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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:AMN1-FAR2 (FusionGDB2 ID:HG196394TG55711)

Fusion Gene Summary for AMN1-FAR2

check button Fusion gene summary
Fusion gene informationFusion gene name: AMN1-FAR2
Fusion gene ID: hg196394tg55711
HgeneTgene
Gene symbol

AMN1

FAR2

Gene ID

196394

55711

Gene nameantagonist of mitotic exit network 1 homologfatty acyl-CoA reductase 2
Synonyms-HEL-S-81|MLSTD1|SDR10E2
Cytomap('AMN1')('FAR2')

12p11.21

12p11.22

Type of geneprotein-codingprotein-coding
Descriptionprotein AMN1 homologfatty acyl-CoA reductase 2epididymis secretory protein Li 81male sterility domain-containing protein 1short chain dehydrogenase/reductase family 10E, member 2
Modification date2020031320200313
UniProtAcc

Q8IY45

.
Ensembl transtripts involved in fusion geneENST00000281471, ENST00000536761, 
ENST00000537562, ENST00000541931, 
ENST00000542781, ENST00000541541, 
Fusion gene scores* DoF score2 X 2 X 2=84 X 3 X 4=48
# samples 24
** MAII scorelog2(2/8*10)=1.32192809488736log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: AMN1 [Title/Abstract] AND FAR2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAMN1(31841941)-FAR2(29460591), # samples:1
Anticipated loss of major functional domain due to fusion event.AMN1-FAR2 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
AMN1-FAR2 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
AMN1-FAR2 seems lost the major protein functional domain in Tgene partner, which is a essential 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
TgeneFAR2

GO:0035336

long-chain fatty-acyl-CoA metabolic process

15220348


check buttonFusion gene breakpoints across AMN1 (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 FAR2 (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
ChimerDB4LUADTCGA-80-5611-01AAMN1chr12

31841941

-FAR2chr12

29460591

+


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Fusion Gene ORF analysis for AMN1-FAR2

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-intronENST00000281471ENST00000182377AMN1chr12

