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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:PPP1CB-SALL4

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PPP1CB-SALL4
FusionPDB ID: 67712
FusionGDB2.0 ID: 67712
HgeneTgene
Gene symbol

PPP1CB

SALL4

Gene ID

5500

57167

Gene nameprotein phosphatase 1 catalytic subunit betaspalt like transcription factor 4
SynonymsHEL-S-80p|MP|NSLH2|PP-1B|PP1B|PP1beta|PP1c|PPP1CD|PPP1betaDRRS|HSAL4|ZNF797
Cytomap

2p23.2

20q13.2

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein phosphatase PP1-beta catalytic subunitepididymis secretory sperm binding protein Li 80pmyosin phosphataseprotein phosphatase 1, catalytic subunit, beta isoformprotein phosphatase 1, catalytic subunit, beta isozymeprotein phossal-like protein 4zinc finger protein 797zinc finger protein SALL4
Modification date2020031320200322
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000296122, ENST00000358506, 
ENST00000395366, 
ENST00000483130, 
ENST00000371539, ENST00000395997, 
ENST00000217086, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score18 X 17 X 11=33663 X 3 X 3=27
# samples 353
** MAII scorelog2(35/3366*10)=-3.26560834949762
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)

PubMed: PPP1CB [Title/Abstract] AND SALL4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PPP1CB(29006844)-SALL4(50408891), # samples:2
Anticipated loss of major functional domain due to fusion event.PPP1CB-SALL4 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.
PPP1CB-SALL4 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
HgenePPP1CB

GO:0030155

regulation of cell adhesion

20354225


check buttonFusion gene breakpoints across PPP1CB (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 SALL4 (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
ChimerDB4ESCATCGA-L5-A4OFPPP1CBchr2

29006844

+SALL4chr20

50408891

-


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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)
ENST00000358506PPP1CBchr229006844+ENST00000217086SALL4chr2050408891-40077524637831245
ENST00000296122PPP1CBchr229006844+ENST00000217086SALL4chr2050408891-40457905438211255
ENST00000395366PPP1CBchr229006844+ENST00000217086SALL4chr2050408891-411986423338951220

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
ENST00000358506ENST00000217086PPP1CBchr229006844+SALL4chr2050408891-0.0010131380.9989869
ENST00000296122ENST00000217086PPP1CBchr229006844+SALL4chr2050408891-0.0009663830.9990337
ENST00000395366ENST00000217086PPP1CBchr229006844+SALL4chr2050408891-0.0008851410.9991148

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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

>67712_67712_1_PPP1CB-SALL4_PPP1CB_chr2_29006844_ENST00000296122_SALL4_chr20_50408891_ENST00000217086_length(amino acids)=1255AA_BP=244
MGLTRPCSRGPLLFIYLFSVRERRAVAAASAAEKPLFPLLGRRVCADKMADGELNVDSLITRLLEVRGCRPGKIVQMTEAEVRGLCIKSR
EIFLSQPILLELEAPLKICGDIHGQYTDLLRLFEYGGFPPEANYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRI
YGFYDECKRRFNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDTGAPVNHPGNDEVASEDEATVKRLRR
EETHVCEKCCAEFFSISEFLEHKKNCTKNPPVLIMNDSEGPVPSEDFSGAVLSHQPTSPGSKDCHRENGGSSEDMKEKPDAESVVYLKTE
TALPPTPQDISYLAKGKVANTNVTLQALRGTKVAVNQRSADALPAPVPGANSIPWVLEQILCLQQQQLQQIQLTEQIRIQVNMWASHALH
SSGAGADTLKTLGSHMSQQVSAAVALLSQKAGSQGLSLDALKQAKLPHANIPSATSSLSPGLAPFTLKPDGTRVLPNVMSRLPSALLPQA
PGSVLFQSPFSTVALDTSKKGKGKPPNISAVDVKPKDEAALYKHKCKYCSKVFGTDSSLQIHLRSHTGERPFVCSVCGHRFTTKGNLKVH
FHRHPQVKANPQLFAEFQDKVAAGNGIPYALSVPDPIDEPSLSLDSKPVLVTTSVGLPQNLSSGTNPKDLTGGSLPGDLQPGPSPESEGG
PTLPGVGPNYNSPRAGGFQGSGTPEPGSETLKLQQLVENIDKATTDPNECLICHRVLSCQSSLKMHYRTHTGERPFQCKICGRAFSTKGN
LKTHLGVHRTNTSIKTQHSCPICQKKFTNAVMLQQHIRMHMGGQIPNTPLPENPCDFTGSEPMTVGENGSTGAICHDDVIESIDVEEVSS
QEAPSSSSKVPTPLPSIHSASPTLGFAMMASLDAPGKVGPAPFNLQRQGSRENGSVESDGLTNDSSSLMGDQEYQSRSPDILETTSFQAL
SPANSQAESIKSKSPDAGSKAESSENSRTEMEGRSSLPSTFIRAPPTYVKVEVPGTFVGPSTLSPGMTPLLAAQPRRQAKQHGCTRCGKN
FSSASALQIHERTHTGEKPFVCNICGRAFTTKGNLKVHYMTHGANNNSARRGRKLAIENTMALLGTDGKRVSEIFPKEILAPSVNVDPVV

