FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:HMBOX1-SCARA3 (FusionGDB2 ID:36631)

Fusion Gene Summary for HMBOX1-SCARA3

check button Fusion gene summary
Fusion gene informationFusion gene name: HMBOX1-SCARA3
Fusion gene ID: 36631
HgeneTgene
Gene symbol

HMBOX1

SCARA3

Gene ID

79618

51435

Gene namehomeobox containing 1scavenger receptor class A member 3
SynonymsHNF1LA|HOT1|PBHNF|TAH1APC7|CSR|CSR1|MSLR1|MSRL1
Cytomap

8p21.1-p12

8p21.1

Type of geneprotein-codingprotein-coding
Descriptionhomeobox-containing protein 1homeobox telomere-binding protein 1homeobox-containing protein PBHNFtelomere-associated homeobox-containing protein 1scavenger receptor class A member 3cellular stress response gene proteincellular stress response proteinmacrophage scavenger receptor-like 1
Modification date2020031320200313
UniProtAcc

Q6NT76

.
Ensembl transtripts involved in fusion geneENST00000403668, ENST00000444075, 
ENST00000287701, ENST00000558662, 
ENST00000523613, ENST00000397358, 
ENST00000519047, ENST00000355231, 
ENST00000524238, ENST00000517386, 
ENST00000337221, ENST00000301904, 
Fusion gene scores* DoF score15 X 13 X 8=15605 X 5 X 4=100
# samples 165
** MAII scorelog2(16/1560*10)=-3.28540221886225
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/100*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HMBOX1 [Title/Abstract] AND SCARA3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHMBOX1(28749001)-SCARA3(27507219), # samples:1
HMBOX1(28748536)-SCARA3(27507219), # 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
HgeneHMBOX1

GO:0000122

negative regulation of transcription by RNA polymerase II

21839858

HgeneHMBOX1

GO:0032212

positive regulation of telomere maintenance via telomerase

23685356

HgeneHMBOX1

GO:0045892

negative regulation of transcription, DNA-templated

19757162

HgeneHMBOX1

GO:0051972

regulation of telomerase activity

23685356

HgeneHMBOX1

GO:0051973

positive regulation of telomerase activity

23685356


check buttonFusion gene breakpoints across HMBOX1 (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 SCARA3 (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
ChimerDB4LUADTCGA-38-4630-01AHMBOX1chr8

28749001

+SCARA3chr8

27507219

+
ChimerDB4LUADTCGA-38-4630-01AHMBOX1chr8

28748536

-SCARA3chr8

27507219

+


Top

Fusion Gene ORF analysis for HMBOX1-SCARA3

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
intron-3CDSENST00000403668ENST00000337221HMBOX1chr8

