![]() |
||||||
|
![]() | |
![]() | |
![]() | |
![]() | |
![]() | |
![]() |
Fusion gene ID: 8318 |
FusionGeneSummary for CPSF6_COL16A1 |
![]() |
Fusion gene information | Fusion gene name: CPSF6_COL16A1 | Fusion gene ID: 8318 | Hgene | Tgene | Gene symbol | CPSF6 | COL16A1 | Gene ID | 11052 | 1307 |
Gene name | cleavage and polyadenylation specific factor 6 | collagen type XVI alpha 1 chain | |
Synonyms | CFIM|CFIM68|CFIM72|HPBRII-4|HPBRII-7 | 447AA|FP1572 | |
Cytomap | 12q15 | 1p35.2 | |
Type of gene | protein-coding | protein-coding | |
Description | cleavage 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 date | 20180522 | 20180523 | |
UniProtAcc | Q16630 | Q07092 | |
Ensembl transtripts involved in fusion gene | ENST00000435070, ENST00000456847, ENST00000266679, ENST00000550987, ENST00000551516, | ENST00000271069, ENST00000373672, ENST00000461217, ENST00000373668, | |
Fusion gene scores | * DoF score | 23 X 6 X 11=1518 | 2 X 2 X 2=8 |
# samples | 26 | 3 | |
** MAII score | log2(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) |
![]() |
Partner | Gene | GO ID | GO term | PubMed ID |
Hgene | CPSF6 | GO:0006397 | mRNA processing | 14690600 |
Hgene | CPSF6 | GO:0051262 | protein tetramerization | 20695905 |
Hgene | CPSF6 | GO:0051290 | protein heterotetramerization | 23187700 |
Hgene | CPSF6 | GO:1990120 | messenger ribonucleoprotein complex assembly | 29276085 |
Tgene | COL16A1 | GO:0007155 | cell adhesion | 16754661 |
Tgene | COL16A1 | GO:0033622 | integrin activation | 16754661 |
Tgene | COL16A1 | GO:0033627 | cell adhesion mediated by integrin | 16754661 |
Tgene | COL16A1 | GO:0051894 | positive regulation of focal adhesion assembly | 24466237 |
![]() (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 type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
TCGA | RV | HNSC | TCGA-KU-A6H7-01A | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
TCGA | RV | HNSC | TCGA-KU-A6H7-06A | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
* LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
![]() * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
3UTR-3CDS | ENST00000435070 | ENST00000271069 | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
3UTR-3CDS | ENST00000435070 | ENST00000373672 | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
3UTR-intron | ENST00000435070 | ENST00000461217 | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
3UTR-intron | ENST00000435070 | ENST00000373668 | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
3UTR-3CDS | ENST00000456847 | ENST00000271069 | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
3UTR-3CDS | ENST00000456847 | ENST00000373672 | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
3UTR-intron | ENST00000456847 | ENST00000461217 | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
3UTR-intron | ENST00000456847 | ENST00000373668 | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
3UTR-3CDS | ENST00000266679 | ENST00000271069 | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
3UTR-3CDS | ENST00000266679 | ENST00000373672 | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
3UTR-intron | ENST00000266679 | ENST00000461217 | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
3UTR-intron | ENST00000266679 | ENST00000373668 | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
intron-3CDS | ENST00000550987 | ENST00000271069 | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
intron-3CDS | ENST00000550987 | ENST00000373672 | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
intron-intron | ENST00000550987 | ENST00000461217 | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
intron-intron | ENST00000550987 | ENST00000373668 | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
In-frame | ENST00000551516 | ENST00000271069 | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
Frame-shift | ENST00000551516 | ENST00000373672 | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
5CDS-intron | ENST00000551516 | ENST00000461217 | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
5CDS-intron | ENST00000551516 | ENST00000373668 | CPSF6 | chr12 | 69656342 | + | COL16A1 | chr1 | 32118454 | - |
Top |
FusionProtFeatures for CPSF6_COL16A1 |
![]() |
Hgene | Tgene |
CPSF6 | COL16A1 |
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}. |
![]() * 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. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
- In-frame and not-retained protein feature among the 13 regional features. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
Top |
FusionGeneSequence for CPSF6_COL16A1 |
![]() (nt: nucleotides, aa: amino acids) |
* Fusion amino acid sequences. |
>In-frame_CPSF6_ENST00000551516_chr12_69656342_+_COL16A1_ENST00000271069_chr1_32118454_-_123aa MADGVDHIDIYADVGEEFNQEAEYEREAENERGTGIVTETVTESVTESANIVIVRRSSRSSRLWQDGCNRTNGPARHPWHPWAPGSHGPA |
* 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 |
Top |
FusionGenePPI for CPSF6_COL16A1 |
![]() |
![]() |
Hgene | Hgene's interactors | Tgene | Tgene's interactors |
CPSF6 | PLSCR1, 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 | COL16A1 |
![]() |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
![]() |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
![]() |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
Top |
RelatedDrugs for CPSF6_COL16A1 |
![]() (DrugBank Version 5.1.0 2018-04-02) |
Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for CPSF6_COL16A1 |
![]() (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |