5UTR-intronENST00000542567ENST00000402629A2Mchr12

9232690

-SERPINA1chr14

94844977

-
5UTR-intronENST00000542567ENST00000555289A2Mchr12

9232690

-SERPINA1chr14

94844977

-
Frame-shiftENST00000318602ENST00000355814A2Mchr12

9232690

-SERPINA1chr14

94844977

-
Frame-shiftENST00000318602ENST00000393087A2Mchr12

9232690

-SERPINA1chr14

94844977

-
Frame-shiftENST00000318602ENST00000404814A2Mchr12

9232690

-SERPINA1chr14

94844977

-
Frame-shiftENST00000318602ENST00000437397A2Mchr12

9232690

-SERPINA1chr14

94844977

-
Frame-shiftENST00000318602ENST00000440909A2Mchr12

9232690

-SERPINA1chr14

94844977

-
Frame-shiftENST00000318602ENST00000448921A2Mchr12

9232690

-SERPINA1chr14

94844977

-
Frame-shiftENST00000318602ENST00000449399A2Mchr12

9232690

-SERPINA1chr14

94844977

-
In-frameENST00000318602ENST00000393088A2Mchr12

9232690

-SERPINA1chr14

94844977

-

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)
ENST00000318602A2Mchr129232690-ENST00000393088SERPINA1chr1494844977-342731623083172954

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
ENST00000318602ENST00000393088A2Mchr129232690-SERPINA1chr1494844977-0.0002225540.9997775

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Fusion Genomic Features for A2M-SERPINA1


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.
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.

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Fusion Protein Features for A2M-SERPINA1


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/chr12:9232690/chr14:94844977)
- 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
A2M

P01023

.
FUNCTION: Is able to inhibit all four classes of proteinases by a unique 'trapping' mechanism. This protein has a peptide stretch, called the 'bait region' which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein which traps the proteinase. The entrapped enzyme remains active against low molecular weight substrates (activity against high molecular weight substrates is greatly reduced). Following cleavage in the bait region, a thioester bond is hydrolyzed and mediates the covalent binding of the protein to the proteinase.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
HgeneA2Mchr12:9232690chr14:94844977ENST00000318602-2336690_7289511475.0RegionNote=Bait region
HgeneA2Mchr12:9232690chr14:94844977ENST00000318602-2336704_7099511475.0RegionNote=Inhibitory
HgeneA2Mchr12:9232690chr14:94844977ENST00000318602-2336719_7239511475.0RegionNote=Inhibitory
HgeneA2Mchr12:9232690chr14:94844977ENST00000318602-2336730_7359511475.0RegionNote=Inhibitory
TgeneSERPINA1chr12:9232690chr14:94844977ENST0000035581435368_392355419.0RegionNote=RCL
TgeneSERPINA1chr12:9232690chr14:94844977ENST0000039308735368_392355419.0RegionNote=RCL
TgeneSERPINA1chr12:9232690chr14:94844977ENST0000039308857368_392355419.0RegionNote=RCL
TgeneSERPINA1chr12:9232690chr14:94844977ENST0000040262904368_3920360.0RegionNote=RCL
TgeneSERPINA1chr12:9232690chr14:94844977ENST0000040481446368_392355419.0RegionNote=RCL
TgeneSERPINA1chr12:9232690chr14:94844977ENST0000043739746368_392355419.0RegionNote=RCL
TgeneSERPINA1chr12:9232690chr14:94844977ENST0000044090935368_392355419.0RegionNote=RCL
TgeneSERPINA1chr12:9232690chr14:94844977ENST0000044892157368_392355419.0RegionNote=RCL
TgeneSERPINA1chr12:9232690chr14:94844977ENST0000044939946368_392355419.0RegionNote=RCL

- 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 A2M-SERPINA1


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.
>30_30_1_A2M-SERPINA1_A2M_chr12_9232690_ENST00000318602_SERPINA1_chr14_94844977_ENST00000393088_length(transcript)=3427nt_BP=3162nt
GAAAAGCTTATTAGCTGCTGTACGGTAAAAGTGAGCTCTTACGGGAATGGGAATGTAGTTTTAGCCCTCCAGGGATTCTATTTAGCCCGC
CAGGAATTAACCTTGACTATAAATAGGCCATCAATGACCTTTCCAGAGAATGTTCAGAGACCTCAACTTTGTTTAGAGATCTTGTGTGGG
TGGAACTTCCTGTTTGCACACAGAGCAGCATAAAGCCCAGTTGCTTTGGGAAGTGTTTGGGACCAGATGGATTGTAGGGAGTAGGGTACA
ATACAGTCTGTTCTCCTCCAGCTCCTTCTTTCTGCAACATGGGGAAGAACAAACTCCTTCATCCAAGTCTGGTTCTTCTCCTCTTGGTCC
TCCTGCCCACAGACGCCTCAGTCTCTGGAAAACCGCAGTATATGGTTCTGGTCCCCTCCCTGCTCCACACTGAGACCACTGAGAAGGGCT
GTGTCCTTCTGAGCTACCTGAATGAGACAGTGACTGTAAGTGCTTCCTTGGAGTCTGTCAGGGGAAACAGGAGCCTCTTCACTGACCTGG
AGGCGGAGAATGACGTACTCCACTGTGTCGCCTTCGCTGTCCCAAAGTCTTCATCCAATGAGGAGGTAATGTTCCTCACTGTCCAAGTGA
AAGGACCAACCCAAGAATTTAAGAAGCGGACCACAGTGATGGTTAAGAACGAGGACAGTCTGGTCTTTGTCCAGACAGACAAATCAATCT
ACAAACCAGGGCAGACAGTGAAATTTCGTGTTGTCTCCATGGATGAAAACTTTCACCCCCTGAATGAGTTGATTCCACTAGTATACATTC
AGGATCCCAAAGGAAATCGCATCGCACAATGGCAGAGTTTCCAGTTAGAGGGTGGCCTCAAGCAATTTTCTTTTCCCCTCTCATCAGAGC
CCTTCCAGGGCTCCTACAAGGTGGTGGTACAGAAGAAATCAGGTGGAAGGACAGAGCACCCTTTCACCGTGGAGGAATTTGTTCTTCCCA
AGTTTGAAGTACAAGTAACAGTGCCAAAGATAATCACCATCTTGGAAGAAGAGATGAATGTATCAGTGTGTGGCCTATACACATATGGGA
AGCCTGTCCCTGGACATGTGACTGTGAGCATTTGCAGAAAGTATAGTGACGCTTCCGACTGCCACGGTGAAGATTCACAGGCTTTCTGTG
AGAAATTCAGTGGACAGCTAAACAGCCATGGCTGCTTCTATCAGCAAGTAAAAACCAAGGTCTTCCAGCTGAAGAGGAAGGAGTATGAAA
TGAAACTTCACACTGAGGCCCAGATCCAAGAAGAAGGAACAGTGGTGGAATTGACTGGAAGGCAGTCCAGTGAAATCACAAGAACCATAA
CCAAACTCTCATTTGTGAAAGTGGACTCACACTTTCGACAGGGAATTCCCTTCTTTGGGCAGGTGCGCCTAGTAGATGGGAAAGGCGTCC
CTATACCAAATAAAGTCATATTCATCAGAGGAAATGAAGCAAACTATTACTCCAATGCTACCACGGATGAGCATGGCCTTGTACAGTTCT
CTATCAACACCACCAATGTTATGGGTACCTCTCTTACTGTTAGGGTCAATTACAAGGATCGTAGTCCCTGTTACGGCTACCAGTGGGTGT
CAGAAGAACACGAAGAGGCACATCACACTGCTTATCTTGTGTTCTCCCCAAGCAAGAGCTTTGTCCACCTTGAGCCCATGTCTCATGAAC
TACCCTGTGGCCATACTCAGACAGTCCAGGCACATTATATTCTGAATGGAGGCACCCTGCTGGGGCTGAAGAAGCTCTCCTTCTATTATC
TGATAATGGCAAAGGGAGGCATTGTCCGAACTGGGACTCATGGACTGCTTGTGAAGCAGGAAGACATGAAGGGCCATTTTTCCATCTCAA
TCCCTGTGAAGTCAGACATTGCTCCTGTCGCTCGGTTGCTCATCTATGCTGTTTTACCTACCGGGGACGTGATTGGGGATTCTGCAAAAT
ATGATGTTGAAAATTGTCTGGCCAACAAGGTGGATTTGAGCTTCAGCCCATCACAAAGTCTCCCAGCCTCACACGCCCACCTGCGAGTCA
CAGCGGCTCCTCAGTCCGTCTGCGCCCTCCGTGCTGTGGACCAAAGCGTGCTGCTCATGAAGCCTGATGCTGAGCTCTCGGCGTCCTCGG
TTTACAACCTGCTACCAGAAAAGGACCTCACTGGCTTCCCTGGGCCTTTGAATGACCAGGACAATGAAGACTGCATCAATCGTCATAATG
TCTATATTAATGGAATCACATATACTCCAGTATCAAGTACAAATGAAAAGGATATGTACAGCTTCCTAGAGGACATGGGCTTAAAGGCAT
TCACCAACTCAAAGATTCGTAAACCCAAAATGTGTCCACAGCTTCAACAGTATGAAATGCATGGACCTGAAGGTCTACGTGTAGGTTTTT
ATGAGTCAGATGTAATGGGAAGAGGCCATGCACGCCTGGTGCATGTTGAAGAGCCTCACACGGAGACCGTACGAAAGTACTTCCCTGAGA
CATGGATCTGGGATTTGGTGGTGGTAAACTCAGCAGGTGTGGCTGAGGTAGGAGTAACAGTCCCTGACACCATCACCGAGTGGAAGGCAG
GGGCCTTCTGCCTGTCTGAAGATGCTGGACTTGGTATCTCTTCCACTGCCTCTCTCCGAGCCTTCCAGCCCTTCTTTGTGGAGCTCACAA
TGCCTTACTCTGTGATTCGTGGAGAGGCCTTCACACTCAAGGCCACGGTCCTAAACTACCTTCCCAAATGCATCCGGGTCAGTGTGCAGC
TGGAAGCCTCTCCCGCCTTCCTAGCTGTCCCAGTGGAGAAGGAACAAGCGCCTCACTGCATCTGTGCAAACGGGCGGCAAACTGTGTCCT
GGGCAGTAACCCCAAAGTCATTAGGAAATGTGAATTTCACTGTGAGCGCAGAGGCACTAGAGTCTCAAGAGCTGTGTGGGACTGAGGTGC
CTTCAGTTCCTGAACACGGAAGGAAAGACACAGTCATCAAGCCTCTGTTGGTTGAACCTGAAGGACTAGAGAAGGAAACAACATTCAACT
CCCTACTTTGTCCATCAGGTGGTGAGGTTTCTGAAGAATTATCCCTGAAACTGCCACCAAATGTGGTAGAAGAATCTGCCCGAGCTTCTG
TCTCAGTTTTGGGCCGTGCATAAGGCTGTGCTGACCATCGACGAGAAAGGGACTGAAGCTGCTGGGGCCATGTTTTTAGAGGCCATACCC
ATGTCTATCCCCCCCGAGGTCAAGTTCAACAAACCCTTTGTCTTCTTAATGATTGAACAAAATACCAAGTCTCCCCTCTTCATGGGAAAA
GTGGTGAATCCCACCCAAAAATAACTGCCTCTCGCTCCTCAACCCCTCCCCTCCATCCCTGGCCCCCTCCCTGGATGACATTAAAGAAGG

>30_30_1_A2M-SERPINA1_A2M_chr12_9232690_ENST00000318602_SERPINA1_chr14_94844977_ENST00000393088_length(amino acids)=954AA_BP=
MGKNKLLHPSLVLLLLVLLPTDASVSGKPQYMVLVPSLLHTETTEKGCVLLSYLNETVTVSASLESVRGNRSLFTDLEAENDVLHCVAFA
VPKSSSNEEVMFLTVQVKGPTQEFKKRTTVMVKNEDSLVFVQTDKSIYKPGQTVKFRVVSMDENFHPLNELIPLVYIQDPKGNRIAQWQS
FQLEGGLKQFSFPLSSEPFQGSYKVVVQKKSGGRTEHPFTVEEFVLPKFEVQVTVPKIITILEEEMNVSVCGLYTYGKPVPGHVTVSICR
KYSDASDCHGEDSQAFCEKFSGQLNSHGCFYQQVKTKVFQLKRKEYEMKLHTEAQIQEEGTVVELTGRQSSEITRTITKLSFVKVDSHFR
QGIPFFGQVRLVDGKGVPIPNKVIFIRGNEANYYSNATTDEHGLVQFSINTTNVMGTSLTVRVNYKDRSPCYGYQWVSEEHEEAHHTAYL
VFSPSKSFVHLEPMSHELPCGHTQTVQAHYILNGGTLLGLKKLSFYYLIMAKGGIVRTGTHGLLVKQEDMKGHFSISIPVKSDIAPVARL
LIYAVLPTGDVIGDSAKYDVENCLANKVDLSFSPSQSLPASHAHLRVTAAPQSVCALRAVDQSVLLMKPDAELSASSVYNLLPEKDLTGF
PGPLNDQDNEDCINRHNVYINGITYTPVSSTNEKDMYSFLEDMGLKAFTNSKIRKPKMCPQLQQYEMHGPEGLRVGFYESDVMGRGHARL
VHVEEPHTETVRKYFPETWIWDLVVVNSAGVAEVGVTVPDTITEWKAGAFCLSEDAGLGISSTASLRAFQPFFVELTMPYSVIRGEAFTL
KATVLNYLPKCIRVSVQLEASPAFLAVPVEKEQAPHCICANGRQTVSWAVTPKSLGNVNFTVSAEALESQELCGTEVPSVPEHGRKDTVI

--------------------------------------------------------------

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Fusion Gene PPI Analysis for A2M-SERPINA1


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 A2M-SERPINA1


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 A2M-SERPINA1


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