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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 35824

FusionGeneSummary for SPSB3_IFT140

check button Fusion gene summary
Fusion gene informationFusion gene name: SPSB3_IFT140
Fusion gene ID: 35824
HgeneTgene
Gene symbol

SPSB3

IFT140

Gene ID

90864

9742

Gene namesplA/ryanodine receptor domain and SOCS box containing 3intraflagellar transport 140
SynonymsC16orf31|SSB3MZSDS|RP80|SRTD9|WDTC2|c305C8.4|c380F5.1|gs114
Cytomap

16p13.3

16p13.3

Type of geneprotein-codingprotein-coding
DescriptionSPRY domain-containing SOCS box protein 3SPRY domain-containing SOCS box protein SSB-3intraflagellar transport protein 140 homologWD and tetratricopeptide repeats protein 2intraflagellar transport 140 homolog
Modification date2018052320180527
UniProtAcc

Q6PJ21

Q96RY7

Ensembl transtripts involved in fusion geneENST00000566339, ENST00000301717, 
ENST00000361339, ENST00000426508, 
ENST00000439987, 
Fusion gene scores* DoF score3 X 2 X 3=188 X 9 X 7=504
# samples 311
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(11/504*10)=-2.19592020997526
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SPSB3 [Title/Abstract] AND IFT140 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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 button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGALDBLCATCGA-UY-A9PD-01ASPSB3chr16

1831359

-IFT140chr16

1561151

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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
Frame-shiftENST00000566339ENST00000361339SPSB3chr16

1831359

-IFT140chr16

1561151

-
In-frameENST00000566339ENST00000426508SPSB3chr16

1831359

-IFT140chr16

1561151

-
5CDS-intronENST00000566339ENST00000439987SPSB3chr16

1831359

-IFT140chr16

1561151

-
In-frameENST00000301717ENST00000361339SPSB3chr16

1831359

-IFT140chr16

1561151

-
Frame-shiftENST00000301717ENST00000426508SPSB3chr16

1831359

-IFT140chr16

1561151

-
5CDS-intronENST00000301717ENST00000439987SPSB3chr16

1831359

-IFT140chr16

1561151

-

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FusionProtFeatures for SPSB3_IFT140


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SPSB3

Q6PJ21

IFT140

Q96RY7

May be a substrate recognition component of a SCF-likeECS (Elongin BC-CUL2/5-SOCS-box protein) E3 ubiquitin-proteinligase complex which mediates the ubiquitination and subsequentproteasomal degradation of target proteins. {ECO:0000250}. Component of the IFT complex A (IFT-A), a complexrequired for retrograde ciliary transport. Plays a pivotal role inproper development and function of ciliated cells. Involved inciliogenesis and cilia maintenance (PubMed:22503633). May play arole in ciliary assembly. Required for the development andmaintenance of the outer segments of rod and cone photoreceptorcells. Plays a role in maintenance and the delivery of opsin tothe outer segment of photoreceptor cells (By similarity).{ECO:0000250|UniProtKB:E9PY46, ECO:0000269|PubMed:22503633}.

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

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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FusionGeneSequence for SPSB3_IFT140


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.
>In-frame_SPSB3_ENST00000566339_chr16_1831359_-_IFT140_ENST00000426508_chr16_1561151_-_111aa
MARRPRNSRAWHFVLSAARRDADARAVALAGSTNWGYDSDGQAYRFLEEMRRRLPLANMSYYVSPQAVDAVHRGLGLPLPRTVPEQVRHN

>In-frame_SPSB3_ENST00000301717_chr16_1831359_-_IFT140_ENST00000361339_chr16_1561151_-_111aa
MARRPRNSRAWHFVLSAARRDADARAVALAGSTNWGYDSDGQAYRFLEEMRRRLPLANMSYYVSPQAVDAVHRGLGLPLPRTVPEQVRHN


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_SPSB3_ENST00000566339_chr16_1831359_-_IFT140_ENST00000426508_chr16_1561151_-_333nt
ATGGCCAGACGCCCCCGGAACAGCAGGGCCTGGCACTTCGTCCTGAGTGCAGCCCGCCGAGACGCAGATGCCCGGGCCGTGGCTCTAGCA
GGCTCCACTAACTGGGGCTACGACTCTGATGGGCAGGCCTACAGATTCCTGGAGGAGATGCGGCGGCGGCTTCCCTTGGCCAACATGTCC
TACTACGTGAGCCCGCAGGCCGTGGACGCCGTGCACCGGGGGCTGGGTCTCCCACTGCCACGCACCGTCCCCGAGCAGGTCCGCCACAAC

>In-frame_SPSB3_ENST00000301717_chr16_1831359_-_IFT140_ENST00000361339_chr16_1561151_-_333nt
ATGGCCAGACGCCCCCGGAACAGCAGGGCCTGGCACTTCGTCCTGAGTGCAGCCCGCCGAGACGCAGATGCCCGGGCCGTGGCTCTAGCA
GGCTCCACTAACTGGGGCTACGACTCTGATGGGCAGGCCTACAGATTCCTGGAGGAGATGCGGCGGCGGCTTCCCTTGGCCAACATGTCC
TACTACGTGAGCCCGCAGGCCGTGGACGCCGTGCACCGGGGGCTGGGTCTCCCACTGCCACGCACCGTCCCCGAGCAGGTCCGCCACAAC


