FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

FusionGeneSummary

leaf

FusionProtFeature

leaf

FusionGeneSequence

leaf

FusionGenePPI

leaf

RelatedDrugs

leaf

RelatedDiseases

Fusion gene ID: 24385

FusionGeneSummary for NIPBL_CLSPN

check button Fusion gene summary
Fusion gene informationFusion gene name: NIPBL_CLSPN
Fusion gene ID: 24385
HgeneTgene
Gene symbol

NIPBL

CLSPN

Gene ID

25836

63967

Gene nameNIPBL, cohesin loading factorclaspin
SynonymsCDLS|CDLS1|IDN3|IDN3-B|Scc2-
Cytomap

5p13.2

1p34.3

Type of geneprotein-codingprotein-coding
Descriptionnipped-B-like proteinNipped-B homologSCC2 homologdelanginsister chromatid cohesion 2 homologclaspinclaspin homolog
Modification date2018052720180522
UniProtAcc

Q6KC79

Q9HAW4

Ensembl transtripts involved in fusion geneENST00000282516, ENST00000448238, 
ENST00000504430, 		ENST00000251195, 
ENST00000466308, ENST00000373220, 
ENST00000520551, ENST00000318121, 
Fusion gene scores* DoF score18 X 9 X 11=17825 X 4 X 4=80
# samples 246
** MAII scorelog2(24/1782*10)=-2.8923910259134
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/80*10)=-0.415037499278844
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NIPBL [Title/Abstract] AND CLSPN [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
HgeneNIPBL

GO:0000122

negative regulation of transcription by RNA polymerase II

18854353

HgeneNIPBL

GO:0031065

positive regulation of histone deacetylation

18854353

HgeneNIPBL

GO:0045892

negative regulation of transcription, DNA-templated

18854353

HgeneNIPBL

GO:0071921

cohesin loading

22628566

TgeneCLSPN

GO:0007095

mitotic G2 DNA damage checkpoint

18662541

TgeneCLSPN

GO:0018105

peptidyl-serine phosphorylation

16885022

TgeneCLSPN

GO:0032147

activation of protein kinase activity

16885022


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
TCGARVBRCATCGA-A7-A13D-01BNIPBLchr5

36877280

+CLSPNchr1

36230927

-
TCGALDBRCATCGA-A7-A13D-01ANIPBLchr5

36877280

+CLSPNchr1

36230927

-
* 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
5UTR-3CDSENST00000282516ENST00000251195NIPBLchr5

36877280

+CLSPNchr1

36230927

-
5UTR-intronENST00000282516ENST00000466308NIPBLchr5

36877280

+CLSPNchr1

36230927

-
5UTR-intronENST00000282516ENST00000373220NIPBLchr5

36877280

+CLSPNchr1

36230927

-
5UTR-intronENST00000282516ENST00000520551NIPBLchr5

36877280

+CLSPNchr1

36230927

-
5UTR-intronENST00000282516ENST00000318121NIPBLchr5

36877280

+CLSPNchr1

36230927

-
5UTR-3CDSENST00000448238ENST00000251195NIPBLchr5

36877280

+CLSPNchr1

36230927

-
5UTR-intronENST00000448238ENST00000466308NIPBLchr5

36877280

+CLSPNchr1

36230927

-
5UTR-intronENST00000448238ENST00000373220NIPBLchr5

36877280

+CLSPNchr1

36230927

-
5UTR-intronENST00000448238ENST00000520551NIPBLchr5

36877280

+CLSPNchr1

36230927

-
5UTR-intronENST00000448238ENST00000318121NIPBLchr5

36877280

+CLSPNchr1

36230927

-
intron-3CDSENST00000504430ENST00000251195NIPBLchr5

36877280

+CLSPNchr1

36230927

-
intron-intronENST00000504430ENST00000466308NIPBLchr5

36877280

+CLSPNchr1

36230927

-
intron-intronENST00000504430ENST00000373220NIPBLchr5

36877280

+CLSPNchr1

36230927

-
intron-intronENST00000504430ENST00000520551NIPBLchr5

36877280

+CLSPNchr1

36230927

-
intron-intronENST00000504430ENST00000318121NIPBLchr5

36877280

+CLSPNchr1

36230927

-

Top

FusionProtFeatures for NIPBL_CLSPN


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

Q6KC79

CLSPN

Q9HAW4

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}. Required for checkpoint mediated cell cycle arrest inresponse to inhibition of DNA replication or to DNA damage inducedby both ionizing and UV irradiation. Adapter protein which bindsto BRCA1 and the checkpoint kinase CHEK1 and facilitates the ATR-dependent phosphorylation of both proteins. Can also bindspecifically to branched DNA structures and may associate with S-phase chromatin following formation of the pre-replication complex(pre-RC). This may indicate a role for this protein as a sensorwhich monitors the integrity of DNA replication forks.{ECO:0000269|PubMed:12766152, ECO:0000269|PubMed:15096610,ECO:0000269|PubMed:15190204, ECO:0000269|PubMed:15226314,ECO:0000269|PubMed:15707391}.

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


Top

FusionGeneSequence for NIPBL_CLSPN


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).

Top

FusionGenePPI for NIPBL_CLSPN


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
NIPBLPRSS23, CBX5, SP100, CBX3, MLLT3, SMC1A, SMC3, MED23, CDK8, SIRT7, HINFP, TOMM40, PPT1, SF3A2, RAD21, MAU2, CDK6, RPA3, RPA2, RPA1, BRCA1, OBSL1, CCDC8, EED, EWSR1, RPL10, TFG, LDHD, SUCO, USP37, SNW1, CDC5L, ARFGAP1, TRIM25CLSPNBRCA1, CHEK1, ATR, RAD9A, USP7, PCNA, TIMELESS, USP28, BTRC, FBXW11, PLK1, MSH6, PMS2, LTA, RAD17, CDC7, CDK9, FZR1, CDC20, HERC2, CASP7, USP29, CEP250, GINS3, XPO1, GJB2, MPP1, MYH7, LTN1, USP20


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


Top

RelatedDrugs for NIPBL_CLSPN


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

Top

RelatedDiseases for NIPBL_CLSPN


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneNIPBLC0270972Cornelia De Lange Syndrome9CTD_human;ORPHANET;UNIPROT
HgeneNIPBLC0005941Bone Diseases, Developmental1CTD_human
HgeneNIPBLC0018798Congenital Heart Defects1CTD_human
HgeneNIPBLC0260662Hearing problem1CTD_human
HgeneNIPBLC0376634Craniofacial Abnormalities1CTD_human