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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:NR2C2AP-MAP1S (FusionGDB2 ID:60094)

Fusion Gene Summary for NR2C2AP-MAP1S

check button Fusion gene summary
Fusion gene informationFusion gene name: NR2C2AP-MAP1S
Fusion gene ID: 60094
HgeneTgene
Gene symbol

NR2C2AP

MAP1S

Gene ID

126382

55201

Gene namenuclear receptor 2C2 associated proteinmicrotubule associated protein 1S
SynonymsTRA16BPY2IP1|C19orf5|MAP8|VCY2IP-1|VCY2IP1
Cytomap

19p13.11

19p13.11

Type of geneprotein-codingprotein-coding
Descriptionnuclear receptor 2C2-associated proteinTR4 orphan receptor associated protein TRA16TR4 orphan receptor-associated 16 kDa proteinrepressor for TR4 transactivationmicrotubule-associated protein 1SBPY2-interacting protein 1MAP-1SVCY2-interacting protein 1microtubule-associated protein 8variable charge Y chromosome 2-interacting protein 1
Modification date2020031320200313
UniProtAcc

Q86WQ0

Q66K74

Ensembl transtripts involved in fusion geneENST00000420605, ENST00000331552, 
ENST00000538165, ENST00000544883, 
ENST00000544059, ENST00000597681, 
ENST00000324096, 
Fusion gene scores* DoF score2 X 2 X 2=86 X 6 X 6=216
# samples 28
** MAII scorelog2(2/8*10)=1.32192809488736log2(8/216*10)=-1.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NR2C2AP [Title/Abstract] AND MAP1S [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNR2C2AP(19312740)-MAP1S(17835858), # samples:3
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
TgeneMAP1S

GO:0010848

regulation of chromatin disassembly

12762840


check buttonFusion gene breakpoints across NR2C2AP (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 MAP1S (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
ChimerDB4BRCATCGA-LD-A7W6-01ANR2C2APchr19

19312740

-MAP1Schr19

17835858

+


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Fusion Gene ORF analysis for NR2C2AP-MAP1S

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-intronENST00000420605ENST00000544059NR2C2APchr19

19312740

-MAP1Schr19

17835858

+
5CDS-intronENST00000420605ENST00000597681NR2C2APchr19

19312740

-MAP1Schr19

17835858

+
In-frameENST00000420605ENST00000324096NR2C2APchr19

19312740

-MAP1Schr19

17835858

+
intron-3CDSENST00000331552ENST00000324096NR2C2APchr19

19312740

-MAP1Schr19

17835858

+
intron-3CDSENST00000538165ENST00000324096NR2C2APchr19

19312740

-MAP1Schr19

17835858

+
intron-3CDSENST00000544883ENST00000324096NR2C2APchr19

19312740

-MAP1Schr19

17835858

+
intron-intronENST00000331552ENST00000544059NR2C2APchr19

19312740

-MAP1Schr19

17835858

+
intron-intronENST00000331552ENST00000597681NR2C2APchr19

19312740

-MAP1Schr19

17835858

+
intron-intronENST00000538165ENST00000544059NR2C2APchr19

19312740

-MAP1Schr19

17835858

+
intron-intronENST00000538165ENST00000597681NR2C2APchr19

19312740

-MAP1Schr19

17835858

+
intron-intronENST00000544883ENST00000544059NR2C2APchr19

19312740

-MAP1Schr19

17835858

+
intron-intronENST00000544883ENST00000597681NR2C2APchr19

19312740

-MAP1Schr19

17835858

+

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)
ENST00000420605NR2C2APchr1919312740-ENST00000324096MAP1Schr1917835858+367671125535871110

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
ENST00000420605ENST00000324096NR2C2APchr1919312740-MAP1Schr1917835858+0.0122957180.9877043

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Fusion Genomic Features for NR2C2AP-MAP1S


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)
NR2C2APchr1919312739-MAP1Schr1917835857+5.89E-050.9999411
NR2C2APchr1919312739-MAP1Schr1917835857+5.89E-050.9999411

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 NR2C2AP-MAP1S


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/chr19:19312740/chr19:17835858)
- 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
NR2C2AP

Q86WQ0

MAP1S

Q66K74

FUNCTION: May act as a repressor of NR2C2-mediated transactivation by suppressing the binding between NR2C2/TR4 and the TR4-response element in target genes. {ECO:0000269|PubMed:12486131}.FUNCTION: Microtubule-associated protein that mediates aggregation of mitochondria resulting in cell death and genomic destruction (MAGD). Plays a role in anchoring the microtubule organizing center to the centrosomes. Binds to DNA. Plays a role in apoptosis. Involved in the formation of microtubule bundles (By similarity). {ECO:0000250, ECO:0000269|PubMed:15899810, ECO:0000269|PubMed:17234756}.

