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Center for Computational Systems Medicine level2
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:IFNGR2-NUDCD3

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: IFNGR2-NUDCD3
FusionPDB ID: 38393
FusionGDB2.0 ID: 38393
HgeneTgene
Gene symbol

IFNGR2

NUDCD3

Gene ID

3460

23386

Gene nameinterferon gamma receptor 2NudC domain containing 3
SynonymsAF-1|IFGR2|IFNGT1|IMD28NudCL
Cytomap

21q22.11

7p13

Type of geneprotein-codingprotein-coding
Descriptioninterferon gamma receptor 2IFN-gamma receptor 2IFN-gamma-R-betaIFN-gamma-R2interferon gamma receptor accessory factor-1interferon gamma receptor beta chaininterferon gamma transducer 1nudC domain-containing protein 3NudC-like protein
Modification date2020031320200313
UniProtAcc

P38484

.
Ensembl transtripts involved in fusion geneENST idsENST00000290219, ENST00000381995, 
ENST00000405436, 
ENST00000460110, 
ENST00000355451, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score4 X 5 X 3=6012 X 10 X 4=480
# samples 512
** MAII scorelog2(5/60*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(12/480*10)=-2
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: IFNGR2 [Title/Abstract] AND NUDCD3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)IFNGR2(34805178)-NUDCD3(44444182), # samples:4
NUDCD3(44465499)-IFNGR2(34809135), # samples:2
Anticipated loss of major functional domain due to fusion event.IFNGR2-NUDCD3 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.
IFNGR2-NUDCD3 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.
IFNGR2-NUDCD3 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.
IFNGR2-NUDCD3 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

check buttonFusion gene breakpoints across IFNGR2 (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 NUDCD3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4PAADTCGA-L1-A7W4-01AIFNGR2chr21

34805178

-NUDCD3chr7

44444182

-
ChimerDB4PAADTCGA-L1-A7W4-01AIFNGR2chr21

34805178

+NUDCD3chr7

44444182

-
ChimerDB4PAADTCGA-L1-A7W4IFNGR2chr21

34805178

+NUDCD3chr7

44444182

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000290219IFNGR2chr2134805178+ENST00000355451NUDCD3chr744444182-886115271681970600
ENST00000381995IFNGR2chr2134805178+ENST00000355451NUDCD3chr744444182-83821048311491486
ENST00000405436IFNGR2chr2134805178+ENST00000355451NUDCD3chr744444182-834310091571452431

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
ENST00000290219ENST00000355451IFNGR2chr2134805178+NUDCD3chr744444182-0.0013736340.99862635
ENST00000381995ENST00000355451IFNGR2chr2134805178+NUDCD3chr744444182-0.0029220770.99707794
ENST00000405436ENST00000355451IFNGR2chr2134805178+NUDCD3chr744444182-0.0033338890.99666613

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>38393_38393_1_IFNGR2-NUDCD3_IFNGR2_chr21_34805178_ENST00000290219_NUDCD3_chr7_44444182_ENST00000355451_length(amino acids)=600AA_BP=453
MCDQAPERRVGGGQEGWGLQGKPGGLGRGLAGPFRKDRGPRRWASRGAPVSRTFREAPRSGRPAAWGPRAAAAEAPQGRGSRSGKVPRGG
GGLGGGTGRGRGRGRPSRIPSTGTPRCCSGRGGPCAPCARHGGLGGDVSGSADPERGPGRDLSRRRAPGAMRPTLLWSLLLLLGVFAAAA
AAPPDPLSQLPAPQHPKIRLYNAEQVLSWEPVALSNSTRPVVYQVQFKYTDSKWFTADIMSIGVNCTQITATECDFTAASPSAGFPMDFN
VTLRLRAELGALHSAWVTMPWFQHYRNVTVGPPENIEVTPGEGSLIIRFSSPFDIADTSTAFFCYYVHYWEKGGIQQVKGPFRSNSISLD
NLKPSRVYCLQVQAQLLWNKSNIFRVGHLSNISCYETMADASTELQQVILISVGTFSLLSVLAGACFFLVLKYRGLIKYWFHTPPSIPLQ
IEEVSVALSSSSIRVAMLEENGERVLMEGKLTHKINTESSLWSLEPGKCVLVNLSKVGEYWWNAILEGEEPIDIDKINKERSMATVDEEE

