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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:HMGN2-NECAB3 (FusionGDB2 ID:HG3151TG63941)

Fusion Gene Summary for HMGN2-NECAB3

check button Fusion gene summary
Fusion gene informationFusion gene name: HMGN2-NECAB3
Fusion gene ID: hg3151tg63941
HgeneTgene
Gene symbol

HMGN2

NECAB3

Gene ID

3151

63941

Gene namehigh mobility group nucleosomal binding domain 2N-terminal EF-hand calcium binding protein 3
SynonymsHMG17APBA2BP|EFCBP3|NIP1|STIP3|SYTIP2|XB51|dJ63M2.4|dJ63M2.5
Cytomap('HMGN2')('NECAB3')

1p36.11

20q11.22

Type of geneprotein-codingprotein-coding
Descriptionnon-histone chromosomal protein HMG-17high mobility group nucleosome-binding domain-containing protein 2high mobility group protein N2high-mobility group (nonhistone chromosomal) protein 17nonhistone chromosomal protein HMG-17N-terminal EF-hand calcium-binding protein 3EF-hand calcium binding protein 3Nek2-interacting protein 1X11L-binding protein 51amyloid beta (A4) precursor protein-binding, family A, member 2 binding proteinamyloid beta A4 protein-binding family A memb
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000361427, ENST00000493418, 
Fusion gene scores* DoF score9 X 4 X 4=1447 X 4 X 4=112
# samples 87
** MAII scorelog2(8/144*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(7/112*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HMGN2 [Title/Abstract] AND NECAB3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHMGN2(26799118)-NECAB3(32248201), # samples:1
Anticipated loss of major functional domain due to fusion event.HMGN2-NECAB3 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.
HMGN2-NECAB3 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.
HMGN2-NECAB3 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.
HMGN2-NECAB3 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
TgeneNECAB3

GO:0019538

protein metabolic process

12780348

TgeneNECAB3

GO:0042984

regulation of amyloid precursor protein biosynthetic process

10833507


check buttonFusion gene breakpoints across HMGN2 (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 NECAB3 (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
ChimerDB4Non-CancerERR315404HMGN2chr1

26799118

+NECAB3chr20

32248201

-


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Fusion Gene ORF analysis for HMGN2-NECAB3

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-5UTRENST00000361427ENST00000606525HMGN2chr1

26799118

+NECAB3chr20

32248201

-
In-frameENST00000361427ENST00000246190HMGN2chr1

26799118

+NECAB3chr20

32248201

-
In-frameENST00000361427ENST00000375238HMGN2chr1

26799118

+NECAB3chr20

32248201

-
intron-3CDSENST00000493418ENST00000246190HMGN2chr1

26799118

+NECAB3chr20

32248201

-
intron-3CDSENST00000493418ENST00000375238HMGN2chr1

26799118

+NECAB3chr20

32248201

-
intron-5UTRENST00000493418ENST00000606525HMGN2chr1

26799118

+NECAB3chr20

32248201

-

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)
ENST00000361427HMGN2chr126799118+ENST00000246190NECAB3chr2032248201-165510994912272
ENST00000361427HMGN2chr126799118+ENST00000375238NECAB3chr2032248201-155310994810238

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
ENST00000361427ENST00000246190HMGN2chr126799118+NECAB3chr2032248201-0.257947980.742052
ENST00000361427ENST00000375238HMGN2chr126799118+NECAB3chr2032248201-0.070796370.9292036

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Fusion Genomic Features for HMGN2-NECAB3


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

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Fusion Protein Features for HMGN2-NECAB3


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/chr1:26799118/chr20:32248201)
- 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
..
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}.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
TgeneNECAB3chr1:26799118chr20:32248201ENST00000246190412296_385129397.0DomainNote=ABM
TgeneNECAB3chr1:26799118chr20:32248201ENST00000375238413296_385129363.0DomainNote=ABM

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneNECAB3chr1:26799118chr20:32248201ENST0000024619041249_60129397.0Calcium bindingOntology_term=ECO:0000255
TgeneNECAB3chr1:26799118chr20:32248201ENST0000037523841349_60129363.0Calcium bindingOntology_term=ECO:0000255
TgeneNECAB3chr1:26799118chr20:32248201ENST0000024619041236_71129397.0DomainEF-hand
TgeneNECAB3chr1:26799118chr20:32248201ENST0000037523841336_71129363.0DomainEF-hand


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Fusion Gene Sequence for HMGN2-NECAB3


