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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:KIF13B-IFT52 (FusionGDB2 ID:42553)

Fusion Gene Summary for KIF13B-IFT52

check button Fusion gene summary
Fusion gene informationFusion gene name: KIF13B-IFT52
Fusion gene ID: 42553
HgeneTgene
Gene symbol

KIF13B

IFT52

Gene ID

23303

51098

Gene namekinesin family member 13Bintraflagellar transport 52
SynonymsGAKINC20orf9|CGI-53|NGD2|NGD5
Cytomap

8p12

20q13.12

Type of geneprotein-codingprotein-coding
Descriptionkinesin-like protein KIF13Bguanylate kinase associated kinesinkinesin 13Bkinesin-like protein GAKINintraflagellar transport protein 52 homologprotein NGD5 homolog
Modification date2020031320200315
UniProtAcc

Q9NQT8

Q9Y366

Ensembl transtripts involved in fusion geneENST00000521515, ENST00000524189, 
ENST00000404075, 
ENST00000471199, 
ENST00000373030, ENST00000373039, 
Fusion gene scores* DoF score23 X 22 X 14=70847 X 7 X 6=294
# samples 277
** MAII scorelog2(27/7084*10)=-4.71353289970108
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(7/294*10)=-2.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: KIF13B [Title/Abstract] AND IFT52 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKIF13B(29120497)-IFT52(42247580), # samples:1
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
HgeneKIF13B

GO:0050770

regulation of axonogenesis

20194617


check buttonFusion gene breakpoints across KIF13B (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 IFT52 (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
ChimerDB4STADTCGA-KB-A93H-01AKIF13Bchr8

29120497

-IFT52chr20

42247580

+


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Fusion Gene ORF analysis for KIF13B-IFT52

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-intronENST00000521515ENST00000471199KIF13Bchr8

29120497

-IFT52chr20

42247580

+
5CDS-intronENST00000524189ENST00000471199KIF13Bchr8

29120497

-IFT52chr20

42247580

+
In-frameENST00000521515ENST00000373030KIF13Bchr8

29120497

-IFT52chr20

42247580

+
In-frameENST00000521515ENST00000373039KIF13Bchr8

29120497

-IFT52chr20

42247580

+
In-frameENST00000524189ENST00000373030KIF13Bchr8

29120497

-IFT52chr20

42247580

+
In-frameENST00000524189ENST00000373039KIF13Bchr8

29120497

-IFT52chr20

42247580

+
intron-3CDSENST00000404075ENST00000373030KIF13Bchr8

29120497

-IFT52chr20

42247580

+
intron-3CDSENST00000404075ENST00000373039KIF13Bchr8

29120497

-IFT52chr20

42247580

+
intron-intronENST00000404075ENST00000471199KIF13Bchr8

29120497

-IFT52chr20

42247580

+

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)
ENST00000524189KIF13Bchr829120497-ENST00000373030IFT52chr2042247580+110994109795228
ENST00000524189KIF13Bchr829120497-ENST00000373039IFT52chr2042247580+103594109795228
ENST00000521515KIF13Bchr829120497-ENST00000373030IFT52chr2042247580+1133118133819228
ENST00000521515KIF13Bchr829120497-ENST00000373039IFT52chr2042247580+1059118133819228

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
ENST00000524189ENST00000373030KIF13Bchr829120497-IFT52chr2042247580+0.0005560780.99944395
ENST00000524189ENST00000373039KIF13Bchr829120497-IFT52chr2042247580+0.0006530860.9993469
ENST00000521515ENST00000373030KIF13Bchr829120497-IFT52chr2042247580+0.0005628820.99943715
ENST00000521515ENST00000373039KIF13Bchr829120497-IFT52chr2042247580+0.0006856160.9993144

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Fusion Genomic Features for KIF13B-IFT52


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)
KIF13Bchr829120496-IFT52chr2042247579+8.59E-070.99999917
KIF13Bchr829120496-IFT52chr2042247579+8.59E-070.99999917

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 KIF13B-IFT52


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/chr8:29120497/chr20:42247580)
- 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
KIF13B

Q9NQT8

IFT52

Q9Y366

FUNCTION: Involved in reorganization of the cortical cytoskeleton. Regulates axon formation by promoting the formation of extra axons. May be functionally important for the intracellular trafficking of MAGUKs and associated protein complexes. {ECO:0000269|PubMed:20194617}.FUNCTION: Involved in ciliogenesis as part of a complex involved in intraflagellar transport (IFT), the bi-directional movement of particles required for the assembly, maintenance and functioning of primary cilia (PubMed:27466190). Required for the anterograde transport of IFT88 (PubMed:27466190). {ECO:0000269|PubMed:27466190}.