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

>38393_38393_2_IFNGR2-NUDCD3_IFNGR2_chr21_34805178_ENST00000381995_NUDCD3_chr7_44444182_ENST00000355451_length(amino acids)=486AA_BP=339
MGGDVSGSADPERGPGRDLSRRRAPGAMRPTLLWSLLLLLGVFAAAAAAPPAQLTLETYQEWCNDSAATHDPLSQLPAPQHPKIRLYNAE
QVLSWEPVALSNSTRPVVYQVQFKYTDSKWFTADIMSIGVNCTQITATECDFTAASPSAGFPMDFNVTLRLRAELGALHSAWVTMPWFQH
YRNVTVGPPENIEVTPGEGSLIIRFSSPFDIADTSTAFFCYYVHYWEKGGIQQVKGPFRSNSISLDNLKPSRVYCLQVQAQLLWNKSNIF
RVGHLSNISCYETMADASTELQQVILISVGTFSLLSVLAGACFFLVLKYRGLIKYWFHTPPSIPLQIEEVSVALSSSSIRVAMLEENGER
VLMEGKLTHKINTESSLWSLEPGKCVLVNLSKVGEYWWNAILEGEEPIDIDKINKERSMATVDEEEQAVLDRLTFDYHQKLQGKPQSHEL

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

>38393_38393_3_IFNGR2-NUDCD3_IFNGR2_chr21_34805178_ENST00000405436_NUDCD3_chr7_44444182_ENST00000355451_length(amino acids)=431AA_BP=284
METYQEWCNDSAATHDPLSQLPAPQHPKIRLYNAEQVLSWEPVALSNSTRPVVYQVQFKYTDSKWFTADIMSIGVNCTQITATECDFTAA
SPSAGFPMDFNVTLRLRAELGALHSAWVTMPWFQHYRNVTVGPPENIEVTPGEGSLIIRFSSPFDIADTSTAFFCYYVHYWEKGGIQQVK
GPFRSNSISLDNLKPSRVYCLQVQAQLLWNKSNIFRVGHLSNISCYETMADASTELQQVILISVGTFSLLSVLAGACFFLVLKYRGLIKY
WFHTPPSIPLQIEEVSVALSSSSIRVAMLEENGERVLMEGKLTHKINTESSLWSLEPGKCVLVNLSKVGEYWWNAILEGEEPIDIDKINK

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

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Fusion Protein Functional Features


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/chr21:34805178/chr7:44444182)
- 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
IFNGR2

P38484

.
FUNCTION: Associates with IFNGR1 to form a receptor for the cytokine interferon gamma (IFNG) (PubMed:8124716, PubMed:7673114,PubMed:7615558). Ligand binding stimulates activation of the JAK/STAT signaling pathway (PubMed:8124716, PubMed:7673114, PubMed:15356148). Required for signal transduction in contrast to other receptor subunit responsible for ligand binding (PubMed:7673114). {ECO:0000269|PubMed:15356148, ECO:0000269|PubMed:7615558, ECO:0000269|PubMed:7673114, ECO:0000269|PubMed:8124716}.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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneIFNGR2chr21:34805178chr7:44444182ENST00000290219+67142_240293.0338.0DomainFibronectin type-III 2
HgeneIFNGR2chr21:34805178chr7:44444182ENST00000290219+6731_129293.0338.0DomainFibronectin type-III 1
HgeneIFNGR2chr21:34805178chr7:44444182ENST00000290219+6728_247293.0338.0Topological domainExtracellular
HgeneIFNGR2chr21:34805178chr7:44444182ENST00000290219+67248_268293.0338.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneIFNGR2chr21:34805178chr7:44444182ENST00000290219+67269_337293.0338.0Topological domainCytoplasmic
TgeneNUDCD3chr21:34805178chr7:44444182ENST0000035545126185_277214.0362.0DomainCS


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Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file >>>1270_IFNGR2_34805178_NUDCD3_44444182_1270_IFNGR2_34805178_NUDCD3_44444182_ranked_0.pdbIFNGR23480517834805178ENST00000355451NUDCD3chr744444182-
MCDQAPERRVGGGQEGWGLQGKPGGLGRGLAGPFRKDRGPRRWASRGAPVSRTFREAPRSGRPAAWGPRAAAAEAPQGRGSRSGKVPRGG
GGLGGGTGRGRGRGRPSRIPSTGTPRCCSGRGGPCAPCARHGGLGGDVSGSADPERGPGRDLSRRRAPGAMRPTLLWSLLLLLGVFAAAA
AAPPDPLSQLPAPQHPKIRLYNAEQVLSWEPVALSNSTRPVVYQVQFKYTDSKWFTADIMSIGVNCTQITATECDFTAASPSAGFPMDFN
VTLRLRAELGALHSAWVTMPWFQHYRNVTVGPPENIEVTPGEGSLIIRFSSPFDIADTSTAFFCYYVHYWEKGGIQQVKGPFRSNSISLD
NLKPSRVYCLQVQAQLLWNKSNIFRVGHLSNISCYETMADASTELQQVILISVGTFSLLSVLAGACFFLVLKYRGLIKYWFHTPPSIPLQ
IEEVSVALSSSSIRVAMLEENGERVLMEGKLTHKINTESSLWSLEPGKCVLVNLSKVGEYWWNAILEGEEPIDIDKINKERSMATVDEEE
600


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pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
IFNGR2_pLDDT.png
all structure
all structure
NUDCD3_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
all structure


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Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots

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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
IFNGR2
NUDCD3


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to IFNGR2-NUDCD3


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to IFNGR2-NUDCD3


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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