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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:SERPINA1-CPD (FusionGDB2 ID:80144)

Fusion Gene Summary for SERPINA1-CPD

check button Fusion gene summary
Fusion gene informationFusion gene name: SERPINA1-CPD
Fusion gene ID: 80144
HgeneTgene
Gene symbol

SERPINA1

CPD

Gene ID

5265

9455

Gene nameserpin family A member 1homer scaffold protein 2
SynonymsA1A|A1AT|AAT|PI|PI1|PRO2275|alpha1AT|nNIFACPD|CPD|DFNA68|HOMER-2|VESL-2
Cytomap

14q32.13

15q25.2

Type of geneprotein-codingprotein-coding
Descriptionalpha-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 proteinhomer protein homolog 2cupidinhomer homolog 2homer homolog 3homer scaffolding protein 2homer, neuronal immediate early gene, 2
Modification date2020032720200313
UniProtAcc.

O75976

Ensembl transtripts involved in fusion geneENST00000440909, ENST00000448921, 
ENST00000437397, ENST00000355814, 
ENST00000393087, ENST00000393088, 
ENST00000404814, ENST00000449399, 
ENST00000402629, ENST00000555289, 
ENST00000225719, ENST00000543464, 
ENST00000584051, 
Fusion gene scores* DoF score28 X 24 X 6=403211 X 13 X 7=1001
# samples 2813
** MAII scorelog2(28/4032*10)=-3.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/1001*10)=-2.94485844580754
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

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

Most frequent breakpointSERPINA1(94844713)-CPD(28783274), # samples:2
Anticipated loss of major functional domain due to fusion event.SERPINA1-CPD seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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 SERPINA1 (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 CPD (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
ChimerDB4LIHCTCGA-DD-A3A4-01ASERPINA1chr14

94844713

-CPDchr17

28783274

+
ChimerDB4LIHCTCGA-ED-A459-01ASERPINA1chr14

94844713

-CPDchr17

28783274

+


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Fusion Gene ORF analysis for SERPINA1-CPD

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-3CDSENST00000440909ENST00000225719SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3CDSENST00000440909ENST00000543464SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3UTRENST00000440909ENST00000584051SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3CDSENST00000448921ENST00000225719SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3CDSENST00000448921ENST00000543464SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3UTRENST00000448921ENST00000584051SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3CDSENST00000437397ENST00000225719SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3CDSENST00000437397ENST00000543464SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3UTRENST00000437397ENST00000584051SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3CDSENST00000355814ENST00000225719SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3CDSENST00000355814ENST00000543464SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3UTRENST00000355814ENST00000584051SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3CDSENST00000393087ENST00000225719SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3CDSENST00000393087ENST00000543464SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3UTRENST00000393087ENST00000584051SERPINA1chr14

94844713

-CPDchr17

28783274

+
Frame-shiftENST00000393088ENST00000225719SERPINA1chr14

94844713

-CPDchr17

28783274

+
Frame-shiftENST00000393088ENST00000543464SERPINA1chr14

94844713

-CPDchr17

28783274

+
5CDS-3UTRENST00000393088ENST00000584051SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3CDSENST00000404814ENST00000225719SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3CDSENST00000404814ENST00000543464SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3UTRENST00000404814ENST00000584051SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3CDSENST00000449399ENST00000225719SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3CDSENST00000449399ENST00000543464SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3UTRENST00000449399ENST00000584051SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3CDSENST00000402629ENST00000225719SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3CDSENST00000402629ENST00000543464SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3UTRENST00000402629ENST00000584051SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3CDSENST00000555289ENST00000225719SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3CDSENST00000555289ENST00000543464SERPINA1chr14

94844713

-CPDchr17

28783274

+
intron-3UTRENST00000555289ENST00000584051SERPINA1chr14

94844713

-CPDchr17

28783274

+

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 SERPINA1-CPD


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)
SERPINA1chr1494844712-CPDchr1728783273+0.0076800710.9923199
SERPINA1chr1494844712-CPDchr1728783273+0.0076800710.9923199