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.
>36938_36938_1_HMGN2-NECAB3_HMGN2_chr1_26799118_ENST00000361427_NECAB3_chr20_32248201_ENST00000246190_length(transcript)=1655nt_BP=109nt
AAGAGGCGAGAACGACCCCCGGACCGACCAAAGCCCGCGCGCCGCTGCATCCCGCGTCCAGCACCTACGTCCCGCTGCCGTCGCCGCCGC
CACCATGCCCAAGAGAAAGGAGTACGAGAGGGCCTCCAAAGTGGACCAGTTTGTGACGCGCTTCCTGCTGCGGGAGACGGTGAGCCAGCT
GCAAGCCCTTCAGAGCTCGCTGGAGGGGGCGTCAGATACCCTGGAGGCCCAGGCCCATGGCTGGCGGTCAGATGCAGAGAGCGTGGAGGC
GCAGAGCAGGCTCTGCGGCAGCCGGCGGGCAGGACGCCGAGCCCTGAGGAGTGTCAGCCGGTCATCCACCTGGTCCCCCGGCTCTTCTGA
CACAGGGCGCAGCTCAGAGGCCGAGATGCAGTGGCGGCTCCAGGTGAACCGCCTCCAGGAGCTCATCGACCAGCTCGAGTGCAAGGTGAG
GGCCGTGGGGCCAGGGCCCCACAAGGGAGGACCCTCCTGGTATCCACCAGAGCCAGGCCCATGCTGGAGGCCCGGCCCACACTCTGTGCC
CTCACAGGCCCCCCGGCTGGAACCCCTGCGTGAAGAGGACCTGGCCAAGGGGCCTGACTTGCACATCCTCATGGCCCAGAGGCAGGTCCA
GGTGGCAGAGGAAGGCCTGCAGGACTTCCACCGAGCCCTGCGCTGCTATGTGGACTTCACAGGGGCCCAGAGCCATTGTCTGCATGTGTC
CGCCCAGAAGATGCTGGACGGTGCCTCCTTCACCCTGTATGAGTTCTGGCAGGATGAGGCCTCCTGGAGAAGGCACCAGCAGTCGCCTGG
CAGCAAGGCCTTCCAGCGCATCCTCATCGACCACCTGCGGGCCCCGGACACCCTCACCACTGTGTTCTTCCCAGCCTCCTGGTGGATAAT
GAATAACAACTGAGCCAGACCTGCACACGCCGAGGGCCCCGGGACCCTGCCTGCCTCCCTCTGGAGCCTTCTGGACTGGCCAGCCCAGCG
CAAAGACCAGGACTTGTCTCCTCCTGGACTTGGGCCTGGTGGAAGGGCTCTCAGCCCAGGGATCAGGGACTGGGCTGCTTGCTTTCTATT
TATTATTGATTTATTTATCCCTGTATTTTATTGTTTGTCACTTCAGCCTCCAAGCTACTTTGGCTTCTGCCTGGCTCAGGAGACCTGGAT
TCTGGTCCCTGCTGTCCCTGCCTGGCTGAGCGACCCAGGGCAGGTCCCGTCCCTGTCTGGGTGGGCCTCAGGCCATCTGGCCGCCTAGCG
AGGGTCCTGCTTTCTTCCTGCTGTCTTGGGACCAGGCTTCTGCTCCTCCTCAGCCAGCGGCAGAAGCAGGGCTGATGCTCAGGGACCCCC
CAACCCTCAAACCTTGCCTCCGAGGCTGGGCCTGAGCTGGGTGCCCCGTCGCCCTCCCAGGCCACTAGGCTCTGACTCTTCCAGCACCCA
TGGATGTGCCAGAGGCCTCTGGGTTGGTTTGCATGTCATTTGCATATCGTTTGCATGCCCTCATCCCACCCATTCTCAGGGCAGTATGGG
AAGCCCCAAGGTGACCTGGCCAAGTAGCAATAATTTGGGTCCAGGGTCACCTATTGCCCCCAGAGGCCTCTGAACCCCAGGCTGGGACCC

>36938_36938_1_HMGN2-NECAB3_HMGN2_chr1_26799118_ENST00000361427_NECAB3_chr20_32248201_ENST00000246190_length(amino acids)=272AA_BP=5
MPKRKEYERASKVDQFVTRFLLRETVSQLQALQSSLEGASDTLEAQAHGWRSDAESVEAQSRLCGSRRAGRRALRSVSRSSTWSPGSSDT
GRSSEAEMQWRLQVNRLQELIDQLECKVRAVGPGPHKGGPSWYPPEPGPCWRPGPHSVPSQAPRLEPLREEDLAKGPDLHILMAQRQVQV
AEEGLQDFHRALRCYVDFTGAQSHCLHVSAQKMLDGASFTLYEFWQDEASWRRHQQSPGSKAFQRILIDHLRAPDTLTTVFFPASWWIMN