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
TgeneIFT52chr8:29120497chr20:42247580ENST00000373030614348_351204438.0Compositional biasNote=Poly-Pro
TgeneIFT52chr8:29120497chr20:42247580ENST00000373039614348_351204438.0Compositional biasNote=Poly-Pro

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneKIF13Bchr8:29120497chr20:42247580ENST00000524189-1401096_1143181827.0Coiled coilOntology_term=ECO:0000255
HgeneKIF13Bchr8:29120497chr20:42247580ENST00000524189-140364_439181827.0Coiled coilOntology_term=ECO:0000255
HgeneKIF13Bchr8:29120497chr20:42247580ENST00000524189-140607_710181827.0Coiled coilOntology_term=ECO:0000255
HgeneKIF13Bchr8:29120497chr20:42247580ENST00000524189-140752_772181827.0Coiled coilOntology_term=ECO:0000255
HgeneKIF13Bchr8:29120497chr20:42247580ENST00000524189-1401721_1763181827.0DomainCAP-Gly
HgeneKIF13Bchr8:29120497chr20:42247580ENST00000524189-140471_535181827.0DomainNote=FHA
HgeneKIF13Bchr8:29120497chr20:42247580ENST00000524189-1405_353181827.0DomainKinesin motor
HgeneKIF13Bchr8:29120497chr20:42247580ENST00000524189-140103_110181827.0Nucleotide bindingATP


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Fusion Gene Sequence for KIF13B-IFT52


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.
>42553_42553_1_KIF13B-IFT52_KIF13B_chr8_29120497_ENST00000521515_IFT52_chr20_42247580_ENST00000373030_length(transcript)=1133nt_BP=118nt
CCCCGAAGAGTCGCCGGTGGCCGCGGCAGACGGAAGCCGAACGAGTTCCTCGGCGGCTGCAGGATGGGGGACTCCAAAGTGAAAGTGGCG
GTGCGGATACGACCCATGAACCGGCGAGAACCAAGGTGGGAAGCTGGCAGTGCTTGGTTCATGTCACATGTTCAGTGATCAATATTTGGA
CAAAGAAGAAAACAGCAAAATCATGGATGTTGTTTTCCAGTGGCTCACGACAGGAGACATCCACCTAAACCAGATTGATGCTGAGGACCC
AGAGATTTCTGACTACATGATGCTGCCCTACACAGCCACCCTATCAAAGCGGAATCGAGAGTGTCTCCAGGAGAGTGATGAGATCCCAAG
GGACTTTACCACCCTCTTCGACCTGTCCATCTTCCAGCTGGATACCACCTCCTTCCACAGCGTCATCGAGGCTCACGAGCAGCTAAATGT
GAAACATGAACCACTCCAGCTCATCCAGCCTCAGTTTGAGACGCCGCTGCCAACCCTTCAGCCTGCGGTTTTTCCTCCCAGTTTCCGGGA
GTTACCACCTCCTCCTCTGGAGCTATTTGATTTAGATGAAACGTTCTCCTCTGAGAAGGCACGGCTGGCTCAGATTACCAATAAGTGTAC
TGAAGAAGACCTGGAATTTTATGTCAGGAAGTGTGGTGATATTCTTGGAGTAACCAGTAAACTACCAAAGGACCAACAGGATGCCAAACA
TATCCTTGAGCACGTCTTCTTCCAAGTGGTGGAGTTCAAGAAATTGAACCAGGAACATGACATCGATACAAGTGAAACAGCATTCCAGAA
CAATTTCTGAAGACCATGCCTCTTGAAGCTTTTTCTGCCTCCTGATTCTCTCTTTGTAAACTATTTTCAAATTGTTTTTCAACTCCTTAT
CAAAATTGTTTATACACTCTTTCCTCCATGAGCTCTGGAAGGTATATGCATCTTCTGTAATACTCAGATAGGTATAAGATTTTTCACAAA
ATCCTTATGTAAGATACATTCCATTTTTAAAAATTAAATGTATGGTTGCATCTGTCTTTTTATACCCTATGAAACAGTCTTGATTTTTTT

>42553_42553_1_KIF13B-IFT52_KIF13B_chr8_29120497_ENST00000521515_IFT52_chr20_42247580_ENST00000373030_length(amino acids)=228AA_BP=
MAVLGSCHMFSDQYLDKEENSKIMDVVFQWLTTGDIHLNQIDAEDPEISDYMMLPYTATLSKRNRECLQESDEIPRDFTTLFDLSIFQLD
TTSFHSVIEAHEQLNVKHEPLQLIQPQFETPLPTLQPAVFPPSFRELPPPPLELFDLDETFSSEKARLAQITNKCTEEDLEFYVRKCGDI

