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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:PACS1-RHOD (FusionGDB2 ID:61859)

Fusion Gene Summary for PACS1-RHOD

check button Fusion gene summary
Fusion gene informationFusion gene name: PACS1-RHOD
Fusion gene ID: 61859
HgeneTgene
Gene symbol

PACS1

RHOD

Gene ID

55690

29984

Gene namephosphofurin acidic cluster sorting protein 1ras homolog family member D
SynonymsMRD17|SHMSARHD|RHOHP1|RHOM|Rho
Cytomap

11q13.1-q13.2

11q13.2

Type of geneprotein-codingprotein-coding
Descriptionphosphofurin acidic cluster sorting protein 1PACS-1cytosolic sorting protein PACS-1rho-related GTP-binding protein RhoDRho-related protein HP1ras homolog Dras homolog gene family, member Aras homolog gene family, member D
Modification date2020031320200313
UniProtAcc.

GRK7

Ensembl transtripts involved in fusion geneENST00000320580, ENST00000529757, 
ENST00000524815, 		ENST00000308831, 
ENST00000533360, ENST00000532559, 
Fusion gene scores* DoF score18 X 7 X 11=138610 X 6 X 6=360
# samples 1915
** MAII scorelog2(19/1386*10)=-2.86685593380627
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(15/360*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PACS1 [Title/Abstract] AND RHOD [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPACS1(65961044)-RHOD(66833367), # samples:2
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

check buttonFusion gene breakpoints across PACS1 (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 RHOD (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-A0YI-01APACS1chr11

65961044

+RHODchr11

66833367

+
ChimerDB4BRCATCGA-A2-A0YI-01APACS1chr11

65961044

+RHODchr11

66833367

+


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Fusion Gene ORF analysis for PACS1-RHOD

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
In-frameENST00000320580ENST00000308831PACS1chr11

65961044

+RHODchr11

66833367

+
In-frameENST00000320580ENST00000533360PACS1chr11

65961044

+RHODchr11

66833367

+
5CDS-intronENST00000320580ENST00000532559PACS1chr11

65961044

+RHODchr11

66833367

+
intron-3CDSENST00000529757ENST00000308831PACS1chr11

65961044

+RHODchr11

66833367

+
intron-3CDSENST00000529757ENST00000533360PACS1chr11

65961044

+RHODchr11

66833367

+
intron-intronENST00000529757ENST00000532559PACS1chr11

65961044

+RHODchr11

66833367

+
intron-3CDSENST00000524815ENST00000308831PACS1chr11

65961044

+RHODchr11

66833367

+
intron-3CDSENST00000524815ENST00000533360PACS1chr11

65961044

+RHODchr11

66833367

+
intron-intronENST00000524815ENST00000532559PACS1chr11

65961044

+RHODchr11

66833367

+

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)
ENST00000320580PACS1chr1165961044+ENST00000308831RHODchr1166833367+138947733977314
ENST00000320580PACS1chr1165961044+ENST00000533360RHODchr1166833367+90447733701222

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
ENST00000320580ENST00000308831PACS1chr1165961044+RHODchr1166833367+0.0409284230.9590716
ENST00000320580ENST00000533360PACS1chr1165961044+RHODchr1166833367+0.0020040060.997996

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Fusion Genomic Features for PACS1-RHOD


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)
PACS1chr1165961044+RHODchr1166833366+2.98E-111
PACS1chr1165961044+RHODchr1166833366+2.98E-111

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 PACS1-RHOD


check button Go to

FGviewer for the breakpoints of chr11:65961044-chr11:66833367

.
- 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
.RHOD

GRK7

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.553

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
HgenePACS1chr11:65961044chr11:66833367ENST00000320580+224112_115148.0964.0Compositional biasNote=Poly-Ser
HgenePACS1chr11:65961044chr11:66833367ENST00000320580+22435_40148.0964.0Compositional biasNote=Poly-Gln
HgenePACS1chr11:65961044chr11:66833367ENST00000320580+22455_84148.0964.0Compositional biasNote=Ser-rich
HgenePACS1chr11:65961044chr11:66833367ENST00000320580+2245_44148.0964.0Compositional biasNote=Gly-rich
HgenePACS1chr11:65961044chr11:66833367ENST00000320580+22462_65148.0964.0Compositional biasNote=Poly-Ala
TgeneRHODchr11:65961044chr11:66833367ENST000003088310546_5444.0211.0MotifEffector region
TgeneRHODchr11:65961044chr11:66833367ENST0000030883105129_13244.0211.0Nucleotide bindingGTP
TgeneRHODchr11:65961044chr11:66833367ENST000003088310571_7544.0211.0Nucleotide bindingGTP

