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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:CREBL2-PAFAH1B1 (FusionGDB2 ID:HG1389TG5048)

Fusion Gene Summary for CREBL2-PAFAH1B1

check button Fusion gene summary
Fusion gene informationFusion gene name: CREBL2-PAFAH1B1
Fusion gene ID: hg1389tg5048
HgeneTgene
Gene symbol

CREBL2

PAFAH1B1

Gene ID

1389

5048

Gene namecAMP responsive element binding protein like 2platelet activating factor acetylhydrolase 1b regulatory subunit 1
Synonyms-LIS1|LIS2|MDCR|MDS|NudF|PAFAH
Cytomap('CREBL2')('PAFAH1B1')

12p13.1

17p13.3

Type of geneprotein-codingprotein-coding
DescriptioncAMP-responsive element-binding protein-like 2MHBs-binding protein 1platelet-activating factor acetylhydrolase IB subunit alphalissencephaly 1 proteinplatelet-activating factor acetylhydrolase 1b, regulatory subunit 1 (45kDa)platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit (45kD)platelet-activatin
Modification date2020031320200313
UniProtAcc

O60519

.
Ensembl transtripts involved in fusion geneENST00000540224, ENST00000228865, 
Fusion gene scores* DoF score5 X 2 X 4=4018 X 14 X 8=2016
# samples 418
** MAII scorelog2(4/40*10)=0log2(18/2016*10)=-3.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CREBL2 [Title/Abstract] AND PAFAH1B1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCREBL2(12765121)-PAFAH1B1(2583457), # samples:1
Anticipated loss of major functional domain due to fusion event.CREBL2-PAFAH1B1 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.
CREBL2-PAFAH1B1 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.
CREBL2-PAFAH1B1 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.
CREBL2-PAFAH1B1 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
TgenePAFAH1B1

GO:0007017

microtubule-based process

11940666


check buttonFusion gene breakpoints across CREBL2 (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 PAFAH1B1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check button Fusion gene information
* 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
ChimerDB4OVTCGA-24-1847CREBL2chr12

12765121

+PAFAH1B1chr17

2583457

+


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Fusion Gene ORF analysis for CREBL2-PAFAH1B1

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
3UTR-3CDSENST00000540224ENST00000397195CREBL2chr12

12765121

+PAFAH1B1chr17

2583457

+
3UTR-intronENST00000540224ENST00000451360CREBL2chr12

12765121

+PAFAH1B1chr17

2583457

+
3UTR-intronENST00000540224ENST00000572915CREBL2chr12

12765121

+PAFAH1B1chr17

2583457

+
5CDS-intronENST00000228865ENST00000451360CREBL2chr12

12765121

+PAFAH1B1chr17

2583457

+
5CDS-intronENST00000228865ENST00000572915CREBL2chr12

12765121

+PAFAH1B1chr17

2583457

+
In-frameENST00000228865ENST00000397195CREBL2chr12

12765121

+PAFAH1B1chr17

2583457

+

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)
ENST00000228865CREBL2chr1212765121+ENST00000397195PAFAH1B1chr172583457+43402962912887

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
ENST00000228865ENST00000397195CREBL2chr1212765121+PAFAH1B1chr172583457+0.1176172050.8823828

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Fusion Genomic Features for CREBL2-PAFAH1B1


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)
CREBL2chr1212765121+PAFAH1B1chr172583457+3.14E-060.9999969
CREBL2chr1212765121+PAFAH1B1chr172583457+3.14E-060.9999969

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.
genomic feature

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.
genomic feature of top 1%

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Fusion Protein Features for CREBL2-PAFAH1B1


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/chr12:12765121/chr17:2583457)
- 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
CREBL2

O60519

.
FUNCTION: Probable regulator of CREB1 transcriptional activity which is involved in adipose cells differentiation. May also play a regulatory role in the cell cycle. Identification in a chromosomal region frequently deleted in various cancers suggests that it might act as a tumor suppressor. {ECO:0000269|PubMed:9693048}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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
TgenePAFAH1B1chr12:12765121chr17:2583457ENST00000397195811336_377334411.0RepeatNote=WD 6
TgenePAFAH1B1chr12:12765121chr17:2583457ENST00000397195811378_410334411.0RepeatNote=WD 7

