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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: 7850

FusionGeneSummary for COL16A1_CPSF6

check button Fusion gene summary
Fusion gene informationFusion gene name: COL16A1_CPSF6
Fusion gene ID: 7850
HgeneTgene
Gene symbol

COL16A1

CPSF6

Gene ID

1307

11052

Gene namecollagen type XVI alpha 1 chaincleavage and polyadenylation specific factor 6
Synonyms447AA|FP1572CFIM|CFIM68|CFIM72|HPBRII-4|HPBRII-7
Cytomap

1p35.2

12q15

Type of geneprotein-codingprotein-coding
Descriptioncollagen alpha-1(XVI) chainalpha 1 type XVI collagencollagen XVI, alpha-1 polypeptidecollagen, type XVI, alpha 1cleavage and polyadenylation specificity factor subunit 6CPSF 68 kDa subunitcleavage and polyadenylation specific factor 6, 68kDacleavage and polyadenylation specificity factor 68 kDa subunitcleavage factor Im complex 68 kDa subunitpre-mRNA cleavage
Modification date2018052320180522
UniProtAcc

Q07092

Q16630

Ensembl transtripts involved in fusion geneENST00000271069, ENST00000373672, 
ENST00000461217, ENST00000373668, 
ENST00000435070, ENST00000456847, 
ENST00000266679, ENST00000550987, 
ENST00000551516, 
Fusion gene scores* DoF score5 X 5 X 5=1258 X 6 X 8=384
# samples 611
** MAII scorelog2(6/125*10)=-1.05889368905357
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(11/384*10)=-1.8036027871965
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: COL16A1 [Title/Abstract] AND CPSF6 [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
HgeneCOL16A1

GO:0007155

cell adhesion

16754661

HgeneCOL16A1

GO:0033622

integrin activation

16754661

HgeneCOL16A1

GO:0033627

cell adhesion mediated by integrin

16754661

HgeneCOL16A1

GO:0051894

positive regulation of focal adhesion assembly

24466237

TgeneCPSF6

GO:0006397

mRNA processing

14690600

TgeneCPSF6

GO:0051262

protein tetramerization

20695905

TgeneCPSF6

GO:0051290

protein heterotetramerization

23187700

TgeneCPSF6

GO:1990120

messenger ribonucleoprotein complex assembly

29276085


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
TCGARVHNSCTCGA-KU-A6H7-01ACOL16A1chr1

32119200

-CPSF6chr12

69663292

+
TCGARVHNSCTCGA-KU-A6H7-06ACOL16A1chr1

32119200

-CPSF6chr12

69663292

+
* 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
5CDS-3UTRENST00000271069ENST00000435070COL16A1chr1

