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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: 19167

FusionGeneSummary for KPNA1_SMC1B

check button Fusion gene summary
Fusion gene informationFusion gene name: KPNA1_SMC1B
Fusion gene ID: 19167
HgeneTgene
Gene symbol

KPNA1

SMC1B

Gene ID

3836

27127

Gene namekaryopherin subunit alpha 1structural maintenance of chromosomes 1B
SynonymsIPOA5|NPI-1|RCH2|SRP1SMC1BETA|SMC1L2
Cytomap

3q21.1

22q13.31

Type of geneprotein-codingprotein-coding
Descriptionimportin subunit alpha-5RAG cohort protein 2SRP1-betaimportin alpha 5importin subunit alpha-1importin-alpha-S1karyopherin alpha 1 (importin alpha 5)nucleoprotein interactor 1recombination activating gene cohort 2structural maintenance of chromosomes protein 1BSMC protein 1BSMC1 (structural maintenance of chromosomes 1, yeast)-like 1SMC1 structural maintenance of chromosomes 1-like 2mitosis-specific chromosome segregation protein like protein beta
Modification date2018052320180519
UniProtAcc

P52294

Q8NDV3

Ensembl transtripts involved in fusion geneENST00000344337, ENST00000466923, 
ENST00000357450, ENST00000404354, 
Fusion gene scores* DoF score7 X 4 X 7=1964 X 3 X 4=48
# samples 74
** MAII scorelog2(7/196*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: KPNA1 [Title/Abstract] AND SMC1B [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

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
TCGARVPRADTCGA-KK-A7AU-01AKPNA1chr3

122215284

-SMC1Bchr22

45804779

-
* 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
Frame-shiftENST00000344337ENST00000357450KPNA1chr3

122215284

-SMC1Bchr22

45804779

-
Frame-shiftENST00000344337ENST00000404354KPNA1chr3

122215284

-SMC1Bchr22

45804779

-
intron-3CDSENST00000466923ENST00000357450KPNA1chr3

122215284

-SMC1Bchr22

45804779

-
intron-3CDSENST00000466923ENST00000404354KPNA1chr3

122215284

-SMC1Bchr22

45804779

-

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FusionProtFeatures for KPNA1_SMC1B


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
KPNA1

P52294

SMC1B

Q8NDV3

Functions in nuclear protein import as an adapterprotein for nuclear receptor KPNB1. Binds specifically anddirectly to substrates containing either a simple or bipartite NLSmotif. Docking of the importin/substrate complex to the nuclearpore complex (NPC) is mediated by KPNB1 through binding tonucleoporin FxFG repeats and the complex is subsequentlytranslocated through the pore by an energy requiring, Ran-dependent mechanism. At the nucleoplasmic side of the NPC, Ranbinds to importin-beta and the three components separate andimportin-alpha and -beta are re-exported from the nucleus to thecytoplasm where GTP hydrolysis releases Ran from importin. Thedirectionality of nuclear import is thought to be conferred by anasymmetric distribution of the GTP- and GDP-bound forms of Ranbetween the cytoplasm and nucleus. In vitro, mediates the nuclearimport of human cytomegalovirus UL84 by recognizing a non-classical NLS. Meiosis-specific component of cohesin complex. Requiredfor the maintenance of meiotic cohesion, but not, or only to aminor extent, for its establishment. Contributes to axial element(AE) formation and the organization of chromatin loops along theAE. Plays a key role in synapsis, recombination and chromosomemovements. The cohesin complex is required for the cohesion ofsister chromatids after DNA replication. The cohesin complexapparently forms a large proteinaceous ring within which sisterchromatids can be trapped. At anaphase, the complex is cleaved anddissociates from chromatin, allowing sister chromatids tosegregate. The meiosis-specific cohesin complex probably replacesmitosis specific cohesin complex when it dissociates fromchromatin during prophase I (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

- 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 KPNA1_SMC1B


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 KPNA1_SMC1B


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
KPNA1LYAR, NUP62, NUP54, RANBP2, UBR5, RAG1, CSE1L, KPNB1, RUNX1T1, STAT1, USP1, SLX4, MEPCE, TPX2, PRPF19, PRPF31, PLRG1, AICDA, CTNNBL1, CUL4B, HSPA4, CDKN1B, SKP2, CUL3, CUL1, COPS5, CAND1, NOSIP, DCAF8, TAF9, ANP32A, TP53BP1, LMO4, HDAC6, HDAC1, HDAC2, BCAR3, ANP32B, IL1RAP, ORC4, FOSL1, CRADD, GOPC, CLK3, HECW2, GABPA, DCAF6, KCTD12, LIMCH1, NPM1, TRMT61A, XRN2, NUP50, CLK4, FANCD2, FBL, IPO5, KPNA2, NOP56, NOP58, RPS19, MORF4L1, MORF4L2, RAN, SUB1, NTRK1, NUP153, PHAX, CDKN2AIP, CHD8, LMNB1, TRIM27, SMARCA4, SMARCD2, VPS72, USP7, RUVBL1, RNMT, MTA2, NCOR1, TSSC4, TADA3, RUVBL2, ADNP, SF3B1, MBD3, GATAD2A, SUPT20H, GATAD2B, MTA3, ANP32E, KIAA2013, C12orf45, ARID2, FOXB1, FOXE1, CRY2, MCM2, SNW1, IKBKG, RBBP4, PHB2, MDM2, PTPN2, STYX, SREK1IP1, PKM, NR3C1, SENP2, CD2BP2, G3BP1, LMNA, GTF2IRD1, BRD1SMC1BCDCA5, RAD21, STAG1, STAG2, SMC3, REC8


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 KPNA1_SMC1B


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 KPNA1_SMC1B


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneKPNA1C0036341Schizophrenia1CTD_human
TgeneSMC1BC0005695Bladder Neoplasm1CTD_human