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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:RASSF3-KRT6B

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: RASSF3-KRT6B
FusionPDB ID: 72493
FusionGDB2.0 ID: 72493
HgeneTgene
Gene symbol

RASSF3

KRT6B

Gene ID

283349

3854

Gene nameRas association domain family member 3keratin 6B
SynonymsRASSF5CK-6B|CK6B|K6B|KRTL1|PC2|PC4
Cytomap

12q14.2

12q13.13

Type of geneprotein-codingprotein-coding
Descriptionras association domain-containing protein 3Ras association (RalGDS/AF-6) domain family 3Ras association (RalGDS/AF-6) domain family member 3keratin, type II cytoskeletal 6Bcytokeratin 6Bkeratin 6B, type IIkeratin, epidermal, type II, K6Bkeratin-like 1 (a type II keratin sequence)type-II keratin Kb10
Modification date2020032720200313
UniProtAcc.

P04259

Ensembl transtripts involved in fusion geneENST idsENST00000540088, ENST00000336061, 
ENST00000542104, 
ENST00000252252, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score18 X 7 X 12=15121 X 1 X 1=1
# samples 181
** MAII scorelog2(18/1512*10)=-3.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(1/1*10)=3.32192809488736
Context (manual curation of fusion genes in FusionPDB)

PubMed: RASSF3 [Title/Abstract] AND KRT6B [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)RASSF3(65004523)-KRT6B(52844404), # samples:1
Anticipated loss of major functional domain due to fusion event.RASSF3-KRT6B seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
RASSF3-KRT6B seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
RASSF3-KRT6B seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
RASSF3-KRT6B seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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

check buttonFusion gene breakpoints across RASSF3 (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 KRT6B (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4SARCTCGA-3B-A9HO-01ARASSF3chr12

65004523

+KRT6Bchr12

52844404

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000336061RASSF3chr1265004523+ENST00000252252KRT6Bchr1252844404-184815411308435
ENST00000542104RASSF3chr1265004523+ENST00000252252KRT6Bchr1252844404-1925231121385457

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
ENST00000336061ENST00000252252RASSF3chr1265004523+KRT6Bchr1252844404-0.0011157160.99888426
ENST00000542104ENST00000252252RASSF3chr1265004523+KRT6Bchr1252844404-0.0011581080.99884194

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>72493_72493_1_RASSF3-KRT6B_RASSF3_chr12_65004523_ENST00000336061_KRT6B_chr12_52844404_ENST00000252252_length(amino acids)=435AA_BP=48
LHKDCPGLRDGTGSMSSGYSSLEEDAEDFFFTARTSFFRRAPQGKPRSGQQVRFLEQQNKVLDTKWTLLQEQGTKTVRQNLEPLFEQYIN
NLRRQLDNIVGERGRLDSELRNMQDLVEDLKNKYEDEINKRTAAENEFVTLKKDVDAAYMNKVELQAKADTLTDEINFLRALYDAELSQM
QTHISDTSVVLSMDNNRNLDLDSIIAEVKAQYEEIAQRSRAEAESWYQTKYEELQITAGRHGDDLRNTKQEIAEINRMIQRLRSEIDHVK
KQCANLQAAIADAEQRGEMALKDAKNKLEGLEDALQKAKQDLARLLKEYQELMNVKLALDVEIATYRKLLEGEECRLNGEGVGQVNISVV

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

>72493_72493_2_RASSF3-KRT6B_RASSF3_chr12_65004523_ENST00000542104_KRT6B_chr12_52844404_ENST00000252252_length(amino acids)=457AA_BP=70
MPGAARREPRGAGGRRTPSLAACAPGRPPARDGTGSMSSGYSSLEEDAEDFFFTARTSFFRRAPQGKPRSGQQVRFLEQQNKVLDTKWTL
LQEQGTKTVRQNLEPLFEQYINNLRRQLDNIVGERGRLDSELRNMQDLVEDLKNKYEDEINKRTAAENEFVTLKKDVDAAYMNKVELQAK
ADTLTDEINFLRALYDAELSQMQTHISDTSVVLSMDNNRNLDLDSIIAEVKAQYEEIAQRSRAEAESWYQTKYEELQITAGRHGDDLRNT
KQEIAEINRMIQRLRSEIDHVKKQCANLQAAIADAEQRGEMALKDAKNKLEGLEDALQKAKQDLARLLKEYQELMNVKLALDVEIATYRK
LLEGEECRLNGEGVGQVNISVVQSTVSSGYGGASGVGSGLGLGGGSSYSYGSGLGVGGGFSSSSGRATGGGLSSVGGGSSTIKYTTTSSS

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Fusion Protein Functional Features


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/chr12:65004523/chr12:52844404)
- 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
.KRT6B

P04259

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneKRT6Bchr12:65004523chr12:52844404ENST0000025225209199_217180.0565.0RegionNote=Linker 1
TgeneKRT6Bchr12:65004523chr12:52844404ENST0000025225209218_309180.0565.0RegionNote=Coil 1B
TgeneKRT6Bchr12:65004523chr12:52844404ENST0000025225209310_333180.0565.0RegionNote=Linker 12
TgeneKRT6Bchr12:65004523chr12:52844404ENST0000025225209334_472180.0565.0RegionNote=Coil 2
TgeneKRT6Bchr12:65004523chr12:52844404ENST0000025225209473_564180.0565.0RegionNote=Tail

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneRASSF3chr12:65004523chr12:52844404ENST00000336061+26187_23437.0239.0DomainSARAH
HgeneRASSF3chr12:65004523chr12:52844404ENST00000336061+2679_18637.0239.0DomainRas-associating
HgeneRASSF3chr12:65004523chr12:52844404ENST00000542104+15187_23437.0239.0DomainSARAH
HgeneRASSF3chr12:65004523chr12:52844404ENST00000542104+1579_18637.0239.0DomainRas-associating
TgeneKRT6Bchr12:65004523chr12:52844404ENST0000025225209163_476180.0565.0DomainIF rod
TgeneKRT6Bchr12:65004523chr12:52844404ENST0000025225209163_198180.0565.0RegionNote=Coil 1A
TgeneKRT6Bchr12:65004523chr12:52844404ENST00000252252092_162180.0565.0RegionNote=Head


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
RASSF3
KRT6B


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to RASSF3-KRT6B


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to RASSF3-KRT6B


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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