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
TgeneMAP1Schr19:19312740chr19:17835858ENST0000032409627560_8501011060.0Compositional biasNote=Pro-rich
TgeneMAP1Schr19:19312740chr19:17835858ENST0000032409627714_9661011060.0RegionNote=Necessary for association with microtubules
TgeneMAP1Schr19:19312740chr19:17835858ENST0000032409627960_10591011060.0RegionNecessary for association with actin
TgeneMAP1Schr19:19312740chr19:17835858ENST0000032409627967_9911011060.0RegionNote=Necessary for the mitochondrial aggregation and genome destruction

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneMAP1Schr19:19312740chr19:17835858ENST00000324096271_7971011060.0RegionNote=Necessary for the microtubule-organizing center localization


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Fusion Gene Sequence for NR2C2AP-MAP1S


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.
>60094_60094_1_NR2C2AP-MAP1S_NR2C2AP_chr19_19312740_ENST00000420605_MAP1S_chr19_17835858_ENST00000324096_length(transcript)=3676nt_BP=711nt
ACAAAAAGCCACCGCCCCCGAAACCCGCGGGAAATCTGTTTCCTGTGAAAGGCCTGGCCTCCGGGCATTGGCGGTTTCCCTGATCCTCTC
TCCCAAATTTTCCGGCAGGGGATTGATCGAGGCGACATTTAGGACTGGGGTGGGCGAGGGAGTGGCGGTTCTCGTCCCAAGTTACAGGTG
AGGACGTTCAGGCCAAGGCGTAGCCAAGATCGCGCCGCCCTGTAGCTTGAGGAGGCGCCGGGATTCGAACCAAGGCTGTGCCCAATCCTA
AGCCCTGCGAGGTCTTGTGGAACCGACATGACCCACTCTTTGGTTTGTCCAGAGACAGTGAGCAGGGTGAGTTCAGTGCTGAATCGCAAC
ACTCGGCAGTTTGGAAAAAAACATCTTTTCGACCAGGATGAGGAGACATGTTGGAACTCAGACCAGGGCCCCTCCCAGTGGGTGACGCTG
GAGTTTCCCCAGCTCATCCGTGTCTCCCAGCTGCAGATCCAGTTTCAGGGTGGCTTCTCCAGTCGCCGGGGCTGCCTGGAAGGTTCACAG
GGCACTCAGGCTCTCCACAAGATTGTAGATTTCTACCCTGAGGACAACAACTCGCTTCAGACTTTCCCCATACCAGCTGCTGAAGTGGAC
CGGCTGAAGGTGACGTTTGAGGATGCCACTGACTTTTTTGGCCGTGTGGTCATCTACCACCTGCGGGTGCTTGGGGAGAAGCTCCGGAAC
CTTCTGTTGGACCCTGCCTCTCACAAGCTACTGGTGTTGGCTGGGCCCTGCCTGGAGGAGACGGGGGAGCTGCTGCTACAGACAGGGGGC
TTCTCGCCTCACCACTTCCTCCAGGTCCTGAAGGACAGAGAGATCCGGGACATCCTGGCCACCACGCCCCCACCTGTGCAGCCGCCCATA
CTCACCATCACCTGCCCCACCTTCGGTGACTGGGCTCAGCTGGCACCCGCTGTGCCTGGCCTTCAGGGGGCGCTCCGGCTCCAGCTGCGG
CTGAACCCCCCGGCGCAGCTGCCCAACTCTGAGGGCCTGTGCGAATTCCTGGAGTACGTGGCTGAGTCTCTGGAGCCACCGTCCCCCTTC
GAGCTGCTGGAGCCCCCGACCTCCGGGGGCTTCCTCAGGCTGGGCCGGCCCTGCTGCTACATCTTCCCTGGAGGCCTCGGGGATGCCGCC
TTCTTCGCCGTCAATGGCTTCACTGTGCTGGTCAACGGTGGCTCAAACCCCAAGTCCAGTTTCTGGAAGCTGGTGCGGCACCTGGACCGC
