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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: 8318

FusionGeneSummary for CPSF6_COL16A1

check button Fusion gene summary
Fusion gene informationFusion gene name: CPSF6_COL16A1
Fusion gene ID: 8318
HgeneTgene
Gene symbol

CPSF6

COL16A1

Gene ID

11052

1307

Gene namecleavage and polyadenylation specific factor 6collagen type XVI alpha 1 chain
SynonymsCFIM|CFIM68|CFIM72|HPBRII-4|HPBRII-7447AA|FP1572
Cytomap

12q15

1p35.2

Type of geneprotein-codingprotein-coding
Descriptioncleavage 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 collagen alpha-1(XVI) chainalpha 1 type XVI collagencollagen XVI, alpha-1 polypeptidecollagen, type XVI, alpha 1
Modification date2018052220180523
UniProtAcc

Q16630

Q07092

Ensembl transtripts involved in fusion geneENST00000435070, ENST00000456847, 
ENST00000266679, ENST00000550987, 
ENST00000551516, 
ENST00000271069, 
ENST00000373672, ENST00000461217, 
ENST00000373668, 
Fusion gene scores* DoF score23 X 6 X 11=15182 X 2 X 2=8
# samples 263
** MAII scorelog2(26/1518*10)=-2.54558826238701
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/8*10)=1.90689059560852
Context

PubMed: CPSF6 [Title/Abstract] AND COL16A1 [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
HgeneCPSF6

GO:0006397

mRNA processing

14690600

HgeneCPSF6

GO:0051262

protein tetramerization

20695905

HgeneCPSF6

GO:0051290

protein heterotetramerization

23187700

HgeneCPSF6

GO:1990120

messenger ribonucleoprotein complex assembly

29276085

TgeneCOL16A1

GO:0007155

cell adhesion

16754661

TgeneCOL16A1

GO:0033622

integrin activation

16754661

TgeneCOL16A1

GO:0033627

cell adhesion mediated by integrin

16754661

TgeneCOL16A1

GO:0051894

positive regulation of focal adhesion assembly

24466237


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-A6H7-01ACPSF6chr12

69656342

+COL16A1chr1

32118454

-
TCGARVHNSCTCGA-KU-A6H7-06ACPSF6chr12

69656342

+COL16A1chr1

32118454

-
* 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
3UTR-3CDSENST00000435070ENST00000271069CPSF6chr12

69656342

+COL16A1chr1

32118454

-
3UTR-3CDSENST00000435070ENST00000373672CPSF6chr12

69656342

+COL16A1chr1

32118454

-
3UTR-intronENST00000435070ENST00000461217CPSF6chr12

69656342

+COL16A1chr1

32118454

-
3UTR-intronENST00000435070ENST00000373668CPSF6chr12

69656342

+COL16A1chr1

32118454

-
3UTR-3CDSENST00000456847ENST00000271069CPSF6chr12

69656342

+COL16A1chr1

32118454

-
3UTR-3CDSENST00000456847ENST00000373672CPSF6chr12

69656342

+COL16A1chr1

32118454

-
3UTR-intronENST00000456847ENST00000461217CPSF6chr12

69656342

+COL16A1chr1

32118454

-
3UTR-intronENST00000456847ENST00000373668CPSF6chr12

69656342

+COL16A1chr1

32118454

-
3UTR-3CDSENST00000266679ENST00000271069CPSF6chr12

69656342

+COL16A1chr1

32118454

-
3UTR-3CDSENST00000266679ENST00000373672CPSF6chr12

69656342

+COL16A1chr1

32118454

-
3UTR-intronENST00000266679ENST00000461217CPSF6chr12

69656342

+COL16A1chr1

32118454

-
3UTR-intronENST00000266679ENST00000373668CPSF6chr12

69656342

+COL16A1chr1

32118454

-
intron-3CDSENST00000550987ENST00000271069CPSF6chr12

69656342

+COL16A1chr1

32118454

-
intron-3CDSENST00000550987ENST00000373672CPSF6chr12

69656342

+COL16A1chr1

32118454

-
intron-intronENST00000550987ENST00000461217CPSF6chr12

69656342

+COL16A1chr1

32118454

-
intron-intronENST00000550987ENST00000373668CPSF6chr12

69656342

+COL16A1chr1

32118454

-
In-frameENST00000551516ENST00000271069CPSF6chr12

69656342

+COL16A1chr1

32118454

-
Frame-shitENST00000551516ENST00000373672CPSF6chr12

69656342

+COL16A1chr1

32118454

-
5CDS-intronENST00000551516ENST00000461217CPSF6chr12

69656342

+COL16A1chr1

32118454

-
5CDS-intronENST00000551516ENST00000373668CPSF6chr12

69656342

+COL16A1chr1

32118454

-

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FusionProtFeatures for CPSF6_COL16A1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CPSF6

