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Center for Computational Systems Medicine level1
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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-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:CIT-SPPL3

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CIT-SPPL3
FusionPDB ID: 16873
FusionGDB2.0 ID: 16873
HgeneTgene
Gene symbol

CIT

SPPL3

Gene ID

79947

121665

Gene namedehydrodolichyl diphosphate synthase subunitsignal peptide peptidase like 3
SynonymsCIT|CPT|DEDSM|DS|HDS|RP59|hCITIMP2|MDHV1887|PRO4332|PSH1|PSL4
Cytomap

1p36.11

12q24.31

Type of geneprotein-codingprotein-coding
Descriptiondehydrodolichyl diphosphate synthase complex subunit DHDDScis-IPTasecis-isoprenyltransferasecis-prenyl transferasecis-prenyltransferase subunit hCITdedol-PP synthasedehydrodolichyl diphosphate syntase complex subunit DHDDSepididymis tissue protein signal peptide peptidase-like 3SPP-like 3intramembrane protease 2presenilin homologous protein 1presenilin-like protein 4
Modification date2020031320200313
UniProtAcc

Q96RK1

.
Ensembl transtripts involved in fusion geneENST idsENST00000537607, ENST00000261833, 
ENST00000392521, 		ENST00000353487, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score9 X 9 X 6=48611 X 9 X 5=495
# samples 911
** MAII scorelog2(9/486*10)=-2.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/495*10)=-2.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: CIT [Title/Abstract] AND SPPL3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CIT(120189855)-SPPL3(121204175), # samples:1
Anticipated loss of major functional domain due to fusion event.CIT-SPPL3 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.
CIT-SPPL3 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.
CIT-SPPL3 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.
CIT-SPPL3 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
HgeneCIT

GO:0006489

dolichyl diphosphate biosynthetic process

28842490

TgeneSPPL3

GO:0033619

membrane protein proteolysis

2313285


check buttonFusion gene breakpoints across CIT (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 SPPL3 (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
ChimerDB4UCECTCGA-E6-A8L9-01ACITchr12

120189855

-SPPL3chr12

121204175

-


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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)
ENST00000392521CITchr12120189855-ENST00000353487SPPL3chr12121204175-563129602630671013
ENST00000261833CITchr12120189855-ENST00000353487SPPL3chr12121204175-55022831232938971

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
ENST00000392521ENST00000353487CITchr12120189855-SPPL3chr12121204175-0.0014919220.99850804
ENST00000261833ENST00000353487CITchr12120189855-SPPL3chr12121204175-0.0021845870.9978154

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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

>16873_16873_1_CIT-SPPL3_CIT_chr12_120189855_ENST00000261833_SPPL3_chr12_121204175_ENST00000353487_length(amino acids)=971AA_BP=936
MGVRRAASGEMLKFKYGARNPLDAGAAEPIASRASRLNLFFQGKPPFMTQQQMSPLSREGILDALFVLFEECSQPALMKIKHVSNFVRKY
SDTIAELQELQPSAKDFEVRSLVGCGHFAEVQVVREKATGDIYAMKVMKKKALLAQEQVSFFEEERNILSRSTSPWIPQLQYAFQDKNHL
YLVMEYQPGGDLLSLLNRYEDQLDENLIQFYLAELILAVHSVHLMGYVHRDIKPENILVDRTGHIKLVDFGSAAKMNSNKMVNAKLPIGT
PDYMAPEVLTVMNGDGKGTYGLDCDWWSVGVIAYEMIYGRSPFAEGTSARTFNNIMNFQRFLKFPDDPKVSSDFLDLIQSLLCGQKERLK
FEGLCCHPFFSKIDWNNIRNSPPPFVPTLKSDDDTSNFDEPEKNSWVSSSPCQLSPSGFSGEELPFVGFSYSKALGILGRSESVVSGLDS
PAKTSSMEKKLLIKSKELQDSQDKCHKMEQEMTRLHRRVSEVEAVLSQKEVELKASETQRSLLEQDLATYITECSSLKRSLEQARMEVSQ
EDDKALQLLHDIREQSRKLQEIKEQEYQAQVEEMRLMMNQLEEDLVSARRRSDLYESELRESRLAAEEFKRKATECQHKLLKAKDQGKPE
VGEYAKLEKINAEQQLKIQELQEKLEKAVKASTEATELLQNIRQAKERAERELEKLQNREDSSEGIRKKLVEAEELEEKHREAQVSAQHL
EVHLKQKEQHYEEKIKVLDNQIKKDLADKETLENMMQRHEEEAHEKGKILSEQKAMINAMDSKIRSLEQRIVELSEANKLAANSSLFTQR
NMKAQEEMISELRQQKFYLETQAGKLEAQNRKLEEQLEKISHQDHSDKNRLLELETRLREVSLEHEEQKLELKRQLTELQLSLQERESQL