GTGGATGCCGTGCTGGTGACCCACCCTGGCGCCGACAGCCTCCCCGGCCTCAACAGCCTGCTGCGGCGCAAACTGGCGGAGCGCTCCGAG
GTGGCTGCTGGTGGGGGCTCCTGGGACGACAGGCTGCGCAGGCTCATCTCCCCCAACCTGGGGGTCGTGTTCTTCAACGCCTGCGAGGCC
GCGTCGCGGCTGGCGCGCGGCGAGGATGAGGCGGAGCTGGCGCTGAGCCTCCTGGCGCAGCTGGGCATCACGCCTCTGCCACTCAGCCGC
GGCCCCGTGCCAGCCAAACCCACCGTGCTCTTCGAGAAGATGGGCGTGGGCCGGCTGGACATGTATGTGCTGCACCCGCCCTCCGCCGGC
GCCGAGCGCACGCTGGCCTCTGTGTGCGCCCTGCTGGTGTGGCACCCCGCCGGCCCCGGCGAGAAGGTGGTGCGCGTGCTGTTCCCCGGT
TGCACCCCGCCCGCCTGCCTCCTGGACGGCCTGGTCCGCCTGCAGCACTTGAGGTTCCTGCGAGAGCCCGTGGTGACGCCCCAGGACCTG
GAGGGGCCGGGGCGAGCCGAGAGCAAAGAGAGCGTGGGCTCCCGGGACAGCTCGAAGAGAGAGGGCCTCCTGGCCACCCACCCTAGACCT
GGCCAGGAGCGCCCTGGGGTGGCCCGCAAGGAGCCAGCACGGGCTGAGGCCCCACGCAAGACTGAGAAAGAAGCCAAGACCCCCCGGGAG
TTGAAGAAAGACCCCAAACCGAGTGTCTCCCGGACCCAGCCGCGGGAGGTGCGCCGGGCAGCCTCTTCTGTGCCCAACCTCAAGAAGACG
AATGCCCAGGCGGCACCCAAGCCCCGCAAAGCGCCCAGCACGTCCCACTCTGGCTTCCCGCCGGTGGCAAATGGACCCCGCAGCCCGCCC
AGCCTCCGATGTGGAGAAGCCAGCCCCCCCAGTGCAGCCTGCGGCTCTCCGGCCTCCCAGCTGGTGGCCACGCCCAGCCTGGAGCTGGGG
CCGATCCCAGCCGGGGAGGAGAAGGCACTGGAGCTGCCTTTGGCCGCCAGCTCAATCCCAAGGCCACGCACACCCTCCCCTGAGTCCCAC
CGGAGCCCCGCAGAGGGCAGCGAGCGGCTGTCGCTGAGCCCACTGCGGGGCGGGGAGGCCGGGCCAGACGCCTCACCCACAGTGACCACA
CCCACGGTGACCACGCCCTCACTACCCGCAGAGGTGGGCTCCCCGCACTCGACCGAGGTGGACGAGTCCCTGTCGGTGTCCTTTGAGCAG
GTGCTGCCGCCATCCGCCCCCACCAGTGAGGCTGGGCTGAGCCTCCCGCTGCGTGGCCCCCGGGCGCGGCGCTCGGCTTCCCCACACGAT
GTGGACCTGTGCCTGGTGTCACCCTGTGAATTTGAGCATCGCAAGGCGGTGCCAATGGCACCGGCACCTGCGTCCCCCGGCAGCTCGAAT
GACAGCAGTGCCCGGTCACAGGAACGGGCAGGTGGGCTGGGGGCCGAGGAGACGCCACCCACATCGGTCAGCGAGTCCCTGCCCACCCTG
TCTGACTCGGATCCCGTGCCCCTGGCCCCCGGTGCGGCAGACTCAGACGAAGACACAGAGGGCTTTGGAGTCCCTCGCCACGACCCTTTG
CCTGACCCCCTCAAGGTCCCCCCACCACTGCCTGACCCATCCAGCATCTGCATGGTGGACCCCGAGATGCTGCCCCCCAAGACAGCACGG
CAAACGGAGAACGTCAGCCGCACCCGGAAGCCCCTGGCCCGCCCCAACTCACGCGCTGCCGCCCCCAAAGCCACTCCAGTGGCTGCTGCC
AAAACCAAGGGGCTTGCTGGTGGGGACCGTGCCAGCCGACCACTCAGTGCCCGGAGTGAGCCCAGTGAGAAGGGAGGCCGGGCACCCCTG
TCCAGAAAGTCCTCAACCCCCAAGACTGCCACTCGAGGCCCGTCGGGGTCAGCCAGCAGCCGGCCCGGGGTGTCAGCCACCCCACCCAAG
TCCCCGGTCTACCTGGACCTGGCCTACCTGCCCAGCGGGAGCAGCGCCCACCTGGTGGATGAGGAGTTCTTCCAGCGCGTGCGCGCGCTC
TGCTACGTCATCAGTGGCCAGGACCAGCGCAAGGAGGAAGGCATGCGGGCCGTCCTGGACGCGCTACTGGCCAGCAAGCAGCATTGGGAC
CGTGACCTGCAGGTGACCCTGATCCCCACTTTCGACTCGGTGGCCATGCATACGTGGTACGCAGAGACGCACGCCCGGCACCAGGCGCTG
GGCATCACGGTGTTGGGCAGCAACAGCATGGTGTCCATGCAGGATGACGCCTTCCCGGCCTGCAAGGTGGAGTTCTAGCCCCATCGCCGA