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePACS1chr11:65961044chr11:66833367ENST00000320580+224353_377148.0964.0Coiled coilOntology_term=ECO:0000255
HgenePACS1chr11:65961044chr11:66833367ENST00000320580+224279_283148.0964.0Compositional biasNote=Poly-Glu
HgenePACS1chr11:65961044chr11:66833367ENST00000320580+224168_175148.0964.0RegionNote=Involved in binding to AP-1
TgeneRHODchr11:65961044chr11:66833367ENST000003088310524_3144.0211.0Nucleotide bindingGTP


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Fusion Gene Sequence for PACS1-RHOD


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.
>In-frame_ENST00000320580_ENST00000308831_TCGA-A2-A0YI-01A_PACS1_chr11_65961044_+_RHOD_chr11_66833367_length(transcript)=1389nt_BP=477nt
CCTCGGCCTCCGTAACCCCCGCCTAGCCGGGCCATGGCGGAACGCGGAGGGGCGGGCGGTGGTCCCGGAGGCGCCGGGGGCGGCAGCGGC
CAGCGGGGATCCGGGGTCGCCCAGTCCCCTCAGCAGCCGCCGCCGCAGCAGCAGCAGCAGCAGCCGCCGCAGCAGCCGACGCCCCCCAAG
CTGGCCCAGGCCACCTCGTCGTCCTCGTCCACCTCGGCGGCGGCTGCCTCCTCCTCGTCCTCGTCTACCTCCACCTCCATGGCCGTGGCG
GTGGCCTCGGGCTCCGCGCCTCCCGGTGGCCCGGGGCCAGGCCGCACCCCCGCCCCGGTGCAGATGAACCTGTACGCCACCTGGGAGGTG
GACCGGAGCTCGTCCAGCTGCGTGCCTAGGCTATTCAGCTTGACCCTGAAGAAACTCGTCATGCTAAAAGAAATGGACAAAGATCTTAAC
TCAGTGGTCATCGCTGTGAAGCTGCAGAGCTACACCCCCACGGTGTTTGAGCGGTACATGGTCAACCTGCAAGTGAAAGGCAAACCTGTG
CACCTCCACATCTGGGACACAGCAGGGCAAGATGACTATGACCGCCTGCGGCCCCTGTTCTACCCTGACGCCAGCGTCCTGCTGCTTTGC
TTCGATGTCACCAGCCCGAACAGCTTTGACAACATCTTTAACCGGTGGTACCCAGAAGTGAATCATTTCTGCAAGAAGGTACCCATCATC
GTCGTGGGCTGCAAGACTGACCTGTGCAAGGACAAATCACTGGTGAACAAGCTCCGAAGAAACGGATTGGAGCCTGTGACCTACCACAGG
GGCCAGGAGATGGCGAGGTCCGTGGGCGCGGTGGCCTACCTCGAGTGCTCGGCTCGGCTCCATGACAACGTCCACGCCGTCTTCCAGGAG
GCCGCCGAGGTGGCCCTCAGCAGCCGCGGTCGCAACTTCTGGCGGCGGATTACCCAGGGCTTTTGCGTGGTGACCTGAGCGGCTCGGGGC
GTCCCAGCGACGCGGGAAGGGGCAGGGCGCTGACCTGCTGCTGAGCTGGCTGGGCTGGACCCGGTCCCTAGGCTGTGACCGCCGAACTCC
ACTGCAACAGACGGGCGCCACCAAAGCCAGGCCCTGAGGCCTGGGAGTCCTGGACTGAGAAAGGGGGTTCCTGGGCCCACCTGCTCTGTG
TAGGGCTCGTCCTGCGGTGCCCGAGAATCACTCGCTAACCCCTATGCCCGGTCCCGGACCGACATCCTGGAGCCGCCTGTGCAGCCTGAT
GCCCCCTCGTGGCTGCTCCCAGGGCTGCACCTGCCAGGACCTAATGTTCTTAGGTCCCTCTGGCCAGAACCCACACCCGGCCCCTTCCCA

>In-frame_ENST00000320580_ENST00000308831_TCGA-A2-A0YI-01A_PACS1_chr11_65961044_+_RHOD_chr11_66833367_length(amino acids)=314AA_start in transcript=33_stop in transcript=977
MAERGGAGGGPGGAGGGSGQRGSGVAQSPQQPPPQQQQQQPPQQPTPPKLAQATSSSSSTSAAAASSSSSSTSTSMAVAVASGSAPPGGP
GPGRTPAPVQMNLYATWEVDRSSSSCVPRLFSLTLKKLVMLKEMDKDLNSVVIAVKLQSYTPTVFERYMVNLQVKGKPVHLHIWDTAGQD
DYDRLRPLFYPDASVLLLCFDVTSPNSFDNIFNRWYPEVNHFCKKVPIIVVGCKTDLCKDKSLVNKLRRNGLEPVTYHRGQEMARSVGAV

