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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: 34852

FusionGeneSummary for SMC1A_SEC31A

check button Fusion gene summary
Fusion gene informationFusion gene name: SMC1A_SEC31A
Fusion gene ID: 34852
HgeneTgene
Gene symbol

SMC1A

SEC31A

Gene ID

8243

22872

Gene namestructural maintenance of chromosomes 1ASEC31 homolog A, COPII coat complex component
SynonymsCDLS2|DXS423E|SB1.8|SMC1|SMC1L1|SMC1alpha|SMCBABP125|ABP130|HSPC275|HSPC334|SEC31L1
Cytomap

Xp11.22

4q21.22

Type of geneprotein-codingprotein-coding
Descriptionstructural maintenance of chromosomes protein 1ASMC protein 1ASMC-1-alphaSMC1 (structural maintenance of chromosomes 1, yeast)-like 1segregation of mitotic chromosomes 1protein transport protein Sec31ASEC31 homolog A, COPII coating complex componentSEC31-like protein 1SEC31-related protein Aweb1-like proteinyeast Sec31p homolog
Modification date2018052220180523
UniProtAcc

Q14683

O94979

Ensembl transtripts involved in fusion geneENST00000322213, ENST00000469129, 
ENST00000375340, 
ENST00000348405, 
ENST00000513858, ENST00000395310, 
ENST00000443462, ENST00000509142, 
ENST00000326950, ENST00000432794, 
ENST00000311785, ENST00000448323, 
ENST00000505472, ENST00000500777, 
ENST00000508502, ENST00000355196, 
ENST00000264405, ENST00000505984, 
ENST00000508479, ENST00000436790, 
Fusion gene scores* DoF score5 X 5 X 4=1008 X 8 X 4=256
# samples 69
** MAII scorelog2(6/100*10)=-0.736965594166206
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(9/256*10)=-1.50814690367033
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SMC1A [Title/Abstract] AND SEC31A [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
HgeneSMC1A

GO:0072423

response to DNA damage checkpoint signaling

11877377

TgeneSEC31A

GO:0051592

response to calcium ion

17196169

TgeneSEC31A

GO:0090110

cargo loading into COPII-coated vesicle

17499046|18843296


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
ChiTaRS3.1DT220653SMC1AchrX

53449439

-SEC31Achr4

83750212

-
ChiTaRS3.1DT219678SMC1AchrX

53449439

-SEC31Achr4

83750212

-
* 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-shiftENST00000322213ENST00000348405SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000322213ENST00000513858SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000322213ENST00000395310SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000322213ENST00000443462SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000322213ENST00000509142SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000322213ENST00000326950SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000322213ENST00000432794SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000322213ENST00000311785SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000322213ENST00000448323SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000322213ENST00000505472SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000322213ENST00000500777SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000322213ENST00000508502SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000322213ENST00000355196SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000322213ENST00000264405SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000322213ENST00000505984SMC1AchrX

53449439

-SEC31Achr4

83750212

-
5CDS-intronENST00000322213ENST00000508479SMC1AchrX

53449439

-SEC31Achr4

83750212

-
5CDS-intronENST00000322213ENST00000436790SMC1AchrX

53449439

-SEC31Achr4

83750212

-
intron-3CDSENST00000469129ENST00000348405SMC1AchrX

53449439

-SEC31Achr4

83750212

-
intron-3CDSENST00000469129ENST00000513858SMC1AchrX

53449439

-SEC31Achr4

83750212

-
intron-3CDSENST00000469129ENST00000395310SMC1AchrX

53449439

-SEC31Achr4

83750212

-
intron-3CDSENST00000469129ENST00000443462SMC1AchrX

53449439

-SEC31Achr4

83750212

-
intron-3CDSENST00000469129ENST00000509142SMC1AchrX

53449439

-SEC31Achr4

83750212

-
intron-3CDSENST00000469129ENST00000326950SMC1AchrX

53449439

-SEC31Achr4

83750212

-
intron-3CDSENST00000469129ENST00000432794SMC1AchrX

53449439

-SEC31Achr4

83750212

-
intron-3CDSENST00000469129ENST00000311785SMC1AchrX

53449439

-SEC31Achr4

83750212

-
intron-3CDSENST00000469129ENST00000448323SMC1AchrX

53449439

-SEC31Achr4

83750212

-
intron-3CDSENST00000469129ENST00000505472SMC1AchrX

53449439

-SEC31Achr4

83750212

-
intron-3CDSENST00000469129ENST00000500777SMC1AchrX

53449439

-SEC31Achr4

83750212

-
intron-3CDSENST00000469129ENST00000508502SMC1AchrX

53449439

-SEC31Achr4

83750212

-
intron-3CDSENST00000469129ENST00000355196SMC1AchrX

53449439

-SEC31Achr4

83750212

-
intron-3CDSENST00000469129ENST00000264405SMC1AchrX

53449439

-SEC31Achr4

83750212

-
intron-3CDSENST00000469129ENST00000505984SMC1AchrX

53449439

-SEC31Achr4

83750212

-
intron-intronENST00000469129ENST00000508479SMC1AchrX

53449439

-SEC31Achr4

83750212

-
intron-intronENST00000469129ENST00000436790SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000375340ENST00000348405SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000375340ENST00000513858SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000375340ENST00000395310SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000375340ENST00000443462SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000375340ENST00000509142SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000375340ENST00000326950SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000375340ENST00000432794SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000375340ENST00000311785SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000375340ENST00000448323SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000375340ENST00000505472SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000375340ENST00000500777SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000375340ENST00000508502SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000375340ENST00000355196SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000375340ENST00000264405SMC1AchrX