31841941

-FAR2chr12

29460591

+
5CDS-intronENST00000281471ENST00000547116AMN1chr12

31841941

-FAR2chr12

29460591

+
5CDS-intronENST00000281471ENST00000549080AMN1chr12

31841941

-FAR2chr12

29460591

+
5CDS-intronENST00000536761ENST00000182377AMN1chr12

31841941

-FAR2chr12

29460591

+
5CDS-intronENST00000536761ENST00000547116AMN1chr12

31841941

-FAR2chr12

29460591

+
5CDS-intronENST00000536761ENST00000549080AMN1chr12

31841941

-FAR2chr12

29460591

+
5CDS-intronENST00000537562ENST00000182377AMN1chr12

31841941

-FAR2chr12

29460591

+
5CDS-intronENST00000537562ENST00000547116AMN1chr12

31841941

-FAR2chr12

29460591

+
5CDS-intronENST00000537562ENST00000549080AMN1chr12

31841941

-FAR2chr12

29460591

+
5CDS-intronENST00000541931ENST00000182377AMN1chr12

31841941

-FAR2chr12

29460591

+
5CDS-intronENST00000541931ENST00000547116AMN1chr12

31841941

-FAR2chr12

29460591

+
5CDS-intronENST00000541931ENST00000549080AMN1chr12

31841941

-FAR2chr12

29460591

+
5CDS-intronENST00000542781ENST00000182377AMN1chr12

31841941

-FAR2chr12

29460591

+
5CDS-intronENST00000542781ENST00000547116AMN1chr12

31841941

-FAR2chr12

29460591

+
5CDS-intronENST00000542781ENST00000549080AMN1chr12

31841941

-FAR2chr12

29460591

+
Frame-shiftENST00000281471ENST00000536681AMN1chr12

31841941

-FAR2chr12

29460591

+
Frame-shiftENST00000536761ENST00000536681AMN1chr12

31841941

-FAR2chr12

29460591

+
Frame-shiftENST00000541931ENST00000536681AMN1chr12

31841941

-FAR2chr12

29460591

+
Frame-shiftENST00000542781ENST00000536681AMN1chr12

31841941

-FAR2chr12

29460591

+
In-frameENST00000537562ENST00000536681AMN1chr12

31841941

-FAR2chr12

29460591

+
intron-3CDSENST00000541541ENST00000536681AMN1chr12

31841941

-FAR2chr12

29460591

+
intron-intronENST00000541541ENST00000182377AMN1chr12

31841941

-FAR2chr12

29460591

+
intron-intronENST00000541541ENST00000547116AMN1chr12

31841941

-FAR2chr12

29460591

+
intron-intronENST00000541541ENST00000549080AMN1chr12

31841941

-FAR2chr12

29460591

+

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)
ENST00000537562AMN1chr1231841941-ENST00000536681FAR2chr1229460591+3930110510552107350

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
ENST00000537562ENST00000536681AMN1chr1231841941-FAR2chr1229460591+0.0004852060.9995148

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Fusion Genomic Features for AMN1-FAR2


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)
AMN1chr1231841940-FAR2chr1229460590+5.92E-070.9999994
AMN1chr1231841940-FAR2chr1229460590+5.92E-070.9999994

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 AMN1-FAR2


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/chr12:31841941/chr12:29460591)
- 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
AMN1

Q8IY45

.
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
TgeneFAR2chr12:31841941chr12:29460591ENST00000182377312485_515181516.0Topological domainPeroxisomal
TgeneFAR2chr12:31841941chr12:29460591ENST00000536681312485_515181516.0Topological domainPeroxisomal
TgeneFAR2chr12:31841941chr12:29460591ENST00000182377312465_484181516.0TransmembraneHelical
TgeneFAR2chr12:31841941chr12:29460591ENST00000536681312465_484181516.0TransmembraneHelical

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneFAR2chr12:31841941chr12:29460591ENST000001823773121_464181516.0Topological domainCytoplasmic
TgeneFAR2chr12:31841941chr12:29460591ENST000005366813121_464181516.0Topological domainCytoplasmic


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Fusion Gene Sequence for AMN1-FAR2