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

>16873_16873_2_CIT-SPPL3_CIT_chr12_120189855_ENST00000392521_SPPL3_chr12_121204175_ENST00000353487_length(amino acids)=1013AA_BP=978
MGVRRAASGEMLKFKYGARNPLDAGAAEPIASRASRLNLFFQGKPPFMTQQQMSPLSREGILDALFVLFEECSQPALMKIKHVSNFVRKY
SDTIAELQELQPSAKDFEVRSLVGCGHFAEVQVVREKATGDIYAMKVMKKKALLAQEQVSFFEEERNILSRSTSPWIPQLQYAFQDKNHL
YLVMEYQPGGDLLSLLNRYEDQLDENLIQFYLAELILAVHSVHLMGYVHRDIKPENILVDRTGHIKLVDFGSAAKMNSNKMVNAKLPIGT
PDYMAPEVLTVMNGDGKGTYGLDCDWWSVGVIAYEMIYGRSPFAEGTSARTFNNIMNFQRFLKFPDDPKVSSDFLDLIQSLLCGQKERLK
FEGLCCHPFFSKIDWNNIRNSPPPFVPTLKSDDDTSNFDEPEKNSWVSSSPCQLSPSGFSGEELPFVGFSYSKALGILGRSESVVSGLDS
PAKTSSMEKKLLIKSKELQDSQDKCHKMEQEMTRLHRRVSEVEAVLSQKEVELKASETQRSLLEQDLATYITECSSLKRSLEQARMEVSQ
EDDKALQLLHDIREQSRKLQEIKEQEYQAQVEEMRLMMNQLEEDLVSARRRSDLYESELRESRLAAEEFKRKATECQHKLLKAKDQGKPE
VGEYAKLEKINAEQQLKIQELQEKLEKAVKASTEATELLQNIRQAKERAERELEKLQNREDSSEGIRKKLVEAEERRHSLENKVKRLETM
ERRENRLKDDIQTKSQQIQQMADKILELEEKHREAQVSAQHLEVHLKQKEQHYEEKIKVLDNQIKKDLADKETLENMMQRHEEEAHEKGK
ILSEQKAMINAMDSKIRSLEQRIVELSEANKLAANSSLFTQRNMKAQEEMISELRQQKFYLETQAGKLEAQNRKLEEQLEKISHQDHSDK
NRLLELETRLREVSLEHEEQKLELKRQLTELQLSLQERESQLTALQAARAALESQLRQAKTELEETTAEAEEEIQALTACSLLLWRLAFT

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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/chr12:120189855/chr12:121204175)
- 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
CIT