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCREBL2chr12:12765121chr17:2583457ENST00000228865+1423_865121.0DomainNote=bZIP
HgeneCREBL2chr12:12765121chr17:2583457ENST00000228865+1429_605121.0RegionBasic motif
HgeneCREBL2chr12:12765121chr17:2583457ENST00000228865+1462_695121.0RegionLeucine-zipper
TgenePAFAH1B1chr12:12765121chr17:2583457ENST0000039719581156_82334411.0Coiled coilOntology_term=ECO:0000255
TgenePAFAH1B1chr12:12765121chr17:2583457ENST000003971958117_39334411.0DomainLisH
TgenePAFAH1B1chr12:12765121chr17:2583457ENST00000397195811106_147334411.0RepeatNote=WD 1
TgenePAFAH1B1chr12:12765121chr17:2583457ENST00000397195811148_187334411.0RepeatNote=WD 2
TgenePAFAH1B1chr12:12765121chr17:2583457ENST00000397195811190_229334411.0RepeatNote=WD 3
TgenePAFAH1B1chr12:12765121chr17:2583457ENST00000397195811232_271334411.0RepeatNote=WD 4
TgenePAFAH1B1chr12:12765121chr17:2583457ENST00000397195811274_333334411.0RepeatNote=WD 5


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Fusion Gene Sequence for CREBL2-PAFAH1B1