* Fusion transcript sequences (Full-length transcript).
>In-frame_SPSB3_ENST00000566339_chr16_1831359_-_IFT140_ENST00000426508_chr16_1561151_-_1181nt
GATGACACGGACCTACTTTCCGGTCAACGCGGCCTGCGGTACCACCTCCCACCCGGGTCCAATGTGCGCGCGAGCTTTGTCTCCAACCGC
TTGGGAACTGACCAATAGGAACGTTGGATTAGGACTGACAGTTCCTGAAACCTCTCGGCAATAGCTTTGTCACCCGACTCCCGCCCCCTC
TCCCGAAGCTCCGAGACAGGTGTGCCCGCCCCTCGCCGCCGGAGCCAATGGGCGCAGGGGGCGGGGATTGTTTACGTCTCGCTCCGGGGC
GGAAAGTGGGTCAGGGCCGGGCCGGCGGAGCGCGCAGCGGGGGCTGCAGATTCTTTCCACCATGGCCAGACGCCCCCGGAACAGCAGGGC
CTGGCACTTCGTCCTGAGTGCAGCCCGCCGAGACGCAGATGCCCGGGCCGTGGCTCTAGCAGGCTCCACTAACTGGGGCTACGACTCTGA
TGGGCAGGCCTACAGATTCCTGGAGGAGATGCGGCGGCGGCTTCCCTTGGCCAACATGTCCTACTACGTGAGCCCGCAGGCCGTGGACGC
CGTGCACCGGGGGCTGGGTCTCCCACTGCCACGCACCGTCCCCGAGCAGGTCCGCCACAACAGCATGGAGGACGCCAGGGAGCTGGACGA
GGAGGTGGTGGAAGAGGCAGATGACGACCCCTGAGGGGCCTGGGCCCCAGGACCAGCGTGCTGCTGCAGAAAGGCATCTTCTGGAATTTT
TTTGTCAGCTGTGGCAAAGCCAGCATTTTTGCTGGGAAAAAACATGTCTGTGTTGGAATACGCGACAGAGCTGGGCGAGAACGCAGCGGC
CCGGGCCGGCGGAGGGTGTGACCCGTCTGCACCTTGCTCTGTCCCACCTGCCTCTGGGTGCCCGGCAGCTCCACTAGATTTTTGGATTCA
TTCCTTTGAAGGGAGTCGGGTTCACCCTTCCATCGTATTCTCCCAACTACACATTGTAAAGCCTGAGAAACTTCTAGAACCTCAGGAAGC
TGCAGCTGGAGGGCTGGGGCACCTGCCCCCCTGCTCCCCACACATCATATCCTCCCCATACTCCTGCAGGGCCCACGGCTCCTGAGCAAC
AGCTGGGACACCCGGGCCTTGGCGGCTGCACCCCCTGCTAGGCTCTGCCCACCGGCCACCAACACTCCTGTAATTCCAATAAAGCAGTTT

>In-frame_SPSB3_ENST00000301717_chr16_1831359_-_IFT140_ENST00000361339_chr16_1561151_-_883nt
AGAGCCTGTGTTTTCTTCTAGATTCTTTCCACCATGGCCAGACGCCCCCGGAACAGCAGGGCCTGGCACTTCGTCCTGAGTGCAGCCCGC
CGAGACGCAGATGCCCGGGCCGTGGCTCTAGCAGGCTCCACTAACTGGGGCTACGACTCTGATGGGCAGGCCTACAGATTCCTGGAGGAG
ATGCGGCGGCGGCTTCCCTTGGCCAACATGTCCTACTACGTGAGCCCGCAGGCCGTGGACGCCGTGCACCGGGGGCTGGGTCTCCCACTG
CCACGCACCGTCCCCGAGCAGGTCCGCCACAACAGCATGGAGGACGCCAGGGAGCTGGACGAGGAGGTGGTGGAAGAGGCAGATGACGAC
CCCTGAGGGGCCTGGGCCCCAGGACCAGCGTGCTGCTGCAGAAAGGCATCTTCTGGAATTTTTTTGTCAGCTGTGGCAAAGCCAGCATTT
TTGCTGGGAAAAAACATGTCTGTGTTGGAATACGCGACAGAGCTGGGCGAGAACGCAGCGGCCCGGGCCGGCGGAGGGTGTGACCCGTCT
GCACCTTGCTCTGTCCCACCTGCCTCTGGGTGCCCGGCAGCTCCACTAGATTTTTGGATTCATTCCTTTGAAGGGAGTCGGGTTCACCCT
TCCATCGTATTCTCCCAACTACACATTGTAAAGCCTGAGAAACTTCTAGAACCTCAGGAAGCTGCAGCTGGAGGGCTGGGGCACCTGCCC
CCCTGCTCCCCACACATCATATCCTCCCCATACTCCTGCAGGGCCCACGGCTCCTGAGCAACAGCTGGGACACCCGGGCCTTGGCGGCTG


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FusionGenePPI for SPSB3_IFT140


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
SPSB3TCEB1, MET, CUL5, HSP90AA1, CSNK2B, NUMBL, ENKD1, MOV10, KLK11, CDK13, MAPK8IP2, UXS1, SMYD1, LYPD1, RPGR, PODN, GNPTG, DOCK5, TRIM25IFT140RANBP2, NEK2, PFDN1, C11orf74, IFT122, FBXW11, CRK, IFT43, TULP3, TULP2, FEZ1, CRYL1, DNAJC7, WDR19, WDR35, PISD, TTC21B, NIPSNAP1, NTPCR, ACSL3


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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RelatedDrugs for SPSB3_IFT140


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for SPSB3_IFT140


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneIFT140C1849437Mainzer-Saldino Disease2ORPHANET;UNIPROT