53449439

-SEC31Achr4

83750212

-
Frame-shiftENST00000375340ENST00000505984SMC1AchrX

53449439

-SEC31Achr4

83750212

-
5CDS-intronENST00000375340ENST00000508479SMC1AchrX

53449439

-SEC31Achr4

83750212

-
5CDS-intronENST00000375340ENST00000436790SMC1AchrX

53449439

-SEC31Achr4

83750212

-

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FusionProtFeatures for SMC1A_SEC31A


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SMC1A

Q14683

SEC31A

O94979

Involved in chromosome cohesion during cell cycle and inDNA repair. Central component of cohesin complex. The cohesincomplex is required for the cohesion of sister chromatids afterDNA replication. The cohesin complex apparently forms a largeproteinaceous ring within which sister chromatids can be trapped.At anaphase, the complex is cleaved and dissociates fromchromatin, allowing sister chromatids to segregate. The cohesincomplex may also play a role in spindle pole assembly duringmitosis. Involved in DNA repair via its interaction with BRCA1 andits related phosphorylation by ATM, or via its phosphorylation byATR. Works as a downstream effector both in the ATM/NBS1 branchand in the ATR/MSH2 branch of S-phase checkpoint.{ECO:0000269|PubMed:11877377}.

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 SMC1A_SEC31A


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 SMC1A_SEC31A


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
SMC1ASTYXL1, CASP4, CDK4, ATM, SMC3, MSH6, CHTF18, SYCP3, SMARCA5, RAD21, NUMA1, STAG1, STAG3, RAE1, SMC1A, USP13, USP32, MLH1, ATRX, AIRE, ATG2A, ATG4C, BECN1, CAMKK2, PRKAA2, MGMT, SRRM1, RPGR, ATR, PHF1, CTCF, PAXIP1, THRA, THRB, KDM1B, EHMT2, SSU72, STAG2, PDS5A, PDS5B, WFDC5, BRCA1, HDAC5, WAPAL, BARD1, SMARCAD1, POLR2A, NIPBL, CDK8, CEBPA, MDC1, CUL3, CDK2, NSMCE2, FBXO6, MCM7, SF3B3, SMC2, RBM14, ACIN1, NOTCH1, METTL21B, MCM6, RFC1, POLA1, HDAC8, HDAC11, CDK20, ANKRD28, ARMCX3, KIF13A, RPA3, RPA2, RPA1, STAU1, CUL7, OBSL1, CCDC8, EED, RNF2, EGFR, SIRT6, ABCE1, ESR1, CDCA5, SDF4, PSMC2, NDC80, PLK1, POLE, SF3A2, SMC4, NTRK1, SCARNA22, HIST1H3E, BPTF, GANC, PEX1, HLTF, YWHAZ, SNX3, MRPL50, AKR7A2, SAP30, KCTD2, OSBPL3, PRPF19, KIAA1191, MTUS1, HAUS3, GCC1, NUF2, MGME1, LSM14B, DDI1, IRF3, TEAD2, FOXB1, FOXG1, FOXJ2, EP300, BRD4, FOXL1, FOXQ1, NF2, USP37, SNW1, CDC5L, RNF126, DERL1, USP15, SPAG9, MCM2, MCM4, EPS15L1, IVNS1ABP, GTF3C4, HSF1, NCL, MTF1SEC31ASEC13, APC, TNNT1, PFDN1, ALG2, STAM, STAM2, CUL3, CDK9, HSPA8, VCAM1, ITGA4, REL, SHMT2, MOV10, NXF1, TFG, SCYL1, C6orf211, ATP6V1C1, ENO2, FDPS, NUDT13, SEC23A, SEC23B, SEC24B, ALDH5A1, ATP6V1D, CBS, CTH, CYB5B, DHX15, HNRNPA1, HSD17B10, NAPRT, NSF, SAR1A, TBCA, TPD52L2, TRIM25, TSTA3, TCEB2, NTRK1, TMEM17, XPO1, TSC22D2, NOP14, SEC23IP, NOC4L, GNPDA1, CCDC88A, BRCA1


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 SMC1A_SEC31A


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 SMC1A_SEC31A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSMC1AC1802395Congenital muscular hypertrophy-cerebral syndrome5UNIPROT
HgeneSMC1AC0005695Bladder Neoplasm1CTD_human
HgeneSMC1AC0010606Adenoid Cystic Carcinoma1CTD_human
HgeneSMC1AC0023470Myeloid Leukemia1CTD_human
TgeneSEC31AC0079744Diffuse Large B-Cell Lymphoma1CTD_human