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Center for Computational Systems Medicine level2
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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 Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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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:FAF1-TTC39A

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: FAF1-TTC39A
FusionPDB ID: 28253
FusionGDB2.0 ID: 28253
HgeneTgene
Gene symbol

FAF1

TTC39A

Gene ID

11124

22996

Gene nameFas associated factor 1tetratricopeptide repeat domain 39A
SynonymsCGI-03|HFAF1s|UBXD12|UBXN3A|hFAF1C1orf34|DEME-6
Cytomap

1p32.3

1p32.3

Type of geneprotein-codingprotein-coding
DescriptionFAS-associated factor 1Fas (TNFRSF6) associated factor 1TNFRSF6-associated factor 1UBX domain protein 3AUBX domain-containing protein 12UBX domain-containing protein 3Atetratricopeptide repeat protein 39ATPR repeat protein 39Adifferentially expressed in MCF7 with estradiol protein 6testicular tissue protein Li 213
Modification date2020031320200313
UniProtAcc

Q9UNN5

.
Ensembl transtripts involved in fusion geneENST idsENST00000371778, ENST00000396153, 
ENST00000472808, ENST00000545823, 
ENST00000530004, ENST00000262676, 
ENST00000534098, ENST00000262675, 
ENST00000371747, ENST00000371750, 
ENST00000413473, ENST00000447632, 
ENST00000451380, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score23 X 21 X 9=43476 X 6 X 4=144
# samples 316
** MAII scorelog2(31/4347*10)=-3.80967997500385
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(6/144*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: FAF1 [Title/Abstract] AND TTC39A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)FAF1(51121114)-TTC39A(51761842), # samples:3
Anticipated loss of major functional domain due to fusion event.FAF1-TTC39A 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.
FAF1-TTC39A 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.
FAF1-TTC39A 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.
FAF1-TTC39A 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.
FAF1-TTC39A seems lost the major protein functional domain in Hgene partner, which is a essential gene 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
HgeneFAF1

GO:0010942

positive regulation of cell death

15596450


check buttonFusion gene breakpoints across FAF1 (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 TTC39A (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
ChimerDB4PRADTCGA-ZG-A9KY-01AFAF1chr1

51121114

-TTC39Achr1

51761842

-
ChimerDB4PRADTCGA-ZG-A9KYFAF1chr1

51121114

-TTC39Achr1

51761842

-


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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)
ENST00000396153FAF1chr151121114-ENST00000447632TTC39Achr151761842-277611961401876578
ENST00000396153FAF1chr151121114-ENST00000413473TTC39Achr151761842-277611961401876578
ENST00000396153FAF1chr151121114-ENST00000262675TTC39Achr151761842-222211961401876578
ENST00000396153FAF1chr151121114-ENST00000451380TTC39Achr151761842-222211961401876578
ENST00000396153FAF1chr151121114-ENST00000371750TTC39Achr151761842-206411961401876578
ENST00000396153FAF1chr151121114-ENST00000371747TTC39Achr151761842-182911961401318392

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
ENST00000396153ENST00000447632FAF1chr151121114-TTC39Achr151761842-0.001360880.99863917
ENST00000396153ENST00000413473FAF1chr151121114-TTC39Achr151761842-0.001360880.99863917
ENST00000396153ENST00000262675FAF1chr151121114-TTC39Achr151761842-0.0022438340.9977562
ENST00000396153ENST00000451380FAF1chr151121114-TTC39Achr151761842-0.0022438340.9977562
ENST00000396153ENST00000371750FAF1chr151121114-TTC39Achr151761842-0.0027995010.9972005
ENST00000396153ENST00000371747FAF1chr151121114-TTC39Achr151761842-0.0017037450.9982963

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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