--------------------------------------------------------------
>42553_42553_2_KIF13B-IFT52_KIF13B_chr8_29120497_ENST00000521515_IFT52_chr20_42247580_ENST00000373039_length(transcript)=1059nt_BP=118nt
CCCCGAAGAGTCGCCGGTGGCCGCGGCAGACGGAAGCCGAACGAGTTCCTCGGCGGCTGCAGGATGGGGGACTCCAAAGTGAAAGTGGCG
GTGCGGATACGACCCATGAACCGGCGAGAACCAAGGTGGGAAGCTGGCAGTGCTTGGTTCATGTCACATGTTCAGTGATCAATATTTGGA
CAAAGAAGAAAACAGCAAAATCATGGATGTTGTTTTCCAGTGGCTCACGACAGGAGACATCCACCTAAACCAGATTGATGCTGAGGACCC
AGAGATTTCTGACTACATGATGCTGCCCTACACAGCCACCCTATCAAAGCGGAATCGAGAGTGTCTCCAGGAGAGTGATGAGATCCCAAG
GGACTTTACCACCCTCTTCGACCTGTCCATCTTCCAGCTGGATACCACCTCCTTCCACAGCGTCATCGAGGCTCACGAGCAGCTAAATGT
GAAACATGAACCACTCCAGCTCATCCAGCCTCAGTTTGAGACGCCGCTGCCAACCCTTCAGCCTGCGGTTTTTCCTCCCAGTTTCCGGGA
GTTACCACCTCCTCCTCTGGAGCTATTTGATTTAGATGAAACGTTCTCCTCTGAGAAGGCACGGCTGGCTCAGATTACCAATAAGTGTAC
TGAAGAAGACCTGGAATTTTATGTCAGGAAGTGTGGTGATATTCTTGGAGTAACCAGTAAACTACCAAAGGACCAACAGGATGCCAAACA
TATCCTTGAGCACGTCTTCTTCCAAGTGGTGGAGTTCAAGAAATTGAACCAGGAACATGACATCGATACAAGTGAAACAGCATTCCAGAA
CAATTTCTGAAGACCATGCCTCTTGAAGCTTTTTCTGCCTCCTGATTCTCTCTTTGTAAACTATTTTCAAATTGTTTTTCAACTCCTTAT
CAAAATTGTTTATACACTCTTTCCTCCATGAGCTCTGGAAGGTATATGCATCTTCTGTAATACTCAGATAGGTATAAGATTTTTCACAAA

>42553_42553_2_KIF13B-IFT52_KIF13B_chr8_29120497_ENST00000521515_IFT52_chr20_42247580_ENST00000373039_length(amino acids)=228AA_BP=
MAVLGSCHMFSDQYLDKEENSKIMDVVFQWLTTGDIHLNQIDAEDPEISDYMMLPYTATLSKRNRECLQESDEIPRDFTTLFDLSIFQLD
TTSFHSVIEAHEQLNVKHEPLQLIQPQFETPLPTLQPAVFPPSFRELPPPPLELFDLDETFSSEKARLAQITNKCTEEDLEFYVRKCGDI

--------------------------------------------------------------
>42553_42553_3_KIF13B-IFT52_KIF13B_chr8_29120497_ENST00000524189_IFT52_chr20_42247580_ENST00000373030_length(transcript)=1109nt_BP=94nt
GGCAGACGGAAGCCGAACGAGTTCCTCGGCGGCTGCAGGATGGGGGACTCCAAAGTGAAAGTGGCGGTGCGGATACGACCCATGAACCGG
CGAGAACCAAGGTGGGAAGCTGGCAGTGCTTGGTTCATGTCACATGTTCAGTGATCAATATTTGGACAAAGAAGAAAACAGCAAAATCAT
GGATGTTGTTTTCCAGTGGCTCACGACAGGAGACATCCACCTAAACCAGATTGATGCTGAGGACCCAGAGATTTCTGACTACATGATGCT
GCCCTACACAGCCACCCTATCAAAGCGGAATCGAGAGTGTCTCCAGGAGAGTGATGAGATCCCAAGGGACTTTACCACCCTCTTCGACCT
GTCCATCTTCCAGCTGGATACCACCTCCTTCCACAGCGTCATCGAGGCTCACGAGCAGCTAAATGTGAAACATGAACCACTCCAGCTCAT
CCAGCCTCAGTTTGAGACGCCGCTGCCAACCCTTCAGCCTGCGGTTTTTCCTCCCAGTTTCCGGGAGTTACCACCTCCTCCTCTGGAGCT
ATTTGATTTAGATGAAACGTTCTCCTCTGAGAAGGCACGGCTGGCTCAGATTACCAATAAGTGTACTGAAGAAGACCTGGAATTTTATGT
CAGGAAGTGTGGTGATATTCTTGGAGTAACCAGTAAACTACCAAAGGACCAACAGGATGCCAAACATATCCTTGAGCACGTCTTCTTCCA
AGTGGTGGAGTTCAAGAAATTGAACCAGGAACATGACATCGATACAAGTGAAACAGCATTCCAGAACAATTTCTGAAGACCATGCCTCTT
GAAGCTTTTTCTGCCTCCTGATTCTCTCTTTGTAAACTATTTTCAAATTGTTTTTCAACTCCTTATCAAAATTGTTTATACACTCTTTCC
TCCATGAGCTCTGGAAGGTATATGCATCTTCTGTAATACTCAGATAGGTATAAGATTTTTCACAAAATCCTTATGTAAGATACATTCCAT
TTTTAAAAATTAAATGTATGGTTGCATCTGTCTTTTTATACCCTATGAAACAGTCTTGATTTTTTTTTCTCAACCCCAGTTCTGGATTTG

