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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 6069

FusionGeneSummary for CCSER1_NIPBL

check button Fusion gene summary
Fusion gene informationFusion gene name: CCSER1_NIPBL
Fusion gene ID: 6069
HgeneTgene
Gene symbol

CCSER1

NIPBL

Gene ID

401145

25836

Gene namecoiled-coil serine rich protein 1NIPBL, cohesin loading factor
SynonymsFAM190ACDLS|CDLS1|IDN3|IDN3-B|Scc2
Cytomap

4q22.1

5p13.2

Type of geneprotein-codingprotein-coding
Descriptionserine-rich coiled-coil domain-containing protein 1family with sequence similarity 190, member Aprotein FAM190Anipped-B-like proteinNipped-B homologSCC2 homologdelanginsister chromatid cohesion 2 homolog
Modification date2018051920180527
UniProtAcc

Q9C0I3

Q6KC79

Ensembl transtripts involved in fusion geneENST00000509176, ENST00000333691, 
ENST00000432775, ENST00000504150, 
ENST00000282516, ENST00000448238, 
ENST00000504430, 
Fusion gene scores* DoF score8 X 7 X 4=2247 X 7 X 4=196
# samples 87
** MAII scorelog2(8/224*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(7/196*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CCSER1 [Title/Abstract] AND NIPBL [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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
TgeneNIPBL

GO:0000122

negative regulation of transcription by RNA polymerase II

18854353

TgeneNIPBL

GO:0031065

positive regulation of histone deacetylation

18854353

TgeneNIPBL

GO:0045892

negative regulation of transcription, DNA-templated

18854353

TgeneNIPBL

GO:0071921

cohesin loading

22628566


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS3.1AW369457CCSER1chr4

91850207

+NIPBLchr5

37037966

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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-intronENST00000509176ENST00000282516CCSER1chr4

91850207

+NIPBLchr5

37037966

+
intron-intronENST00000509176ENST00000448238CCSER1chr4

91850207

+NIPBLchr5

37037966

+
intron-intronENST00000509176ENST00000504430CCSER1chr4

91850207

+NIPBLchr5

37037966

+
intron-intronENST00000333691ENST00000282516CCSER1chr4

91850207

+NIPBLchr5

37037966

+
intron-intronENST00000333691ENST00000448238CCSER1chr4

91850207

+NIPBLchr5

37037966

+
intron-intronENST00000333691ENST00000504430CCSER1chr4

91850207

+NIPBLchr5

37037966

+
intron-intronENST00000432775ENST00000282516CCSER1chr4

91850207

+NIPBLchr5

37037966

+
intron-intronENST00000432775ENST00000448238CCSER1chr4

91850207

+NIPBLchr5

37037966

+
intron-intronENST00000432775ENST00000504430CCSER1chr4

91850207

+NIPBLchr5

37037966

+
intron-intronENST00000504150ENST00000282516CCSER1chr4

91850207

+NIPBLchr5

37037966

+
intron-intronENST00000504150ENST00000448238CCSER1chr4

91850207

+NIPBLchr5

37037966

+
intron-intronENST00000504150ENST00000504430CCSER1chr4

91850207

+NIPBLchr5

37037966

+

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FusionProtFeatures for CCSER1_NIPBL


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CCSER1

Q9C0I3

NIPBL

Q6KC79

Plays an important role in the loading of the cohesincomplex on to DNA. Forms a heterodimeric complex (also known ascohesin loading complex) with MAU2/SCC4 which mediates the loadingof the cohesin complex onto chromatin (PubMed:22628566,PubMed:28914604). Plays a role in cohesin loading at sites of DNAdamage. Its recruitement to double-strand breaks (DSBs) sitesoccurs in a CBX3-, RNF8- and RNF168-dependent manner whereas itsrecruitement to UV irradiation-induced DNA damage sites occurs ina ATM-, ATR-, RNF8- and RNF168-dependent manner (PubMed:28167679).Along with ZNF609, promotes cortical neuron migration during braindevelopment by regulating the transcription of crucial genes inthis process. Preferentially binds promoters containing paused RNApolymerase II. Up-regulates the expression of SEMA3A, NRP1, PLXND1and GABBR2 genes, among others (By similarity).{ECO:0000250|UniProtKB:Q6KCD5, ECO:0000269|PubMed:22628566,ECO:0000269|PubMed:28167679, ECO:0000269|PubMed:28914604}.

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


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FusionGeneSequence for CCSER1_NIPBL


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for CCSER1_NIPBL


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


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RelatedDrugs for CCSER1_NIPBL


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for CCSER1_NIPBL


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCCSER1C0236736Cocaine-Related Disorders1CTD_human
TgeneNIPBLC0270972Cornelia De Lange Syndrome9CTD_human;ORPHANET;UNIPROT
TgeneNIPBLC0005941Bone Diseases, Developmental1CTD_human
TgeneNIPBLC0018798Congenital Heart Defects1CTD_human
TgeneNIPBLC0260662Hearing problem1CTD_human
TgeneNIPBLC0376634Craniofacial Abnormalities1CTD_human