|
||||||
|
 | |
| |
| |
| |
| |
|
Fusion gene ID: 8318 |
FusionGeneSummary for CPSF6_COL16A1 |
 Fusion gene summary |
| 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) |
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| 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 |
| 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 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 |
| 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. |
| 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-shit | 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 |
| Main function of each fusion partner protein. (from UniProt) |
| 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}. |
| Retention 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 . * 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 |
| 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 |
Top |
FusionGenePPI for CPSF6_COL16A1 |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in . |
| Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
| 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 |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
Top |
RelatedDrugs for CPSF6_COL16A1 |
| Drugs targeting genes involved in this fusion gene. (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 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|