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.
>4228_4228_1_AMN1-FAR2_AMN1_chr12_31841941_ENST00000537562_FAR2_chr12_29460591_ENST00000536681_length(transcript)=3930nt_BP=1105nt
CGATGCCTCGCCCACGGCGGGTCAGTCAGCTCCTGGATCTTGATGCTTAGGAAAGATTTTATATCATTAAAAAGAAATTGGGAGGTCACT
TCCAAGATGGCTAAATGGGAACAGCTCCAGTCTGCAGCTCCCAGCAAGATTGACGCAGAAGATGGGCGATTTCTGCATTTCCAACTGAGA
TGCTACTGGACTTGAATGGTTAATAAAATTGCACAATGTTGTTGGTGGCAGTGACTTCTTTCTGTTCAGATTAAGGCCGAGCACAAGGCT
CATGCCTGTAATCCCAGCAGTTTGGGAGGCCAAGGTGGGAGGCTCACTTCAGCCCAGGAGTTCAAGACCGGCCTGGGCAACATATAGAGA
CCCCATCTCTACAAGAAATACAGAAAATTAGCTGATTGTGGTGGTGCATGTCTGTAGTCCCAACTACTTGGGAGGCTGAGATGCCTTTGG
TGCTTCATGAAGAATATTTCCAGATATCTCACAGACATTAAGCCTTTGCCTCCCAACATAAAAGACAGACTGATTAAAATAATGAGTATG
CAGGGACAGATAACAGATTCAAATATAAGTGAGATTTTACATCCTGAAGTCCAAACTCTAGATCTACGGAGCTGCGATATATCAGATGCT
GCTCTCCTGCACCTGTCTAACTGTAGAAAACTGAAGAAATTAAATTTAAATGCTTCAAAAGGGAACCGAGTTTCTGTAACTTCAGAAGGA
ATAAAAGCTGTGGCTTCATCTTGTTCATACCTACACGAAGCTTCTTTGAAAAGATGCTGCAATCTCACTGACGAAGGAGTCGTTGCTCTT
GCACTCAATTGCCAGCTGCTAAAGATCATCGATTTAGGTGGCTGCTTAAGTATTACTGATGTGTCCTTACATGCATTAGGAAAAAACTGC
CCATTTTTGCAGTGTGTCGACTTTTCAGCTACTCAGGTATCTGACAGTGGTGTGATTGCACTTGTTAGTGGACCTTGTGCGAAGAAATTA
GAGGAGATTCATATGGGACATTGTGTAAATCTGACTGATGGGGCTGTCGAAGCTGTCCTTACTTACTGTCCTCAAATACGTATATTACTC
TTCCATGGATGCCCCTTGATAACAGGTGGTTAGACGATGCTATTATTGACGAGATTACACCCAAGCTGATCAGAGATTGGCCCAATATTT
ATACCTACACCAAGGCCTTGGGAGAAATGGTGGTGCAGCAAGAGAGCAGGAACCTGAACATTGCCATCATAAGGCCCTCCATTGTGGGAG
CAACTTGGCAGGAGCCTTTCCCAGGTTGGGTTGATAATATAAATGGACCTAATGGAATCATTATTGCGACTGGGAAAGGGTTTCTTCGGG
CCATAAAAGCTACTCCAATGGCTGTGGCAGACGTAATTCCAGTTGATACAGTCGTCAATCTCATGCTAGCTGTAGGATGGTATACTGCAG
TTCACAGACCTAAGTCAACATTAGTCTACCACATTACATCTGGTAACATGAATCCCTGCAATTGGCACAAAATGGGAGTCCAAGTCTTGG
CAACCTTTGAAAAAATCCCATTTGAGAGACCTTTCAGGAGGCCAAATGCTAATTTTACCAGCAACAGCTTCACATCACAGTACTGGAATG
CGGTCAGCCACCGGGCCCCTGCCATTATCTATGACTGCTATCTGCGGCTCACTGGAAGGAAGCCCAGGATGACAAAGCTCATGAATCGGC
TTTTAAGAACTGTTTCCATGTTGGAGTATTTCATCAACCGGAGTTGGGAATGGAGCACGTACAATACAGAAATGCTGATGTCTGAGCTGA
GTCCTGAAGACCAGAGAGTATTCAACTTTGACGTGCGCCAGTTGAACTGGTTGGAATACATTGAAAATTATGTTTTGGGAGTTAAAAAAT
ACTTATTGAAAGAGGATATGGCTGGGATCCCAAAAGCAAAGCAACGCTTAAAAAGGCTCCGAAATATTCACTACCTCTTTAATACTGCCC
TCTTCCTTATCGCCTGGCGCCTTCTCATTGCAAGATCTCAGATGGCTCGGAATGTCTGGTTCTTCATTGTAAGCTTCTGTTATAAATTCC
TCTCCTACTTTAGAGCATCCAGCACGCTCAAAGTTTAAGAGCATTTAGCCATCGCTTTTTATCTGGAACCTCTCAGATACCTCTAAAACA
GCAAACTGTGATTCTCAAGATTAGAAAGTAACAAGGAATATGCCCAAACTGTCAAATGTCACCTGTTATGTATTCGTCCCTATTCCTTAA
