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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:KDM5B-RABGAP1L (FusionGDB2 ID:41677)

Fusion Gene Summary for KDM5B-RABGAP1L

check button Fusion gene summary
Fusion gene informationFusion gene name: KDM5B-RABGAP1L
Fusion gene ID: 41677
HgeneTgene
Gene symbol

KDM5B

RABGAP1L

Gene ID

10765

9910

Gene namelysine demethylase 5BRAB GTPase activating protein 1 like
SynonymsCT31|JARID1B|MRT65|PLU-1|PLU1|PPP1R98|PUT1|RBBP2H1A|RBP2-H1HHL|TBC1D18
Cytomap

1q32.1

1q25.1

Type of geneprotein-codingprotein-coding
Descriptionlysine-specific demethylase 5Bcancer/testis antigen 31histone demethylase JARID1Bjumonji, AT rich interactive domain 1Bjumonji/ARID domain-containing protein 1Blysine (K)-specific demethylase 5Bprotein phosphatase 1, regulatory subunit 98putative Drab GTPase-activating protein 1-likeTBC1 domain family, member 18expressed in hematopoietic cells, heart, liver (HLL)
Modification date2020032020200313
UniProtAcc

Q9UGL1

.
Ensembl transtripts involved in fusion geneENST00000367265, ENST00000367264, 
ENST00000456180, 		ENST00000367689, 
ENST00000357444, ENST00000251507, 
ENST00000325589, ENST00000367686, 
ENST00000367687, ENST00000347255, 
ENST00000489615, ENST00000478442, 
ENST00000486220, ENST00000392064, 
ENST00000367688, 
Fusion gene scores* DoF score14 X 13 X 9=163816 X 16 X 10=2560
# samples 1719
** MAII scorelog2(17/1638*10)=-3.26832870550331
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(19/2560*10)=-3.75207248655641
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: KDM5B [Title/Abstract] AND RABGAP1L [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKDM5B(202742246)-RABGAP1L(174340117), # samples:3
Anticipated loss of major functional domain due to fusion event.KDM5B-RABGAP1L seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
KDM5B-RABGAP1L seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
KDM5B-RABGAP1L seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted 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
HgeneKDM5B

GO:0034720

histone H3-K4 demethylation

20228790

TgeneRABGAP1L

GO:0032880

regulation of protein localization

16923123


check buttonFusion gene breakpoints across KDM5B (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across RABGAP1L (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChimerDB4BRCATCGA-A2-A1FW-01AKDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
ChimerDB4BRCATCGA-A2-A1FW-01AKDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
ChimerDB4BRCATCGA-A2-A1FW-01AKDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+


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Fusion Gene ORF analysis for KDM5B-RABGAP1L

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-shiftENST00000367265ENST00000367689KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
Frame-shiftENST00000367265ENST00000357444KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
Frame-shiftENST00000367265ENST00000251507KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
5CDS-intronENST00000367265ENST00000325589KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
5CDS-intronENST00000367265ENST00000367686KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
5CDS-intronENST00000367265ENST00000367687KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
5CDS-intronENST00000367265ENST00000347255KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
5CDS-intronENST00000367265ENST00000489615KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
5CDS-intronENST00000367265ENST00000478442KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
5CDS-intronENST00000367265ENST00000486220KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
5CDS-intronENST00000367265ENST00000392064KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
5CDS-intronENST00000367265ENST00000367688KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
Frame-shiftENST00000367264ENST00000367689KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
Frame-shiftENST00000367264ENST00000357444KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
Frame-shiftENST00000367264ENST00000251507KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
5CDS-intronENST00000367264ENST00000325589KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
5CDS-intronENST00000367264ENST00000367686KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
5CDS-intronENST00000367264ENST00000367687KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
5CDS-intronENST00000367264ENST00000347255KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
5CDS-intronENST00000367264ENST00000489615KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
5CDS-intronENST00000367264ENST00000478442KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
5CDS-intronENST00000367264ENST00000486220KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
5CDS-intronENST00000367264ENST00000392064KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
5CDS-intronENST00000367264ENST00000367688KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
intron-3CDSENST00000456180ENST00000367689KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
intron-3CDSENST00000456180ENST00000357444KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
intron-3CDSENST00000456180ENST00000251507KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
intron-intronENST00000456180ENST00000325589KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
intron-intronENST00000456180ENST00000367686KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
intron-intronENST00000456180ENST00000367687KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
intron-intronENST00000456180ENST00000347255KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
intron-intronENST00000456180ENST00000489615KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
intron-intronENST00000456180ENST00000478442KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
intron-intronENST00000456180ENST00000486220KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
intron-intronENST00000456180ENST00000392064KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+
intron-intronENST00000456180ENST00000367688KDM5Bchr1

202742246

-RABGAP1Lchr1

174340117

+

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)

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

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Fusion Genomic Features for KDM5B-RABGAP1L


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)
KDM5Bchr1202742245-RABGAP1Lchr1174340116+1.62E-101
KDM5Bchr1202742245-RABGAP1Lchr1174340116+1.62E-101

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.

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.

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Fusion Protein Features for KDM5B-RABGAP1L


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
KDM5B

Q9UGL1

.
FUNCTION: Histone demethylase that demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code (PubMed:24952722, PubMed:27214403, PubMed:28262558). Does not demethylate histone H3 'Lys-9' or H3 'Lys-27'. Demethylates trimethylated, dimethylated and monomethylated H3 'Lys-4'. Acts as a transcriptional corepressor for FOXG1B and PAX9. Favors the proliferation of breast cancer cells by repressing tumor suppressor genes such as BRCA1 and HOXA5 (PubMed:24952722). In contrast, may act as a tumor suppressor for melanoma. Represses the CLOCK-ARNTL/BMAL1 heterodimer-mediated transcriptional activation of the core clock component PER2 (By similarity). {ECO:0000250|UniProtKB:Q80Y84, ECO:0000269|PubMed:12657635, ECO:0000269|PubMed:16645588, ECO:0000269|PubMed:17320161, ECO:0000269|PubMed:17363312, ECO:0000269|PubMed:24952722, ECO:0000269|PubMed:26645689, ECO:0000269|PubMed:26741168, ECO:0000269|PubMed:27214403, ECO:0000269|PubMed:28262558}.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.
- 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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Fusion Gene Sequence for KDM5B-RABGAP1L


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.

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Fusion Gene PPI Analysis for KDM5B-RABGAP1L


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 KDM5B-RABGAP1L


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 KDM5B-RABGAP1L


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneKDM5BC0004352Autistic Disorder1GENOMICS_ENGLAND
HgeneKDM5BC0007102Malignant tumor of colon1CTD_human
HgeneKDM5BC0009375Colonic Neoplasms1CTD_human
HgeneKDM5BC4748219MENTAL RETARDATION, AUTOSOMAL RECESSIVE 651GENOMICS_ENGLAND
TgeneRABGAP1LC0023893Liver Cirrhosis, Experimental1CTD_human