Q16630

COL16A1

Q07092

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}. Involved in mediating cell attachment and inducingintegrin-mediated cellular reactions, such as cell spreading andalterations in cell morphology. {ECO:0000269|PubMed:16754661}.

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 CPSF6_COL16A1


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.
>In-frame_CPSF6_ENST00000551516_chr12_69656342_+_COL16A1_ENST00000271069_chr1_32118454_-_123aa
MADGVDHIDIYADVGEEFNQEAETEREAENERGTGIVTETVTESVTESANIVIVRRSSRSSRLWQDGCNRTNGPARHPWHPWAPGSHGPA


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_CPSF6_ENST00000551516_chr12_69656342_+_COL16A1_ENST00000271069_chr1_32118454_-_370nt
ATGGCGGACGGCGTGGACCACATAGACATTTACGCGGATGTCGGCGAAGAGTTCAACCAGGAAGCTGAATATGAGAGAGAAGCAGAGAAC
GAGAGAGGCACCGGGATCGTGACCGAGACCGTGACCGAGAGCGTGACCGAGAGCGCGAATATCGTCATCGTTAGAAGGTCCTCAAGGTCC
TCCAGGCTATGGCAAGATGGGTGCAACAGGACCAATGGGCCAGCAAGGCATCCCTGGCATCCCTGGGCCCCCGGGTCCCATGGGCCAGCC
AGGCAAGGCTGGCCACTGTAATCCCTCTGACTGCTTTGGGGCCATGCCGATGGAGCAGCAGTACCCACCCATGAAAACCATGAAGGGGCC


* Fusion transcript sequences (Full-length transcript).
>In-frame_CPSF6_ENST00000551516_chr12_69656342_+_COL16A1_ENST00000271069_chr1_32118454_-_779nt
GGAAGATGGCGGACGGCGTGGACCACATAGACATTTACGCGGATGTCGGCGAAGAGTTCAACCAGGAAGCTGAATATGAGAGAGAAGCAG
AGAACGAGAGAGGCACCGGGATCGTGACCGAGACCGTGACCGAGAGCGTGACCGAGAGCGCGAATATCGTCATCGTTAGAAGGTCCTCAA
GGTCCTCCAGGCTATGGCAAGATGGGTGCAACAGGACCAATGGGCCAGCAAGGCATCCCTGGCATCCCTGGGCCCCCGGGTCCCATGGGC
CAGCCAGGCAAGGCTGGCCACTGTAATCCCTCTGACTGCTTTGGGGCCATGCCGATGGAGCAGCAGTACCCACCCATGAAAACCATGAAG
GGGCCTTTTGGCTGAAATTCCCCACCTGCCTTTGGATGAAAGACTCCGTTGGGAATAAATGGCCAAAGCTTATAGGACTCTGTGACAGGT
TGTGAATGTTTTTTTTGTTGTTGTTGTTGTTTTTAATTGCTGTTAATATTTTTTAAATAATAAAGAAACAAAACTATCTGCCCTTTCCCT
TCCAGTGGGTTCCTCTGGTGCTGCAGCCAGAGCTCCCTGTTGCCCTCCTTTTCCCGTTTAGTCCCAGGAACAAAAAAGGGCATTTTGGGT
ACAGGGGCATATACCTGTAATCCTAGCTATTCAAGGGGCTGAGGTGGGAGGATCGCCTGAGCCCAGGAGTTTGAGACCAGTCTAAGCAAC


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FusionGenePPI for CPSF6_COL16A1


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
CPSF6PLSCR1, 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, G3BP1COL16A1


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 CPSF6_COL16A1


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 CPSF6_COL16A1


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