32119200

-CPSF6chr12

69663292

+
5CDS-3UTRENST00000271069ENST00000456847COL16A1chr1

32119200

-CPSF6chr12

69663292

+
5CDS-3UTRENST00000271069ENST00000266679COL16A1chr1

32119200

-CPSF6chr12

69663292

+
5CDS-intronENST00000271069ENST00000550987COL16A1chr1

32119200

-CPSF6chr12

69663292

+
5CDS-intronENST00000271069ENST00000551516COL16A1chr1

32119200

-CPSF6chr12

69663292

+
5CDS-3UTRENST00000373672ENST00000435070COL16A1chr1

32119200

-CPSF6chr12

69663292

+
5CDS-3UTRENST00000373672ENST00000456847COL16A1chr1

32119200

-CPSF6chr12

69663292

+
5CDS-3UTRENST00000373672ENST00000266679COL16A1chr1

32119200

-CPSF6chr12

69663292

+
5CDS-intronENST00000373672ENST00000550987COL16A1chr1

32119200

-CPSF6chr12

69663292

+
5CDS-intronENST00000373672ENST00000551516COL16A1chr1

32119200

-CPSF6chr12

69663292

+
5CDS-3UTRENST00000461217ENST00000435070COL16A1chr1

32119200

-CPSF6chr12

69663292

+
5CDS-3UTRENST00000461217ENST00000456847COL16A1chr1

32119200

-CPSF6chr12

69663292

+
5CDS-3UTRENST00000461217ENST00000266679COL16A1chr1

32119200

-CPSF6chr12

69663292

+
5CDS-intronENST00000461217ENST00000550987COL16A1chr1

32119200

-CPSF6chr12

69663292

+
5CDS-intronENST00000461217ENST00000551516COL16A1chr1

32119200

-CPSF6chr12

69663292

+
intron-3UTRENST00000373668ENST00000435070COL16A1chr1

32119200

-CPSF6chr12

69663292

+
intron-3UTRENST00000373668ENST00000456847COL16A1chr1

32119200

-CPSF6chr12

69663292

+
intron-3UTRENST00000373668ENST00000266679COL16A1chr1

32119200

-CPSF6chr12

69663292

+
intron-intronENST00000373668ENST00000550987COL16A1chr1

32119200

-CPSF6chr12

69663292

+
intron-intronENST00000373668ENST00000551516COL16A1chr1

32119200

-CPSF6chr12

69663292

+

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FusionProtFeatures for COL16A1_CPSF6


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
COL16A1

Q07092

CPSF6

Q16630

Involved in mediating cell attachment and inducingintegrin-mediated cellular reactions, such as cell spreading andalterations in cell morphology. {ECO:0000269|PubMed:16754661}. Component of the cleavage factor Im (CFIm) complex thatfunctions as an activator of the pre-mRNA 3'-end cleavage andpolyadenylation processing required for the maturation of pre-mRNAinto functional mRNAs (PubMed:9659921, PubMed:8626397,PubMed:14690600, PubMed:29276085). CFIm contributes to therecruitment of multiprotein complexes on specific sequences on thepre-mRNA 3'-end, so called cleavage and polyadenylation signals(pA signals) (PubMed:9659921, PubMed:8626397, PubMed:14690600).Most pre-mRNAs contain multiple pA signals, resulting inalternative cleavage and polyadenylation (APA) producing mRNAswith variable 3'-end formation (PubMed:23187700, PubMed:29276085).The CFIm complex acts as a key regulator of cleavage andpolyadenylation site choice during APA through its binding to 5'-UGUA-3' elements localized in the 3'-untranslated region (UTR) fora huge number of pre-mRNAs (PubMed:20695905, PubMed:29276085).CPSF6 enhances NUDT21/CPSF5 binding to 5'-UGUA-3' elementslocalized upstream of pA signals and promotes RNA looping, andhence activates directly the mRNA 3'-processing machinery(PubMed:15169763, PubMed:29276085, PubMed:21295486). Plays a rolein mRNA export (PubMed:19864460). {ECO:0000269|PubMed:14690600,ECO:0000269|PubMed:15169763, ECO:0000269|PubMed:19864460,ECO:0000269|PubMed:20695905, ECO:0000269|PubMed:21295486,ECO:0000269|PubMed:23187700, ECO:0000269|PubMed:29276085,ECO:0000269|PubMed:8626397, ECO:0000269|PubMed:9659921}.

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 COL16A1_CPSF6


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 COL16A1_CPSF6


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
COL16A1CPSF6PLSCR1, GIN1, WWP1, EWSR1, ARMC7, KLHL12, NUDT21, UBAC1, WWP2, NCK2, RNPS1, CREBBP, PAPOLA, ITCH, NEDD4, WWOX, APBB1, TCERG1, MME, CLP1, ITSN2, HNRNPA1, CUL3, CAND1, UBQLN4, U2AF2, UBAP2L, NONO, WBP11, CPSF7, PUF60, CSTF2, POLR2I, NUP88, TCEA2, ZBTB8B, CSNK1A1, SAFB, MAX, STRN, TBC1D2, TTN, NUP107, BARD1, MDC1, SMURF1, NPM1, FN1, CSNK2A1, TP63, DAB2, CD81, LMNA, SRPK2, PRPF40A, WBP4, FXR2, FUS, PPIL1, TOLLIP, OTUB2, CUL7, OBSL1, CCDC8, EZH2, SUZ12, EED, RSRP1, LUC7L2, DDX17, DDX5, KHSRP, SMARCB1, TXNDC9, PCF11, SMARCC1, SMARCC2, SMEK1, NTRK1, XPO1, VPS26A, NF2, SNW1, JMJD6, RBBP6, PA2G4, TRAP1, SND1, ANXA5, MYL12B, SNRPB2, UBE2N, COQ2, DLD, HSD17B10, PARK7, G3BP1


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 COL16A1_CPSF6


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 COL16A1_CPSF6


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