	FusionGeneSummary
	FusionProtFeature
	FusionGeneSequence
	FusionGenePPI
	RelatedDrugs
	RelatedDiseases

Fusion gene ID: 30369

FusionGeneSummary for RAP1A_ABCD3

Fusion gene summary

Fusion gene information	Fusion gene name: RAP1A_ABCD3
	Fusion gene ID: 30369
		Hgene	Tgene
	Gene symbol	RAP1A	ABCD3
	Gene ID	5906	5825
	Gene name	RAP1A, member of RAS oncogene family	ATP binding cassette subfamily D member 3
	Synonyms	C21KG\|G-22K\|KREV-1\|KREV1\|RAP1\|SMGP21	ABC43\|CBAS5\|PMP70\|PXMP1\|ZWS2
	Cytomap	1p13.2	1p21.3
	Type of gene	protein-coding	protein-coding
	Description	ras-related protein Rap-1AGTP-binding protein smg p21ARas-related protein Krev-1	ATP-binding cassette sub-family D member 370 kDa peroxisomal membrane proteinATP-binding cassette, sub-family D (ALD), member 3Peroxisomal membrane protein-1 (70kD)dJ824O18.1 (ATP-binding cassette, sub-family D (ALD), member 3 (PMP70, PXMP1))peroxiso
	Modification date	20180522	20180519
	UniProtAcc	P62834	P28288
	Ensembl transtripts involved in fusion gene	ENST00000356415, ENST00000436150, ENST00000369709, ENST00000545460, ENST00000494982,	ENST00000394233, ENST00000454898, ENST00000536817, ENST00000370214, ENST00000315713, ENST00000484213,
Fusion gene scores	* DoF score	9 X 10 X 5=450	4 X 3 X 4=48
	# samples	11	4
	** MAII score	log2(11/450*10)=-2.03242147769238 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(4/48*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: RAP1A [Title/Abstract] AND ABCD3 [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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	RAP1A	GO:0015031	protein transport	17916086
Hgene	RAP1A	GO:0071320	cellular response to cAMP	21840392
Tgene	ABCD3	GO:0007031	peroxisome organization	9425230

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 type	Source	Cancer type	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
TCGA	RV	STAD	TCGA-CD-8532-01A	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+

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

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.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
intron-3CDS	ENST00000356415	ENST00000394233	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
intron-3CDS	ENST00000356415	ENST00000454898	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
intron-intron	ENST00000356415	ENST00000536817	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
intron-intron	ENST00000356415	ENST00000370214	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
intron-intron	ENST00000356415	ENST00000315713	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
intron-intron	ENST00000356415	ENST00000484213	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
5UTR-3CDS	ENST00000436150	ENST00000394233	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
5UTR-3CDS	ENST00000436150	ENST00000454898	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
5UTR-intron	ENST00000436150	ENST00000536817	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
5UTR-intron	ENST00000436150	ENST00000370214	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
5UTR-intron	ENST00000436150	ENST00000315713	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
5UTR-intron	ENST00000436150	ENST00000484213	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
5UTR-3CDS	ENST00000369709	ENST00000394233	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
5UTR-3CDS	ENST00000369709	ENST00000454898	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
5UTR-intron	ENST00000369709	ENST00000536817	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
5UTR-intron	ENST00000369709	ENST00000370214	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
5UTR-intron	ENST00000369709	ENST00000315713	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
5UTR-intron	ENST00000369709	ENST00000484213	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
intron-3CDS	ENST00000545460	ENST00000394233	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
intron-3CDS	ENST00000545460	ENST00000454898	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
intron-intron	ENST00000545460	ENST00000536817	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
intron-intron	ENST00000545460	ENST00000370214	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
intron-intron	ENST00000545460	ENST00000315713	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
intron-intron	ENST00000545460	ENST00000484213	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
intron-3CDS	ENST00000494982	ENST00000394233	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
intron-3CDS	ENST00000494982	ENST00000454898	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
intron-intron	ENST00000494982	ENST00000536817	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
intron-intron	ENST00000494982	ENST00000370214	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
intron-intron	ENST00000494982	ENST00000315713	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+
intron-intron	ENST00000494982	ENST00000484213	RAP1A	chr1	112162556	+	ABCD3	chr1	94924163	+