Q96RK1

.
FUNCTION: Acts as transcriptional coactivator for TFAP2/AP-2. Enhances estrogen-dependent transactivation mediated by estrogen receptors. May function as an inhibitor of transactivation by HIF1A by disrupting HIF1A interaction with CREBBP. May be involved in regulation of gene expression during development and differentiation of blood cells, endothelial cells and mammary epithelial cells. {ECO:0000269|PubMed:11744733, ECO:0000269|PubMed:15342390}.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
HgeneCITchr12:120189855chr12:121204175ENST00000261833-2247361_431926.02028.0DomainAGC-kinase C-terminal
HgeneCITchr12:120189855chr12:121204175ENST00000261833-224797_360926.02028.0DomainProtein kinase
HgeneCITchr12:120189855chr12:121204175ENST00000392521-2348361_431968.02070.0DomainAGC-kinase C-terminal
HgeneCITchr12:120189855chr12:121204175ENST00000392521-234897_360968.02070.0DomainProtein kinase
HgeneCITchr12:120189855chr12:121204175ENST00000261833-2247103_111926.02028.0Nucleotide bindingATP
HgeneCITchr12:120189855chr12:121204175ENST00000392521-2348103_111968.02070.0Nucleotide bindingATP
TgeneSPPL3chr12:120189855chr12:121204175ENST00000353487811374_379324.3333333333333385.0Compositional biasNote=Poly-Ser
TgeneSPPL3chr12:120189855chr12:121204175ENST00000353487811341_343324.3333333333333385.0MotifNote=PAL
TgeneSPPL3chr12:120189855chr12:121204175ENST00000353487811333_339324.3333333333333385.0Topological domainLumenal
TgeneSPPL3chr12:120189855chr12:121204175ENST00000353487811361_384324.3333333333333385.0Topological domainCytoplasmic
TgeneSPPL3chr12:120189855chr12:121204175ENST00000353487811340_360324.3333333333333385.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCITchr12:120189855chr12:121204175ENST00000261833-2247453_1297926.02028.0Coiled coilOntology_term=ECO:0000255
HgeneCITchr12:120189855chr12:121204175ENST00000392521-2348453_1297968.02070.0Coiled coilOntology_term=ECO:0000255
HgeneCITchr12:120189855chr12:121204175ENST00000261833-22471443_1563926.02028.0DomainPH
HgeneCITchr12:120189855chr12:121204175ENST00000261833-22471591_1881926.02028.0DomainCNH
HgeneCITchr12:120189855chr12:121204175ENST00000392521-23481443_1563968.02070.0DomainPH
HgeneCITchr12:120189855chr12:121204175ENST00000392521-23481591_1881968.02070.0DomainCNH
HgeneCITchr12:120189855chr12:121204175ENST00000261833-22471953_1958926.02028.0MotifSH3-binding
HgeneCITchr12:120189855chr12:121204175ENST00000392521-23481953_1958968.02070.0MotifSH3-binding
HgeneCITchr12:120189855chr12:121204175ENST00000261833-22471362_1411926.02028.0Zinc fingerPhorbol-ester/DAG-type
HgeneCITchr12:120189855chr12:121204175ENST00000392521-23481362_1411968.02070.0Zinc fingerPhorbol-ester/DAG-type
TgeneSPPL3chr12:120189855chr12:121204175ENST00000353487811119_136324.3333333333333385.0Topological domainCytoplasmic
TgeneSPPL3chr12:120189855chr12:121204175ENST00000353487811160_164324.3333333333333385.0Topological domainLumenal
TgeneSPPL3chr12:120189855chr12:121204175ENST00000353487811186_190324.3333333333333385.0Topological domainCytoplasmic
TgeneSPPL3chr12:120189855chr12:121204175ENST000003534878111_8324.3333333333333385.0Topological domainLumenal
TgeneSPPL3chr12:120189855chr12:121204175ENST00000353487811212_262324.3333333333333385.0Topological domainLumenal
TgeneSPPL3chr12:120189855chr12:121204175ENST00000353487811284_311324.3333333333333385.0Topological domainCytoplasmic
TgeneSPPL3chr12:120189855chr12:121204175ENST0000035348781130_74324.3333333333333385.0Topological domainCytoplasmic
TgeneSPPL3chr12:120189855chr12:121204175ENST0000035348781196_97324.3333333333333385.0Topological domainLumenal
TgeneSPPL3chr12:120189855chr12:121204175ENST00000353487811137_159324.3333333333333385.0TransmembraneHelical
TgeneSPPL3chr12:120189855chr12:121204175ENST00000353487811165_185324.3333333333333385.0TransmembraneHelical
TgeneSPPL3chr12:120189855chr12:121204175ENST00000353487811191_211324.3333333333333385.0TransmembraneHelical
TgeneSPPL3chr12:120189855chr12:121204175ENST00000353487811263_283324.3333333333333385.0TransmembraneHelical
TgeneSPPL3chr12:120189855chr12:121204175ENST00000353487811312_332324.3333333333333385.0TransmembraneHelical
TgeneSPPL3chr12:120189855chr12:121204175ENST0000035348781175_95324.3333333333333385.0TransmembraneHelical
TgeneSPPL3chr12:120189855chr12:121204175ENST0000035348781198_118324.3333333333333385.0TransmembraneHelical
TgeneSPPL3chr12:120189855chr12:121204175ENST000003534878119_29324.3333333333333385.0TransmembraneHelical


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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
CIT
SPPL3


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
HgeneCITchr12:120189855chr12:121204175ENST00000261833-22471091_1302926.02028.0Rho/Rac
HgeneCITchr12:120189855chr12:121204175ENST00000392521-23481091_1302968.02070.0Rho/Rac


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Related Drugs to CIT-SPPL3


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 CIT-SPPL3


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