>42553_42553_3_KIF13B-IFT52_KIF13B_chr8_29120497_ENST00000524189_IFT52_chr20_42247580_ENST00000373030_length(amino acids)=228AA_BP=
MAVLGSCHMFSDQYLDKEENSKIMDVVFQWLTTGDIHLNQIDAEDPEISDYMMLPYTATLSKRNRECLQESDEIPRDFTTLFDLSIFQLD
TTSFHSVIEAHEQLNVKHEPLQLIQPQFETPLPTLQPAVFPPSFRELPPPPLELFDLDETFSSEKARLAQITNKCTEEDLEFYVRKCGDI

--------------------------------------------------------------
>42553_42553_4_KIF13B-IFT52_KIF13B_chr8_29120497_ENST00000524189_IFT52_chr20_42247580_ENST00000373039_length(transcript)=1035nt_BP=94nt
GGCAGACGGAAGCCGAACGAGTTCCTCGGCGGCTGCAGGATGGGGGACTCCAAAGTGAAAGTGGCGGTGCGGATACGACCCATGAACCGG
CGAGAACCAAGGTGGGAAGCTGGCAGTGCTTGGTTCATGTCACATGTTCAGTGATCAATATTTGGACAAAGAAGAAAACAGCAAAATCAT
GGATGTTGTTTTCCAGTGGCTCACGACAGGAGACATCCACCTAAACCAGATTGATGCTGAGGACCCAGAGATTTCTGACTACATGATGCT
GCCCTACACAGCCACCCTATCAAAGCGGAATCGAGAGTGTCTCCAGGAGAGTGATGAGATCCCAAGGGACTTTACCACCCTCTTCGACCT
GTCCATCTTCCAGCTGGATACCACCTCCTTCCACAGCGTCATCGAGGCTCACGAGCAGCTAAATGTGAAACATGAACCACTCCAGCTCAT
CCAGCCTCAGTTTGAGACGCCGCTGCCAACCCTTCAGCCTGCGGTTTTTCCTCCCAGTTTCCGGGAGTTACCACCTCCTCCTCTGGAGCT
ATTTGATTTAGATGAAACGTTCTCCTCTGAGAAGGCACGGCTGGCTCAGATTACCAATAAGTGTACTGAAGAAGACCTGGAATTTTATGT
CAGGAAGTGTGGTGATATTCTTGGAGTAACCAGTAAACTACCAAAGGACCAACAGGATGCCAAACATATCCTTGAGCACGTCTTCTTCCA
AGTGGTGGAGTTCAAGAAATTGAACCAGGAACATGACATCGATACAAGTGAAACAGCATTCCAGAACAATTTCTGAAGACCATGCCTCTT
GAAGCTTTTTCTGCCTCCTGATTCTCTCTTTGTAAACTATTTTCAAATTGTTTTTCAACTCCTTATCAAAATTGTTTATACACTCTTTCC
TCCATGAGCTCTGGAAGGTATATGCATCTTCTGTAATACTCAGATAGGTATAAGATTTTTCACAAAATCCTTATGTAAGATACATTCCAT

>42553_42553_4_KIF13B-IFT52_KIF13B_chr8_29120497_ENST00000524189_IFT52_chr20_42247580_ENST00000373039_length(amino acids)=228AA_BP=
MAVLGSCHMFSDQYLDKEENSKIMDVVFQWLTTGDIHLNQIDAEDPEISDYMMLPYTATLSKRNRECLQESDEIPRDFTTLFDLSIFQLD
TTSFHSVIEAHEQLNVKHEPLQLIQPQFETPLPTLQPAVFPPSFRELPPPPLELFDLDETFSSEKARLAQITNKCTEEDLEFYVRKCGDI

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

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Fusion Gene PPI Analysis for KIF13B-IFT52


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 KIF13B-IFT52


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 KIF13B-IFT52


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