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>67712_67712_2_PPP1CB-SALL4_PPP1CB_chr2_29006844_ENST00000358506_SALL4_chr20_50408891_ENST00000217086_length(amino acids)=1245AA_BP=234
MRVGPSAALVRERRAVAAASAAEKPLFPLLGRRVCADKMADGELNVDSLITRLLEVRGCRPGKIVQMTEAEVRGLCIKSREIFLSQPILL
ELEAPLKICGDIHGQYTDLLRLFEYGGFPPEANYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRR
FNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDTGAPVNHPGNDEVASEDEATVKRLRREETHVCEKCC
AEFFSISEFLEHKKNCTKNPPVLIMNDSEGPVPSEDFSGAVLSHQPTSPGSKDCHRENGGSSEDMKEKPDAESVVYLKTETALPPTPQDI
SYLAKGKVANTNVTLQALRGTKVAVNQRSADALPAPVPGANSIPWVLEQILCLQQQQLQQIQLTEQIRIQVNMWASHALHSSGAGADTLK
TLGSHMSQQVSAAVALLSQKAGSQGLSLDALKQAKLPHANIPSATSSLSPGLAPFTLKPDGTRVLPNVMSRLPSALLPQAPGSVLFQSPF
STVALDTSKKGKGKPPNISAVDVKPKDEAALYKHKCKYCSKVFGTDSSLQIHLRSHTGERPFVCSVCGHRFTTKGNLKVHFHRHPQVKAN
PQLFAEFQDKVAAGNGIPYALSVPDPIDEPSLSLDSKPVLVTTSVGLPQNLSSGTNPKDLTGGSLPGDLQPGPSPESEGGPTLPGVGPNY
NSPRAGGFQGSGTPEPGSETLKLQQLVENIDKATTDPNECLICHRVLSCQSSLKMHYRTHTGERPFQCKICGRAFSTKGNLKTHLGVHRT
NTSIKTQHSCPICQKKFTNAVMLQQHIRMHMGGQIPNTPLPENPCDFTGSEPMTVGENGSTGAICHDDVIESIDVEEVSSQEAPSSSSKV
PTPLPSIHSASPTLGFAMMASLDAPGKVGPAPFNLQRQGSRENGSVESDGLTNDSSSLMGDQEYQSRSPDILETTSFQALSPANSQAESI
KSKSPDAGSKAESSENSRTEMEGRSSLPSTFIRAPPTYVKVEVPGTFVGPSTLSPGMTPLLAAQPRRQAKQHGCTRCGKNFSSASALQIH
ERTHTGEKPFVCNICGRAFTTKGNLKVHYMTHGANNNSARRGRKLAIENTMALLGTDGKRVSEIFPKEILAPSVNVDPVVWNQYTSMLNG