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 SERPINA1-CPD


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
.CPD

O75976

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

- 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 SERPINA1-CPD


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 SERPINA1-CPD


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 SERPINA1-CPD


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 SERPINA1-CPD


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSERPINA1C0023895Liver diseases6CTD_human
HgeneSERPINA1C0086565Liver Dysfunction6CTD_human
HgeneSERPINA1C0221757alpha 1-Antitrypsin Deficiency6CTD_human;GENOMICS_ENGLAND
HgeneSERPINA1C0023890Liver Cirrhosis3CTD_human
HgeneSERPINA1C0239946Fibrosis, Liver3CTD_human
HgeneSERPINA1C0005586Bipolar Disorder2CTD_human;PSYGENET
HgeneSERPINA1C0024117Chronic Obstructive Airway Disease2CTD_human
HgeneSERPINA1C0030328Panniculitis, Nodular Nonsuppurative2CTD_human
HgeneSERPINA1C0525045Mood Disorders2PSYGENET
HgeneSERPINA1C1527303Chronic Airflow Obstruction2CTD_human
HgeneSERPINA1C2239176Liver carcinoma2CTD_human
HgeneSERPINA1C0001418Adenocarcinoma1CTD_human
HgeneSERPINA1C0003469Anxiety Disorders1CTD_human
HgeneSERPINA1C0003850Arteriosclerosis1CTD_human
HgeneSERPINA1C0003949Asbestosis1CTD_human
HgeneSERPINA1C0005587Depression, Bipolar1CTD_human
HgeneSERPINA1C0006267Bronchiectasis1CTD_human
HgeneSERPINA1C0008370Cholestasis1CTD_human
HgeneSERPINA1C0013221Drug toxicity1CTD_human
HgeneSERPINA1C0013990Pathological accumulation of air in tissues1CTD_human
HgeneSERPINA1C0019080Hemorrhage1CTD_human
HgeneSERPINA1C0019693HIV Infections1CTD_human
HgeneSERPINA1C0020615Hypoglycemia1CTD_human
HgeneSERPINA1C0022660Kidney Failure, Acute1CTD_human
HgeneSERPINA1C0024115Lung diseases1CTD_human;GENOMICS_ENGLAND
HgeneSERPINA1C0024121Lung Neoplasms1CTD_human
HgeneSERPINA1C0024623Malignant neoplasm of stomach1CTD_human
HgeneSERPINA1C0024713Manic Disorder1CTD_human
HgeneSERPINA1C0027627Neoplasm Metastasis1CTD_human
HgeneSERPINA1C0034067Pulmonary Emphysema1CTD_human
HgeneSERPINA1C0034069Pulmonary Fibrosis1CTD_human
HgeneSERPINA1C0038356Stomach Neoplasms1CTD_human
HgeneSERPINA1C0039841Thiamine Deficiency1CTD_human
HgeneSERPINA1C0041755Adverse reaction to drug1CTD_human
HgeneSERPINA1C0042384Vasculitis1CTD_human
HgeneSERPINA1C0205641Adenocarcinoma, Basal Cell1CTD_human
HgeneSERPINA1C0205642Adenocarcinoma, Oxyphilic1CTD_human
HgeneSERPINA1C0205643Carcinoma, Cribriform1CTD_human
HgeneSERPINA1C0205644Carcinoma, Granular Cell1CTD_human
HgeneSERPINA1C0205645Adenocarcinoma, Tubular1CTD_human
HgeneSERPINA1C0221227Centriacinar Emphysema1CTD_human
HgeneSERPINA1C0242379Malignant neoplasm of lung1CTD_human
HgeneSERPINA1C0264393Panacinar Emphysema1CTD_human
HgeneSERPINA1C0270715Degenerative Diseases, Central Nervous System1CTD_human
HgeneSERPINA1C0271708Fasting Hypoglycemia1CTD_human
HgeneSERPINA1C0271710Reactive hypoglycemia1CTD_human
HgeneSERPINA1C0338831Manic1CTD_human
HgeneSERPINA1C0376280Anxiety States, Neurotic1CTD_human
HgeneSERPINA1C0524851Neurodegenerative Disorders1CTD_human
HgeneSERPINA1C0751733Degenerative Diseases, Spinal Cord1CTD_human
HgeneSERPINA1C1279420Anxiety neurosis (finding)1CTD_human
HgeneSERPINA1C1565662Acute Kidney Insufficiency1CTD_human
HgeneSERPINA1C1708349Hereditary Diffuse Gastric Cancer1CTD_human
HgeneSERPINA1C2350878Focal Emphysema1CTD_human
HgeneSERPINA1C2609414Acute kidney injury1CTD_human
HgeneSERPINA1C2930617Pulmonary Fibrosis - from Asbestos Exposure1CTD_human
HgeneSERPINA1C2930967Gastro-enteropancreatic neuroendocrine tumor1CTD_human
HgeneSERPINA1C4505456HIV Coinfection1CTD_human
HgeneSERPINA1C4721507Alveolitis, Fibrosing1CTD_human