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.
>19400_19400_1_CREBL2-PAFAH1B1_CREBL2_chr12_12765121_ENST00000228865_PAFAH1B1_chr17_2583457_ENST00000397195_length(transcript)=4340nt_BP=296nt
CAGAGCGTCTGTAAACACCCAGAGACTGTCATGGAGGGGGAGGAGGAGGCGGCGGCGGCGAAGGGAGGCGTTTGGGGCCGCCTCCAGGGT
CCGCTCTGCCATTCCTGAACTGGTCCCTCGTCCCCGTGACTCTGGCATCAGGGAAGCGAACTGTTAGGCGAGAGGAGGAGGCAGCCAGAA
CCATATCCCCTTCTTCCTCGGGGCGGGGGCCGGGCCAGGCCGGCTGAGCCGGGGGAGGGCTCCGGGAGGGAGTGCCTGGCCAGGCCGGCC
TGTCTGCCGCGATGGATGACAGTAAGGTGGGTCATGATAACTGGGTACGTGGAGTTCTGTTCCATTCTGGGGGGAAGTTTATTTTGAGTT
GTGCTGATGACAAGACCCTACGCGTATGGGATTACAAGAACAAGCGATGCATGAAGACCCTCAATGCGCATGAACACTTTGTTACCTCCT
TGGATTTCCACAAGACGGCACCCTATGTCGTCACTGGCAGCGTAGATCAAACAGTAAAAGTGTGGGAGTGCCGTTGATTGTGTCTCCTTC
GGCCCCTCCTCCCTCTTTTCCTCTGGATGCACTCTGATGATACCATGGTTACCCCATTGAGCTCTGTTTAAATAAATATTGTCCTTTCAT
GTAAATTATTCTGGATGTAGATTGAGCTTATTAAATGTTACACACAAAGTATTCATGCATGGTGAATCCAAATTGTATACTGTAAATTTA
CATACGTTGTCTAGAAGTACCATAGGGTTTAAAAACCTGGGCTGGCATTGGTCACACCAGGCCTAAGAAGGCAGAAGTTGAATCAATTGA
ACTAGGGCACTAAACTGAATAGTTGACAGTGTCATTTTATGTTGGATTATTAATTCCTGTTTTTCTTTCTGCTATCTGTTGGTGCCTGAC
TTGATGGCCTCATTTGGGGAAAAGTGGTGGTTATTAGGGCTTTTTCTGAAATGTGTATCTATGTAACATCACTTAAGTGTGCTTAATAAA
TCTTCTGTAAGGATTTTAGATGATAAGGCTACAATTCAGAATCTTCTGAACCATCTATGTAATGAATGGGGATTATACATTGGAATTTTT
GTCATGACACATTTGCCAAATCAGTAGGATATATTTGTTTTGGCAGCCTATCACGCAGAGGCTAGTGGTATATTTATGTAAGAAAATGAC
TGTAAATCTCAAGAAAAATCTCAGCAGCTAATAGCAACTCATTTATTTCATTTTGGTCTTAATGCTTTGTAAACAGGTCAAAAAATACTG
TCATACTCTAAGCTTCTATTTTCCACACTGGACATACTTCTAGTTGTATTCTCCATACTATTAGACTGTGTAGTGATGTGACTTCCAAGT
AGAATTTAATCTCCCCATTGAGTGTGTCATGGTACAAATCACTATTCGTTTTTGGTGTTTTTTAGGGATGTGCAATGTGCATTACATAAT
GACAGAAATACTGAGAAGGTTCTGTGTGCCCATTTGAAAGGAGTGGGAGGAATACAGCAGTTTGTTTTTCAACATGAATCTGATATTGAT
TTAAACTGTGTTTCACTTACAAGTTTTAAAAAAATGACAGGGTTTAATGGAGCGTGCATAAAAATGTACTGTTTTCACCTTTTGTTTATA
TGTAAATGTTTGTAAGTATATGGGCCTATCTGTAAGTGGATAAGTCTGTATGTGTGTATCATACACATCAACCTCCATGTCCTTAGTCCT
GGGTTTTTGAAAAAGTGCTAAAACGGACAAGTAGAATAAATGTTGCTGTGGAATGCCATGCTTTAGAACAAACCCTTTTTGATCTTAATG
CTTCTGAAAACTAGGTCTGACTCTGGGGATTTTTTTCCAGCCGAAGGAAAATCACTTCCGTTATGTCCCCCTCTAATTTAGCCGCTCGAC
ATTTTACACAACCCGGATATGTTGTATATTTTGACCCAAAGTTACAGGTAGGTTTAAGAGAATTTTTAGCCATGACTTTTGGAGCACTAT
TCCATTGTCAGTTATTAATAAAGAATTCCATTGCTTAGCTAACCAACAGGTTTTTTTTGTTTCCAAGAGAGTTATTTGAAAAGTTAACAG
AACAATGAGATAACAGTGACAGTTTAACAAAGATAAAATTCTGAACTGCGTTTTATTCATTTGTGTACTATGTGATTTTTTAAATGTCCC
CTTTAGTATTTAATGGAAAATTGGTTCCTGCAAAAGACAAAGGGTGAGAGTTAGCGTCCTGTAGATACACACAGAGACTAGGCCGTATAT
TAACTAGAAGCAGCTTTATGTCTAGCTTGTGTCTTTTTGTTTGTTTGCTTGTTTGTTTTTAGATTCCTGAGAGATGTCTCTGGAAGGGAA
AGTTTTGAGAACTAATGGCTATTTTTGAGGACAAAAATTACATCTTAAGCTAATTCCTTAAATACATACAGTAGGTGAATTTTCAGGACA
ATATTGCCTCACAACCCTGCTTACATTGAAAAGTCTTTTTCCCTTAGCTCTTCTGACTGGATTTTTCTACAAAAACTATGGAAAATATCT
TTGTTCTTGTTTGCTGCTATTTTCTGTCCTATTTTGAGAAATATAAATACATAGAAATGGTGCATCTTAACATTTGTTTGTACATGTATA
AATGTCTTGTATTTTAATTCATTTTTAGCATGAATTGTTTAAGGGTAAGCCACAACATCTAGAAATCACTCATAGATATTGAACAATAAA
GGAGAATGGTACCGATGCAGGAGGAAGCAAGCGTGTCTTCCCCTGCAGCACACAGCGACTTGCGTTGACAAAGGAGGAGGAAACGATTAC
TCTGTAAACAAAGTTATCCTTACTTGGGAGATTGCCACAGCCTGCTGCTGAGTTGAGTTACCAGACATCCTCCATGTGAGAAGCAGCGAA
CATTGAATCTCAGGGATGGCCCACAACTGGGTCCACATGTAATGAGCCCTGTTTAATAACGAAGGGGTGGGGGAGAGCAGTCCGTCTACA
ACCTGGAATCAGATTTGCAAAATTTCCTGCACTGCTGTCTGACACTGTCCTGTTGATGCCCTTTCTGACTGTGTTCTCTGTTTTCTCTGT
CTGCTGTCTAACCCTGTGCCTTGCCTGGGATAAGGACAATGATGAGGTTACTGGTTTGGATTGTAAGTAGAGGACTTTTATTAATTGGTT
TAGAGGTTCACTGCTGCTTTGTCACTTTCTCAATCAAATTGGCCACTTAAGAAATAAAGAGCTGGTAGAATTGCATCCTCAGATGATTAT
TGACTGTGTGTGTGTGTGAAAACAGACATTCCAGTGCCACCCAAATATATATCTGTAACGTGCCCAAGAAATCCTAGCTGCGCTCTTGAG
AGTGCATGCCATGGAGACTGGTTTAGACACCGCGTGGAGCCTAGTTGCCTGTTGTCACGGCATCTTGCACTTTAGGAGACTAAGACCGTC
CTGGTTCGTCTGTGTGTGGTGTGACCAATGGTGTGCCCAGAGCACTACTCTCAAAATCACTAGTGTTAGCAAGTCGTCCCGGGCTGGGGA
GCGTTCGCCGTAGTCTTTGGAAGCTTTGGCTTTAGATTTACCAAGCCCCGCCTCCCCGCTGCCAGTGCCCTGCTCTCCCGTTCGCCTCTT
TCTGTTTCTGTGTGAACTTTCCCGGTAATATCACTCGTTAAATAGGTTTTCTTTAAACTTAATTAAAGAAAAACTATTTAAAGGTAAAGG
ATATTTTGTTGACATCGGTGGCTCGATCATCCTTAAGCAACTGAAGTTAAAATTGTTGAAGGAAAAGGCACTTAAATTGGTTACTTTCAT
GTCCAGCTGTATATAAGTCCAGTGTGTTCATCTAGATGACGCAAAGAATCTCCTGGTAGAGAAGCGACATGTAAAAAACTGGTGGAAAAA
GGTTTTGGATTTTTTTTCCAGTGGGGTGGGGGGAGGGCAAGCTGGATTTACAGGTCACGGCTGGACTGAATGGGCCTTTTTATCTTCCCA
CTGTATCATGGAAGTAGCTGCTTGCTTGTACTGTCCATCCTTCAGGCATCCCTAAAGCTCACTCTGAAGATGTTAGAGACAAACACAAAC
TCTTCGAGTTAAAGTTGATCCTGACACTGACATGAAGGCAAGCCTTGATTTCGTATGAACGTTGCTGAAGTGGTAATTGAGGAAAACAGT
TCCCCAGATTGTTAAGAGTTCACTGAAGATATTGACACAATTTTAAAAAATCAGTAAAGGAATGTATATAATATTGCTCTCGTGTTTTAC
AGTAAGATTTGTTGCTCTCAGACTGTGTAAAACAAAATTTATTCATGTTTTCTGCATATTAAAAAATCTTATTGTACCAACTGGTAAACT