>28253_28253_1_FAF1-TTC39A_FAF1_chr1_51121114_ENST00000396153_TTC39A_chr1_51761842_ENST00000262675_length(amino acids)=578AA_BP=352
MPSSWPATVRPDPHPDQSSCPGCCDAGSAGCRRAAGAPEGYRVHERLALPALPRPLARRPARRLARQPLGARRRRRRWRRRSQEVPSASQ
VRASLPEPRNSAAAMASNMDREMILADFQACTGIENIDEAITLLEQNNWDLVAAINGVIPQENGILQSEYGGETIPGPAFNPASHPASAP
TSSSSSAFRPVMPSRQIVERQPRMLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGDVEDSTVLKSLHLPKNNS
LYVLTPDLPPPSSSSHAGALQESLNQNFMLIITHREVQREYNLNFSGSSTIQEVKRNVYDLTSIPVRHQLWEGWPTSATDDSATYIYMKA
AYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAGKSLPTEKFAIRKSRRYFSSNPISLPVPALEMMYIWNGYAVIGKQPKLTDGILEIIT
KAEEMLEKGPENEYSVDDECLVKLLKGLCLKYLGRVQEAEENFRSISANEKKIKYDHYLIPNALLELALLLMEQDRNEEAIKLLESAKQN

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

>28253_28253_2_FAF1-TTC39A_FAF1_chr1_51121114_ENST00000396153_TTC39A_chr1_51761842_ENST00000371747_length(amino acids)=392AA_BP=352
MPSSWPATVRPDPHPDQSSCPGCCDAGSAGCRRAAGAPEGYRVHERLALPALPRPLARRPARRLARQPLGARRRRRRWRRRSQEVPSASQ
VRASLPEPRNSAAAMASNMDREMILADFQACTGIENIDEAITLLEQNNWDLVAAINGVIPQENGILQSEYGGETIPGPAFNPASHPASAP
TSSSSSAFRPVMPSRQIVERQPRMLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGDVEDSTVLKSLHLPKNNS
LYVLTPDLPPPSSSSHAGALQESLNQNFMLIITHREVQREYNLNFSGSSTIQEVKRNVYDLTSIPVRHQLWEGWPTSATDDSATYIYMKA

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

>28253_28253_3_FAF1-TTC39A_FAF1_chr1_51121114_ENST00000396153_TTC39A_chr1_51761842_ENST00000371750_length(amino acids)=578AA_BP=352
MPSSWPATVRPDPHPDQSSCPGCCDAGSAGCRRAAGAPEGYRVHERLALPALPRPLARRPARRLARQPLGARRRRRRWRRRSQEVPSASQ
VRASLPEPRNSAAAMASNMDREMILADFQACTGIENIDEAITLLEQNNWDLVAAINGVIPQENGILQSEYGGETIPGPAFNPASHPASAP
TSSSSSAFRPVMPSRQIVERQPRMLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGDVEDSTVLKSLHLPKNNS
LYVLTPDLPPPSSSSHAGALQESLNQNFMLIITHREVQREYNLNFSGSSTIQEVKRNVYDLTSIPVRHQLWEGWPTSATDDSATYIYMKA
AYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAGKSLPTEKFAIRKSRRYFSSNPISLPVPALEMMYIWNGYAVIGKQPKLTDGILEIIT
KAEEMLEKGPENEYSVDDECLVKLLKGLCLKYLGRVQEAEENFRSISANEKKIKYDHYLIPNALLELALLLMEQDRNEEAIKLLESAKQN