CTATGTATTTTTATTTCAGTGAGAGAAGGAAAGTTGTAAACTAGCCCATAGTCACCTATATTTTAGGGAAAAAAATCCAAATTGTTTCCT
AACATTCTATTTTATGCCCTTGCGTATTAAACGTGAAAGTACTCCCACTTTTCTATATTTAGTTTTTCTTTTCTCTCTGAGATGATTCAT
TTAAACTCAGTAAATATGGAAAGATGCATGGCAGAAGCTGAAATGAGCTCAAGCAGTACTAACCTTGGAACCATTCTGGGTACCCAAAAG
AAAAATTTAAAATCAAGATGAGTAAAAGGAGAATGGTCTCAATATCCTCAAAAATGCAGTAAGAGAAGTAATTCCCCACTGAAAATGTCT
CTCTTTCTTTCTATGTTATACCCTGGAGTCCTGGTTGAGGGGTGGGGGAATCAGAAAAGTAGGTTTACATTTAACATTTTTCTTAACTAC
ATTCACTTCTTAAAAAGGAACAAGAAGTGTAAATAAGTATGTATAGAGTGAGGGATTAAGCATATTTGCATTGGGGACTCGTGTATTATG
CTTTTAAGTCAAAATTAATATTCTCAAATTCGAATTTGATAGCTATTATTTCTAAATCTTTTTAATCCTCAATTTTCCTGGTAACCTTCT
TTCAAGAGTCTCCTTCTTCTAAAAGTTGCCAAACCCTTTATATTTAAGCTTTTTCCACTCAGGACTCAATTAGAGTGGTCAACAGGGAGA
GGGATGGTCCCATTTGATCTTTGCCACTGAGCAAAACAAAACTTCAAATGAACTTTTAAACTGTAGCTTTAGTCTTCTGGTATAAAGTGG
GGAAGATTACACTTATGTGATCACCAAAGGATTTACTAGTATCTTGGTCATTCCAATTGCACAATGTTAACTGTACAACACACAGCAGAA
AAGTGAATAGACTTCACTAAGGGATTCTAAGTTTAGAAAATAGGTTTTGTTTTCTTAAAAAATTTTGTGTATAATACAAACTAATGAAAA
CTATACATATTCTCCAATTCCTATAGTAATAATAATGTAACTGTTACACCAACTTTCCTCATATTTGAGAGATGAGTACATGTTGGATTG
CAGCATTTCTTCATGTTAAAAACATGGAATATTATTCAAATATAGTACTTGGGGCCTAAACAACTAAAATTAGTCACCGCATAACTAGTT
GAAAATGGCATAGGCATAAAATGTTAATAAAGAATGGCAGTTATATTTATGCTCACTTCCTGGAGTAATTGGGTAATATTCAGAAAGGCA
CATCGTGGTAGTTTAAGTGTACAAGGCCTTAGGGCAGTATCTAGCCCAGTATTATTCCAGATTCTCCTGAGCTCTATATAAAGGGCATTT
TGGAGGAACTCTTCTGGGCAATATCTTTCCCAATCTCATCTAAATTCTGGGAAATATTTTCCATAGCAGACAACCCAGCTCTGAAACTAA
GCACCTGGTGATCTTTAGTTTGAGATGTCTATATGGTACTTTTGAGTTATATCAATTAAGATACAAGCTATAGACATGATAAAAATATGA
AATCAAGATATAGCTCAGTGGGATTGGATTAAGACATAATAATAGTTCTAAGAATTCACTTTTGATTGTATGTTTTACCAATTCAATAAT

>4228_4228_1_AMN1-FAR2_AMN1_chr12_31841941_ENST00000537562_FAR2_chr12_29460591_ENST00000536681_length(amino acids)=350AA_BP=16
MSSNTYITLPWMPLDNRWLDDAIIDEITPKLIRDWPNIYTYTKALGEMVVQQESRNLNIAIIRPSIVGATWQEPFPGWVDNINGPNGIII
ATGKGFLRAIKATPMAVADVIPVDTVVNLMLAVGWYTAVHRPKSTLVYHITSGNMNPCNWHKMGVQVLATFEKIPFERPFRRPNANFTSN
SFTSQYWNAVSHRAPAIIYDCYLRLTGRKPRMTKLMNRLLRTVSMLEYFINRSWEWSTYNTEMLMSELSPEDQRVFNFDVRQLNWLEYIE

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

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Fusion Gene PPI Analysis for AMN1-FAR2


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 AMN1-FAR2


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 AMN1-FAR2


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