Top

FusionProtFeatures for RAP1A_ABCD3

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
RAP1A P62834	ABCD3 P28288
Induces morphological reversion of a cell linetransformed by a Ras oncogene. Counteracts the mitogenic functionof Ras, at least partly because it can interact with Ras GAPs andRAF in a competitive manner. Together with ITGB1BP1, regulatesKRIT1 localization to microtubules and membranes. Plays a role innerve growth factor (NGF)-induced neurite outgrowth. Plays a rolein the regulation of embryonic blood vessel formation. Involved inthe establishment of basal endothelial barrier function. May beinvolved in the regulation of the vascular endothelial growthfactor receptor KDR expression at endothelial cell-cell junctions.{ECO:0000269\|PubMed:17916086, ECO:0000269\|PubMed:21840392}.	Probable transporter involved in the transport ofbranched-chain fatty acids and C27 bile acids into the peroxisome;the latter function is a crucial step in bile acid biosynthesis(PubMed:25168382). The nucleotide-binding fold acts as an ATP-binding subunit with ATPase activity (PubMed:11248239).{ECO:0000269\|PubMed:11248239, ECO:0000269\|PubMed:25168382}.

Retention 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.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

- In-frame and not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Top

FusionGeneSequence for RAP1A_ABCD3

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.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

Top

FusionGenePPI for RAP1A_ABCD3

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page
.

Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)

Hgene	Hgene's interactors	Tgene	Tgene's interactors
RAP1A	PDE6D, RAP1GDS1, KRIT1, RGL4, TSC2, GABARAPL2, ARHGEF1, RUNDC3A, MLLT4, RALGDS, RAPGEF3, RAPGEF4, RAPGEF5, MTOR, RAP1GAP, RHEB, RAF1, RGS14, BRAF, NTRK1, RAPGEF2, RAPGEF6, PPP2R1A, ELAVL1, RADIL, GNB1, CDC42, ILF3, DNAJC8, PON2, FEN1, HNRNPM, GNG12, CDK11B, RAB1A, DGKI, SIRT1, MTNR1A, GANAB, UNK, ARHGDIA, ECHS1, RAB5A, RAB5B, RAB5C, RAB7A, RAB8A, RAB8B, UQCRC2, BIN1, BMX, SMARCA2, TNFRSF10C, TCEB3, FADD, FAF1, FAS, HDAC1, HSPA4, IQGAP1, LIMA1, RASGRP4, DUSP19, DUSP22, DUSP9, KIFAP3, MRPL34, EXOC6, CPLX2, MGST3, TBRG4, DLST, SOD1, TRIM25, RAPGEF1	ABCD3	C20orf24, PTP4A3, PELO, MLF2, MEST, PGRMC1, BRF2, ABCD1, PEX19, USP50, USP32, CLN3, CUL3, PEX3, NDUFV1, MPV17, TAP1, ATP6V1C1, AGPS, NNT, SURF1, SYNJ2BP, MRPL41, ZNF454, TIMMDC1, NDUFB11, NDUFS4, TOMM40, ECT2, MDC1, PEX14, MMS19, TUFT1, PSMA1, DYRK1B, DYRK1A, HIPK4, MOV10, NXF1, OBSL1, RNF2, EGFR, FAF2, SLC39A4, UNK, NTRK1, DHX9, EEF2, BTRC, PCM1, TMEM67, KRAS, PTPN1, RAB7A, VAPA, GOLT1B, TMEM63B, FAM134A, MYH14, COQ9, NDUFA4, C15orf48, OCIAD1, ZNF746, CTDNEP1, TPTE, STOM, PDHA1, TRIM25, UBE2A

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

Top

RelatedDrugs for RAP1A_ABCD3

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

Top

RelatedDiseases for RAP1A_ABCD3

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Tgene	ABCD3	C0009404	Colorectal Neoplasms	1	CTD_human
Tgene	ABCD3	C0043459	Zellweger Syndrome	1	CTD_human

Home

Download

Statistics

Examples

Help

Contact

Fusion gene ID: 30369

FusionGeneSummary for RAP1A_ABCD3

FusionProtFeatures for RAP1A_ABCD3

FusionGeneSequence for RAP1A_ABCD3

FusionGenePPI for RAP1A_ABCD3

RelatedDrugs for RAP1A_ABCD3

RelatedDiseases for RAP1A_ABCD3