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

>28253_28253_4_FAF1-TTC39A_FAF1_chr1_51121114_ENST00000396153_TTC39A_chr1_51761842_ENST00000413473_length(amino acids)=578AA_BP=352
MPSSWPATVRPDPHPDQSSCPGCCDAGSAGCRRAAGAPEGYRVHERLALPALPRPLARRPARRLARQPLGARRRRRRWRRRSQEVPSASQ
VRASLPEPRNSAAAMASNMDREMILADFQACTGIENIDEAITLLEQNNWDLVAAINGVIPQENGILQSEYGGETIPGPAFNPASHPASAP
TSSSSSAFRPVMPSRQIVERQPRMLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGDVEDSTVLKSLHLPKNNS
LYVLTPDLPPPSSSSHAGALQESLNQNFMLIITHREVQREYNLNFSGSSTIQEVKRNVYDLTSIPVRHQLWEGWPTSATDDSATYIYMKA
AYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAGKSLPTEKFAIRKSRRYFSSNPISLPVPALEMMYIWNGYAVIGKQPKLTDGILEIIT
KAEEMLEKGPENEYSVDDECLVKLLKGLCLKYLGRVQEAEENFRSISANEKKIKYDHYLIPNALLELALLLMEQDRNEEAIKLLESAKQN

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

>28253_28253_5_FAF1-TTC39A_FAF1_chr1_51121114_ENST00000396153_TTC39A_chr1_51761842_ENST00000447632_length(amino acids)=578AA_BP=352
MPSSWPATVRPDPHPDQSSCPGCCDAGSAGCRRAAGAPEGYRVHERLALPALPRPLARRPARRLARQPLGARRRRRRWRRRSQEVPSASQ
VRASLPEPRNSAAAMASNMDREMILADFQACTGIENIDEAITLLEQNNWDLVAAINGVIPQENGILQSEYGGETIPGPAFNPASHPASAP
TSSSSSAFRPVMPSRQIVERQPRMLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGDVEDSTVLKSLHLPKNNS
LYVLTPDLPPPSSSSHAGALQESLNQNFMLIITHREVQREYNLNFSGSSTIQEVKRNVYDLTSIPVRHQLWEGWPTSATDDSATYIYMKA
AYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAGKSLPTEKFAIRKSRRYFSSNPISLPVPALEMMYIWNGYAVIGKQPKLTDGILEIIT
KAEEMLEKGPENEYSVDDECLVKLLKGLCLKYLGRVQEAEENFRSISANEKKIKYDHYLIPNALLELALLLMEQDRNEEAIKLLESAKQN

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

>28253_28253_6_FAF1-TTC39A_FAF1_chr1_51121114_ENST00000396153_TTC39A_chr1_51761842_ENST00000451380_length(amino acids)=578AA_BP=352
MPSSWPATVRPDPHPDQSSCPGCCDAGSAGCRRAAGAPEGYRVHERLALPALPRPLARRPARRLARQPLGARRRRRRWRRRSQEVPSASQ
VRASLPEPRNSAAAMASNMDREMILADFQACTGIENIDEAITLLEQNNWDLVAAINGVIPQENGILQSEYGGETIPGPAFNPASHPASAP
TSSSSSAFRPVMPSRQIVERQPRMLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGDVEDSTVLKSLHLPKNNS
LYVLTPDLPPPSSSSHAGALQESLNQNFMLIITHREVQREYNLNFSGSSTIQEVKRNVYDLTSIPVRHQLWEGWPTSATDDSATYIYMKA
AYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAGKSLPTEKFAIRKSRRYFSSNPISLPVPALEMMYIWNGYAVIGKQPKLTDGILEIIT
KAEEMLEKGPENEYSVDDECLVKLLKGLCLKYLGRVQEAEENFRSISANEKKIKYDHYLIPNALLELALLLMEQDRNEEAIKLLESAKQN

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

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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/chr1:51121114/chr1:51761842)
- 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
FAF1