--------------------------------------------------------------
>In-frame_ENST00000320580_ENST00000533360_TCGA-A2-A0YI-01A_PACS1_chr11_65961044_+_RHOD_chr11_66833367_length(transcript)=904nt_BP=477nt
CCTCGGCCTCCGTAACCCCCGCCTAGCCGGGCCATGGCGGAACGCGGAGGGGCGGGCGGTGGTCCCGGAGGCGCCGGGGGCGGCAGCGGC
CAGCGGGGATCCGGGGTCGCCCAGTCCCCTCAGCAGCCGCCGCCGCAGCAGCAGCAGCAGCAGCCGCCGCAGCAGCCGACGCCCCCCAAG
CTGGCCCAGGCCACCTCGTCGTCCTCGTCCACCTCGGCGGCGGCTGCCTCCTCCTCGTCCTCGTCTACCTCCACCTCCATGGCCGTGGCG
GTGGCCTCGGGCTCCGCGCCTCCCGGTGGCCCGGGGCCAGGCCGCACCCCCGCCCCGGTGCAGATGAACCTGTACGCCACCTGGGAGGTG
GACCGGAGCTCGTCCAGCTGCGTGCCTAGGCTATTCAGCTTGACCCTGAAGAAACTCGTCATGCTAAAAGAAATGGACAAAGATCTTAAC
TCAGTGGTCATCGCTGTGAAGCTGCAGAGCTACACCCCCACGGTGTTTGAGCGGTACATGGTCAACCTGCAAGTGAAAGGCAAACCTGTG
CACCTCCACATCTGGGACACAGCAGGGCAAGATGACTATGACCGCCTGCGGCCCCTGTTCTACCCTGACGCCAGCGTCCTGCTGCTTTGC
TTCGATGTCACCAGCCCGAACAGCTTTGACAACATCTTTAACCGGTTTCTCCCTAGGTGCTGGCTTTGCTGATTATCCATATCAGAGCTC
AGGCTGGGGAGCAAGAGAGTGGTCCACTGAGAGGGCCAGAACTCTCCAGGGCTCACACATGCCCCCCACATGCCCCCTCGCCCCCCTGCA
GTGGTACCCAGAAGTGAATCATTTCTGCAAGAAGGTACCCATCATCGTCGTGGGCTGCAAGACTGACCTGTGCAAGGACAAATCACTGGT

>In-frame_ENST00000320580_ENST00000533360_TCGA-A2-A0YI-01A_PACS1_chr11_65961044_+_RHOD_chr11_66833367_length(amino acids)=222AA_start in transcript=33_stop in transcript=701
MAERGGAGGGPGGAGGGSGQRGSGVAQSPQQPPPQQQQQQPPQQPTPPKLAQATSSSSSTSAAAASSSSSSTSTSMAVAVASGSAPPGGP
GPGRTPAPVQMNLYATWEVDRSSSSCVPRLFSLTLKKLVMLKEMDKDLNSVVIAVKLQSYTPTVFERYMVNLQVKGKPVHLHIWDTAGQD

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

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Fusion Gene PPI Analysis for PACS1-RHOD


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 PACS1-RHOD


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 PACS1-RHOD


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePACS1C3714756Intellectual Disability2GENOMICS_ENGLAND
HgenePACS1C0005586Bipolar Disorder1CTD_human
HgenePACS1C0005587Depression, Bipolar1CTD_human
HgenePACS1C0013146Drug abuse1CTD_human
HgenePACS1C0013170Drug habituation1CTD_human
HgenePACS1C0013222Drug Use Disorders1CTD_human
HgenePACS1C0024713Manic Disorder1CTD_human
HgenePACS1C0028754Obesity1CTD_human
HgenePACS1C0029231Organic Mental Disorders, Substance-Induced1CTD_human
HgenePACS1C0038580Substance Dependence1CTD_human
HgenePACS1C0038586Substance Use Disorders1CTD_human
HgenePACS1C0236969Substance-Related Disorders1CTD_human
HgenePACS1C0338831Manic1CTD_human
HgenePACS1C0740858Substance abuse problem1CTD_human
HgenePACS1C1510472Drug Dependence1CTD_human
HgenePACS1C3554343MENTAL RETARDATION, AUTOSOMAL DOMINANT 171GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgenePACS1C4316881Prescription Drug Abuse1CTD_human