>60094_60094_1_NR2C2AP-MAP1S_NR2C2AP_chr19_19312740_ENST00000420605_MAP1S_chr19_17835858_ENST00000324096_length(amino acids)=1110AA_BP=152
MCPILSPARSCGTDMTHSLVCPETVSRVSSVLNRNTRQFGKKHLFDQDEETCWNSDQGPSQWVTLEFPQLIRVSQLQIQFQGGFSSRRGC
LEGSQGTQALHKIVDFYPEDNNSLQTFPIPAAEVDRLKVTFEDATDFFGRVVIYHLRVLGEKLRNLLLDPASHKLLVLAGPCLEETGELL
LQTGGFSPHHFLQVLKDREIRDILATTPPPVQPPILTITCPTFGDWAQLAPAVPGLQGALRLQLRLNPPAQLPNSEGLCEFLEYVAESLE
PPSPFELLEPPTSGGFLRLGRPCCYIFPGGLGDAAFFAVNGFTVLVNGGSNPKSSFWKLVRHLDRVDAVLVTHPGADSLPGLNSLLRRKL
AERSEVAAGGGSWDDRLRRLISPNLGVVFFNACEAASRLARGEDEAELALSLLAQLGITPLPLSRGPVPAKPTVLFEKMGVGRLDMYVLH
PPSAGAERTLASVCALLVWHPAGPGEKVVRVLFPGCTPPACLLDGLVRLQHLRFLREPVVTPQDLEGPGRAESKESVGSRDSSKREGLLA
THPRPGQERPGVARKEPARAEAPRKTEKEAKTPRELKKDPKPSVSRTQPREVRRAASSVPNLKKTNAQAAPKPRKAPSTSHSGFPPVANG
PRSPPSLRCGEASPPSAACGSPASQLVATPSLELGPIPAGEEKALELPLAASSIPRPRTPSPESHRSPAEGSERLSLSPLRGGEAGPDAS
PTVTTPTVTTPSLPAEVGSPHSTEVDESLSVSFEQVLPPSAPTSEAGLSLPLRGPRARRSASPHDVDLCLVSPCEFEHRKAVPMAPAPAS
PGSSNDSSARSQERAGGLGAEETPPTSVSESLPTLSDSDPVPLAPGAADSDEDTEGFGVPRHDPLPDPLKVPPPLPDPSSICMVDPEMLP
PKTARQTENVSRTRKPLARPNSRAAAPKATPVAAAKTKGLAGGDRASRPLSARSEPSEKGGRAPLSRKSSTPKTATRGPSGSASSRPGVS
ATPPKSPVYLDLAYLPSGSSAHLVDEEFFQRVRALCYVISGQDQRKEEGMRAVLDALLASKQHWDRDLQVTLIPTFDSVAMHTWYAETHA

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

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Fusion Gene PPI Analysis for NR2C2AP-MAP1S


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 NR2C2AP-MAP1S


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 NR2C2AP-MAP1S


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