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

>67712_67712_3_PPP1CB-SALL4_PPP1CB_chr2_29006844_ENST00000395366_SALL4_chr20_50408891_ENST00000217086_length(amino acids)=1220AA_BP=209
MFPLLGRRVCADKMADGELNVDSLITRLLEVRGCRPGKIVQMTEAEVRGLCIKSREIFLSQPILLELEAPLKICGDIHGQYTDLLRLFEY
GGFPPEANYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRFNIKLWKTFTDCFNCLPIAAIVDEK
IFCCHGGLSPDLQSMEQIRRIMRPTDVPDTGAPVNHPGNDEVASEDEATVKRLRREETHVCEKCCAEFFSISEFLEHKKNCTKNPPVLIM
NDSEGPVPSEDFSGAVLSHQPTSPGSKDCHRENGGSSEDMKEKPDAESVVYLKTETALPPTPQDISYLAKGKVANTNVTLQALRGTKVAV
NQRSADALPAPVPGANSIPWVLEQILCLQQQQLQQIQLTEQIRIQVNMWASHALHSSGAGADTLKTLGSHMSQQVSAAVALLSQKAGSQG
LSLDALKQAKLPHANIPSATSSLSPGLAPFTLKPDGTRVLPNVMSRLPSALLPQAPGSVLFQSPFSTVALDTSKKGKGKPPNISAVDVKP
KDEAALYKHKCKYCSKVFGTDSSLQIHLRSHTGERPFVCSVCGHRFTTKGNLKVHFHRHPQVKANPQLFAEFQDKVAAGNGIPYALSVPD
PIDEPSLSLDSKPVLVTTSVGLPQNLSSGTNPKDLTGGSLPGDLQPGPSPESEGGPTLPGVGPNYNSPRAGGFQGSGTPEPGSETLKLQQ
LVENIDKATTDPNECLICHRVLSCQSSLKMHYRTHTGERPFQCKICGRAFSTKGNLKTHLGVHRTNTSIKTQHSCPICQKKFTNAVMLQQ
HIRMHMGGQIPNTPLPENPCDFTGSEPMTVGENGSTGAICHDDVIESIDVEEVSSQEAPSSSSKVPTPLPSIHSASPTLGFAMMASLDAP
GKVGPAPFNLQRQGSRENGSVESDGLTNDSSSLMGDQEYQSRSPDILETTSFQALSPANSQAESIKSKSPDAGSKAESSENSRTEMEGRS
SLPSTFIRAPPTYVKVEVPGTFVGPSTLSPGMTPLLAAQPRRQAKQHGCTRCGKNFSSASALQIHERTHTGEKPFVCNICGRAFTTKGNL
KVHYMTHGANNNSARRGRKLAIENTMALLGTDGKRVSEIFPKEILAPSVNVDPVVWNQYTSMLNGGLAVKTNEISVIQSGGVPTLPVSLG

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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/chr2:29006844/chr20:50408891)
- 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
..
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.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
TgeneSALL4chr2:29006844chr20:50408891ENST0000021708604382_40443.3333333333333361054.0Zinc fingerC2H2-type 2
TgeneSALL4chr2:29006844chr20:50408891ENST0000021708604410_43243.3333333333333361054.0Zinc fingerC2H2-type 3
TgeneSALL4chr2:29006844chr20:50408891ENST0000021708604566_58843.3333333333333361054.0Zinc fingerC2H2-type 4
TgeneSALL4chr2:29006844chr20:50408891ENST0000021708604594_61643.3333333333333361054.0Zinc fingerC2H2-type 5
TgeneSALL4chr2:29006844chr20:50408891ENST0000021708604626_64843.3333333333333361054.0Zinc fingerC2H2-type 6
TgeneSALL4chr2:29006844chr20:50408891ENST000002170860472_9443.3333333333333361054.0Zinc fingerC2H2-type 1%3B atypical
TgeneSALL4chr2:29006844chr20:50408891ENST0000021708604870_89243.3333333333333361054.0Zinc fingerC2H2-type 7
TgeneSALL4chr2:29006844chr20:50408891ENST0000021708604898_92043.3333333333333361054.0Zinc fingerC2H2-type 8
TgeneSALL4chr2:29006844chr20:50408891ENST0000039599704382_40443.333333333333336617.0Zinc fingerC2H2-type 2
TgeneSALL4chr2:29006844chr20:50408891ENST0000039599704410_43243.333333333333336617.0Zinc fingerC2H2-type 3
TgeneSALL4chr2:29006844chr20:50408891ENST0000039599704566_58843.333333333333336617.0Zinc fingerC2H2-type 4
TgeneSALL4chr2:29006844chr20:50408891ENST0000039599704594_61643.333333333333336617.0Zinc fingerC2H2-type 5
TgeneSALL4chr2:29006844chr20:50408891ENST0000039599704626_64843.333333333333336617.0Zinc fingerC2H2-type 6
TgeneSALL4chr2:29006844chr20:50408891ENST000003959970472_9443.333333333333336617.0Zinc fingerC2H2-type 1%3B atypical
TgeneSALL4chr2:29006844chr20:50408891ENST0000039599704870_89243.333333333333336617.0Zinc fingerC2H2-type 7
TgeneSALL4chr2:29006844chr20:50408891ENST0000039599704898_92043.333333333333336617.0Zinc fingerC2H2-type 8

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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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
PPP1CB
SALL4


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 PPP1CB-SALL4


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 PPP1CB-SALL4


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