>19400_19400_1_CREBL2-PAFAH1B1_CREBL2_chr12_12765121_ENST00000228865_PAFAH1B1_chr17_2583457_ENST00000397195_length(amino acids)=87AA_BP=

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

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Fusion Gene PPI Analysis for CREBL2-PAFAH1B1


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
TgenePAFAH1B1chr12:12765121chr17:2583457ENST00000397195811367_409334.0411.0DCX
TgenePAFAH1B1chr12:12765121chr17:2583457ENST00000397195811388_410334.0411.0NDEL1


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with
TgenePAFAH1B1chr12:12765121chr17:2583457ENST0000039719581183_410334.0411.0dynein and dynactin
TgenePAFAH1B1chr12:12765121chr17:2583457ENST000003971958111_66334.0411.0NDE1
TgenePAFAH1B1chr12:12765121chr17:2583457ENST000003971958111_102334.0411.0NDEL1


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 CREBL2-PAFAH1B1


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 CREBL2-PAFAH1B1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0431375Classical Lissencephaly9GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0036341Schizophrenia1PSYGENET
TgeneC0265219Miller Dieker syndrome1ORPHANET
TgeneC0596263Carcinogenesis1CTD_human
TgeneC1848201Subcortical Band Heterotopia1GENOMICS_ENGLAND;ORPHANET
TgeneC2750748Chromosome 17p13.3 Duplication Syndrome1ORPHANET