--------------------------------------------------------------
>36938_36938_2_HMGN2-NECAB3_HMGN2_chr1_26799118_ENST00000361427_NECAB3_chr20_32248201_ENST00000375238_length(transcript)=1553nt_BP=109nt
AAGAGGCGAGAACGACCCCCGGACCGACCAAAGCCCGCGCGCCGCTGCATCCCGCGTCCAGCACCTACGTCCCGCTGCCGTCGCCGCCGC
CACCATGCCCAAGAGAAAGGAGTACGAGAGGGCCTCCAAAGTGGACCAGTTTGTGACGCGCTTCCTGCTGCGGGAGACGGTGAGCCAGCT
GCAAGCCCTTCAGAGCTCGCTGGAGGGGGCGTCAGATACCCTGGAGGCCCAGGCCCATGGCTGGCGGTCAGATGCAGAGAGCGTGGAGGC
GCAGAGCAGGCTCTGCGGCAGCCGGCGGGCAGGACGCCGAGCCCTGAGGAGTGTCAGCCGGTCATCCACCTGGTCCCCCGGCTCTTCTGA
CACAGGGCGCAGCTCAGAGGCCGAGATGCAGTGGCGGCTCCAGGTGAACCGCCTCCAGGAGCTCATCGACCAGCTCGAGTGCAAGGCCCC
CCGGCTGGAACCCCTGCGTGAAGAGGACCTGGCCAAGGGGCCTGACTTGCACATCCTCATGGCCCAGAGGCAGGTCCAGGTGGCAGAGGA
AGGCCTGCAGGACTTCCACCGAGCCCTGCGCTGCTATGTGGACTTCACAGGGGCCCAGAGCCATTGTCTGCATGTGTCCGCCCAGAAGAT
GCTGGACGGTGCCTCCTTCACCCTGTATGAGTTCTGGCAGGATGAGGCCTCCTGGAGAAGGCACCAGCAGTCGCCTGGCAGCAAGGCCTT
CCAGCGCATCCTCATCGACCACCTGCGGGCCCCGGACACCCTCACCACTGTGTTCTTCCCAGCCTCCTGGTGGATAATGAATAACAACTG
AGCCAGACCTGCACACGCCGAGGGCCCCGGGACCCTGCCTGCCTCCCTCTGGAGCCTTCTGGACTGGCCAGCCCAGCGCAAAGACCAGGA
CTTGTCTCCTCCTGGACTTGGGCCTGGTGGAAGGGCTCTCAGCCCAGGGATCAGGGACTGGGCTGCTTGCTTTCTATTTATTATTGATTT
ATTTATCCCTGTATTTTATTGTTTGTCACTTCAGCCTCCAAGCTACTTTGGCTTCTGCCTGGCTCAGGAGACCTGGATTCTGGTCCCTGC
TGTCCCTGCCTGGCTGAGCGACCCAGGGCAGGTCCCGTCCCTGTCTGGGTGGGCCTCAGGCCATCTGGCCGCCTAGCGAGGGTCCTGCTT
TCTTCCTGCTGTCTTGGGACCAGGCTTCTGCTCCTCCTCAGCCAGCGGCAGAAGCAGGGCTGATGCTCAGGGACCCCCCAACCCTCAAAC
CTTGCCTCCGAGGCTGGGCCTGAGCTGGGTGCCCCGTCGCCCTCCCAGGCCACTAGGCTCTGACTCTTCCAGCACCCATGGATGTGCCAG
AGGCCTCTGGGTTGGTTTGCATGTCATTTGCATATCGTTTGCATGCCCTCATCCCACCCATTCTCAGGGCAGTATGGGAAGCCCCAAGGT
GACCTGGCCAAGTAGCAATAATTTGGGTCCAGGGTCACCTATTGCCCCCAGAGGCCTCTGAACCCCAGGCTGGGACCCCAGCACAGAGGC

>36938_36938_2_HMGN2-NECAB3_HMGN2_chr1_26799118_ENST00000361427_NECAB3_chr20_32248201_ENST00000375238_length(amino acids)=238AA_BP=5
MPKRKEYERASKVDQFVTRFLLRETVSQLQALQSSLEGASDTLEAQAHGWRSDAESVEAQSRLCGSRRAGRRALRSVSRSSTWSPGSSDT
GRSSEAEMQWRLQVNRLQELIDQLECKAPRLEPLREEDLAKGPDLHILMAQRQVQVAEEGLQDFHRALRCYVDFTGAQSHCLHVSAQKML

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

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Fusion Gene PPI Analysis for HMGN2-NECAB3


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 HMGN2-NECAB3


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 HMGN2-NECAB3


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