28749001

+SCARA3chr8

27507219

+
intron-3CDSENST00000403668ENST00000301904HMBOX1chr8

28749001

+SCARA3chr8

27507219

+
intron-3CDSENST00000444075ENST00000337221HMBOX1chr8

28749001

+SCARA3chr8

27507219

+
intron-3CDSENST00000444075ENST00000301904HMBOX1chr8

28749001

+SCARA3chr8

27507219

+
intron-3CDSENST00000287701ENST00000337221HMBOX1chr8

28749001

+SCARA3chr8

27507219

+
intron-3CDSENST00000287701ENST00000301904HMBOX1chr8

28749001

+SCARA3chr8

27507219

+
intron-3CDSENST00000558662ENST00000337221HMBOX1chr8

28749001

+SCARA3chr8

27507219

+
intron-3CDSENST00000558662ENST00000301904HMBOX1chr8

28749001

+SCARA3chr8

27507219

+
intron-3CDSENST00000523613ENST00000337221HMBOX1chr8

28749001

+SCARA3chr8

27507219

+
intron-3CDSENST00000523613ENST00000301904HMBOX1chr8

28749001

+SCARA3chr8

27507219

+
intron-3CDSENST00000397358ENST00000337221HMBOX1chr8

28749001

+SCARA3chr8

27507219

+
intron-3CDSENST00000397358ENST00000301904HMBOX1chr8

28749001

+SCARA3chr8

27507219

+
intron-3CDSENST00000519047ENST00000337221HMBOX1chr8

28749001

+SCARA3chr8

27507219

+
intron-3CDSENST00000519047ENST00000301904HMBOX1chr8

28749001

+SCARA3chr8

27507219

+
5UTR-3CDSENST00000355231ENST00000337221HMBOX1chr8

28749001

+SCARA3chr8

27507219

+
5UTR-3CDSENST00000355231ENST00000301904HMBOX1chr8

28749001

+SCARA3chr8

27507219

+
intron-3CDSENST00000524238ENST00000337221HMBOX1chr8

28749001

+SCARA3chr8

27507219

+
intron-3CDSENST00000524238ENST00000301904HMBOX1chr8

28749001

+SCARA3chr8

27507219

+
intron-3CDSENST00000517386ENST00000337221HMBOX1chr8

28749001

+SCARA3chr8

27507219

+
intron-3CDSENST00000517386ENST00000301904HMBOX1chr8

28749001

+SCARA3chr8

27507219

+
intron-3CDSENST00000403668ENST00000337221HMBOX1chr8

28748536

-SCARA3chr8

27507219

+
intron-3CDSENST00000403668ENST00000301904HMBOX1chr8

28748536

-SCARA3chr8

27507219

+
intron-3CDSENST00000444075ENST00000337221HMBOX1chr8

28748536

-SCARA3chr8

27507219

+
intron-3CDSENST00000444075ENST00000301904HMBOX1chr8

28748536

-SCARA3chr8

27507219

+
intron-3CDSENST00000287701ENST00000337221HMBOX1chr8

28748536

-SCARA3chr8

27507219

+
intron-3CDSENST00000287701ENST00000301904HMBOX1chr8

28748536

-SCARA3chr8

27507219

+
intron-3CDSENST00000558662ENST00000337221HMBOX1chr8

28748536

-SCARA3chr8

27507219

+
intron-3CDSENST00000558662ENST00000301904HMBOX1chr8

28748536

-SCARA3chr8

27507219

+
intron-3CDSENST00000523613ENST00000337221HMBOX1chr8

28748536

-SCARA3chr8

27507219

+
intron-3CDSENST00000523613ENST00000301904HMBOX1chr8

28748536

-SCARA3chr8

27507219

+
5UTR-3CDSENST00000397358ENST00000337221HMBOX1chr8

28748536

-SCARA3chr8

27507219

+
5UTR-3CDSENST00000397358ENST00000301904HMBOX1chr8

28748536

-SCARA3chr8

27507219

+
intron-3CDSENST00000519047ENST00000337221HMBOX1chr8

28748536

-SCARA3chr8

27507219

+
intron-3CDSENST00000519047ENST00000301904HMBOX1chr8

28748536

-SCARA3chr8

27507219

+
intron-3CDSENST00000355231ENST00000337221HMBOX1chr8

28748536

-SCARA3chr8

27507219

+
intron-3CDSENST00000355231ENST00000301904HMBOX1chr8

28748536

-SCARA3chr8

27507219

+
intron-3CDSENST00000524238ENST00000337221HMBOX1chr8

28748536

-SCARA3chr8

27507219

+
intron-3CDSENST00000524238ENST00000301904HMBOX1chr8

28748536

-SCARA3chr8

27507219

+
intron-3CDSENST00000517386ENST00000337221HMBOX1chr8

28748536

-SCARA3chr8

27507219

+
intron-3CDSENST00000517386ENST00000301904HMBOX1chr8

28748536

-SCARA3chr8

27507219

+

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

Top

Fusion Genomic Features for HMBOX1-SCARA3


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)
HMBOX1chr828749001+SCARA3chr827507218+0.0002094910.9997905
HMBOX1chr828749001+SCARA3chr827507218+0.0002094910.9997905

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.

Top

Fusion Protein Features for HMBOX1-SCARA3


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
HMBOX1

Q6NT76

.
FUNCTION: Binds directly to 5'-TTAGGG-3' repeats in telomeric DNA (PubMed:23813958, PubMed:23685356). Associates with the telomerase complex at sites of active telomere processing and positively regulates telomere elongation (PubMed:23685356). Important for TERT binding to chromatin, indicating a role in recruitment of the telomerase complex to telomeres (By similarity). Also plays a role in the alternative lengthening of telomeres (ALT) pathway in telomerase-negative cells where it promotes formation and/or maintenance of ALT-associated promyelocytic leukemia bodies (APBs) (PubMed:23813958). Enhances formation of telomere C-circles in ALT cells, suggesting a possible role in telomere recombination (PubMed:23813958). Might also be involved in the DNA damage response at telomeres (PubMed:23813958). {ECO:0000250|UniProtKB:Q8BJA3, ECO:0000269|PubMed:23685356, ECO:0000269|PubMed:23813958}.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


Top

Fusion Gene Sequence for HMBOX1-SCARA3


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.

Top

Fusion Gene PPI Analysis for HMBOX1-SCARA3


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


Top

Related Drugs for HMBOX1-SCARA3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for HMBOX1-SCARA3


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