Q9UNN5

.
FUNCTION: Ubiquitin-binding protein (PubMed:19722279). Required for the progression of DNA replication forks by targeting DNA replication licensing factor CDT1 for degradation (PubMed:26842564). Potentiates but cannot initiate FAS-induced apoptosis (By similarity). {ECO:0000250|UniProtKB:P54731, ECO:0000269|PubMed:19722279, ECO:0000269|PubMed:26842564}.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
HgeneFAF1chr1:51121114chr1:51761842ENST00000371778-9201_57248.0651.0DomainUBA
HgeneFAF1chr1:51121114chr1:51761842ENST00000396153-8191_57248.0651.0DomainUBA
TgeneTTC39Achr1:51121114chr1:51761842ENST00000262676011315_3480421.0RepeatNote=TPR 1
TgeneTTC39Achr1:51121114chr1:51761842ENST00000262676011505_5380421.0RepeatNote=TPR 2
TgeneTTC39Achr1:51121114chr1:51761842ENST00000262676011546_5790421.0RepeatNote=TPR 3
TgeneTTC39Achr1:51121114chr1:51761842ENST000004134731118505_538355.0582.0RepeatNote=TPR 2
TgeneTTC39Achr1:51121114chr1:51761842ENST000004134731118546_579355.0582.0RepeatNote=TPR 3
TgeneTTC39Achr1:51121114chr1:51761842ENST000004476321118505_538387.0614.0RepeatNote=TPR 2
TgeneTTC39Achr1:51121114chr1:51761842ENST000004476321118546_579387.0614.0RepeatNote=TPR 3
TgeneTTC39Achr1:51121114chr1:51761842ENST000004513801118505_538351.0578.0RepeatNote=TPR 2
TgeneTTC39Achr1:51121114chr1:51761842ENST000004513801118546_579351.0578.0RepeatNote=TPR 3
TgeneTTC39Achr1:51121114chr1:51761842ENST0000053000407315_3480222.0RepeatNote=TPR 1
TgeneTTC39Achr1:51121114chr1:51761842ENST0000053000407505_5380222.0RepeatNote=TPR 2
TgeneTTC39Achr1:51121114chr1:51761842ENST0000053000407546_5790222.0RepeatNote=TPR 3

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneFAF1chr1:51121114chr1:51761842ENST00000371778-920569_646248.0651.0DomainUBX
HgeneFAF1chr1:51121114chr1:51761842ENST00000396153-819569_646248.0651.0DomainUBX
TgeneTTC39Achr1:51121114chr1:51761842ENST000004134731118315_348355.0582.0RepeatNote=TPR 1
TgeneTTC39Achr1:51121114chr1:51761842ENST000004476321118315_348387.0614.0RepeatNote=TPR 1
TgeneTTC39Achr1:51121114chr1:51761842ENST000004513801118315_348351.0578.0RepeatNote=TPR 1


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Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file >>>1234_FAF1_51121114_TTC39A_51761842_1234_FAF1_51121114_TTC39A_51761842_ranked_0.pdbFAF15112111451121114ENST00000371747TTC39Achr151761842-
MPSSWPATVRPDPHPDQSSCPGCCDAGSAGCRRAAGAPEGYRVHERLALPALPRPLARRPARRLARQPLGARRRRRRWRRRSQEVPSASQ
VRASLPEPRNSAAAMASNMDREMILADFQACTGIENIDEAITLLEQNNWDLVAAINGVIPQENGILQSEYGGETIPGPAFNPASHPASAP
TSSSSSAFRPVMPSRQIVERQPRMLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGDVEDSTVLKSLHLPKNNS
LYVLTPDLPPPSSSSHAGALQESLNQNFMLIITHREVQREYNLNFSGSSTIQEVKRNVYDLTSIPVRHQLWEGWPTSATDDSATYIYMKA
AYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAGKSLPTEKFAIRKSRRYFSSNPISLPVPALEMMYIWNGYAVIGKQPKLTDGILEIIT
KAEEMLEKGPENEYSVDDECLVKLLKGLCLKYLGRVQEAEENFRSISANEKKIKYDHYLIPNALLELALLLMEQDRNEEAIKLLESAKQN
578


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pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
FAF1_pLDDT.png
all structure
all structure
TTC39A_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
all structure


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Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots

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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
FAF1
TTC39A


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 FAF1-TTC39A


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 FAF1-TTC39A


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