Q16630 (CPSF6_HUMAN) Reviewed, UniProtKB/Swiss-Prot
Last modified
May 1, 2013.
Version 116.
History...
Names·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
Names·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize orderNames and origin
| Protein names | Recommended name: Cleavage and polyadenylation specificity factor subunit 6 Alternative name(s): Cleavage and polyadenylation specificity factor 68 kDa subunit Short name=CFIm68 Short name=CPSF 68 kDa subunit Pre-mRNA cleavage factor Im 68 kDa subunit Protein HPBRII-4/7 | ||||
| Gene names |
| ||||
| Organism | Homo sapiens (Human) [Reference proteome] | ||||
| Taxonomic identifier | 9606 [NCBI] | ||||
| Taxonomic lineage | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo![]() |
Protein attributes
| Sequence length | 551 AA. |
| Sequence status | Complete. |
| Protein existence | Evidence at protein level |
General annotation (Comments)
| Function | Component of the cleavage factor Im complex (CFIm) that plays a key role in pre-mRNA 3'-processing. Involved in association with NUDT21/CPSF5 in pre-MRNA 3'-end poly(A) site cleavage and poly(A) addition. CPSF6 binds to cleavage and polyadenylation RNA substrates and promotes RNA looping. Ref.1 Ref.7 Ref.8 Ref.14 Ref.16 |
| Subunit structure | Component of the cleavage factor Im (CFIm) complex, composed at least of NUDT21/CPSF5 and CPSF6 or CPSF7. Within the cleavage factor Im complex, the NUDT21/CPSF5 homodimer is at the core of a heterotetramer, and is clasped by two additional subunits (CPSF6 or CPSF7). Interacts with NUDT21/CPSF5, SFRS3, SFRS7, SNRNP70 and TRA2B/SFRS10. Ref.1 Ref.7 Ref.9 Ref.10 Ref.14 Ref.16 |
| Subcellular location | Nucleus. Note: In punctate subnuclear structures localized adjacent to nuclear speckles, called paraspeckles. Ref.1 Ref.9 Ref.14 |
| Sequence similarities | Belongs to the RRM CPSF6/7 family. Contains 1 RRM (RNA recognition motif) domain. |
Ontologies
| Keywords | |
|---|---|
| Biological process | mRNA processing |
| Cellular component | Nucleus |
| Coding sequence diversity | Alternative splicing |
| Ligand | RNA-binding |
| PTM | Phosphoprotein |
| Technical term | 3D-structure Complete proteome Direct protein sequencing Reference proteome |
| Gene Ontology (GO) | |
| Biological_process | mRNA polyadenylation Inferred from mutant phenotype Ref.14. Source: UniProtKB protein tetramerizationInferred from direct assay Ref.14. Source: UniProtKB |
| Cellular_component | mRNA cleavage factor complex Inferred from direct assay Ref.14Ref.1. Source: UniProtKB paraspecklesInferred from direct assay Ref.1. Source: UniProtKB ribonucleoprotein complexInferred from direct assay PubMed 18809582. Source: MGI |
| Molecular_function | mRNA binding Inferred from direct assay Ref.16. Source: UniProtKB nucleotide bindingInferred from electronic annotation. Source: InterPro |
| Complete GO annotation... | |
Binary interactions
With | Entry | #Exp. | IntAct | Notes |
|---|---|---|---|---|
| PLSCR1 | O15162 | 2 | EBI-358410,EBI-740019 | |
| WWP1 | Q9H0M0 | 3 | EBI-358410,EBI-742157 |
Alternative products
| This entry describes 3 isoforms produced by alternative splicing. [Align] [Select] | ||||||
| Isoform 1 (identifier: Q16630-1) This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. | ||||||
| Isoform 2 (identifier: Q16630-2) The sequence of this isoform differs from the canonical sequence as follows: 231-231: P → PGNLIKHLVKGTRPLFLETRIPWHMGHSIEEIPIFGLK | ||||||
| Isoform 3 (identifier: Q16630-3) The sequence of this isoform differs from the canonical sequence as follows: 188-260: Missing. |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||||||||||||||||||||||
Molecule processing | |||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 551 | 551 | Cleavage and polyadenylation specificity factor subunit 6 | PRO_0000081521 | |||||||||||||||||||||||||
Regions | |||||||||||||||||||||||||||||
| Domain | 81 – 161 | 81 | RRM | ||||||||||||||||||||||||||
| Region | 81 – 161 | 81 | Necessary for interaction with NUDT21/CPSF5 | ||||||||||||||||||||||||||
| Region | 510 – 551 | 42 | Sufficient for nuclear targeting | ||||||||||||||||||||||||||
| Compositional bias | 208 – 398 | 191 | Pro-rich | ||||||||||||||||||||||||||
| Compositional bias | 490 – 551 | 62 | Arg-rich | ||||||||||||||||||||||||||
Amino acid modifications | |||||||||||||||||||||||||||||
| Modified residue | 404 | 1 | Phosphothreonine Ref.11 | ||||||||||||||||||||||||||
| Modified residue | 407 | 1 | Phosphothreonine Ref.13 | ||||||||||||||||||||||||||
Natural variations | |||||||||||||||||||||||||||||
| Alternative sequence | 188 – 260 | 73 | Missing in isoform 3. | VSP_017191 | |||||||||||||||||||||||||
| Alternative sequence | 231 | 1 | P → PGNLIKHLVKGTRPLFLETR IPWHMGHSIEEIPIFGLK in isoform 2. | VSP_017192 | |||||||||||||||||||||||||
Experimental info | |||||||||||||||||||||||||||||
| Mutagenesis | 84 | 1 | Y → A: Reduces affinity for UGUA RNA by 40%; when associated with A-128. Ref.16 | ||||||||||||||||||||||||||
| Mutagenesis | 86 | 1 | G → V: Abolishes interaction with NUDT21/CPSF5; when associated with V-87. Ref.9 | ||||||||||||||||||||||||||
| Mutagenesis | 87 | 1 | N → V: Abolishes interaction with NUDT21/CPSF5; when associated with V-86. Ref.9 | ||||||||||||||||||||||||||
| Mutagenesis | 90 – 91 | 2 | WW → AA: Reduces affinity for UGUA RNA by 70%. Strongly reduced affinity for UGUA RNA; when associated with A-94. | ||||||||||||||||||||||||||
| Mutagenesis | 94 | 1 | D → A: Strongly reduced affinity for UGUA RNA; when associated with 90-A-A-91. Ref.16 | ||||||||||||||||||||||||||
| Mutagenesis | 111 | 1 | E → A: Reduces affinity for UGUA RNA by 85%. Ref.16 | ||||||||||||||||||||||||||
| Mutagenesis | 126 | 1 | F → A: Increases affinity for UGUA RNA by 40%. Ref.16 | ||||||||||||||||||||||||||
| Mutagenesis | 128 | 1 | L → A: Reduces affinity for UGUA RNA by 40%; when associated with A-84. Ref.16 | ||||||||||||||||||||||||||
| Sequence conflict | 9 | 1 | D → N in CAA47751. Ref.2 | ||||||||||||||||||||||||||
| Sequence conflict | 9 | 1 | D → N in CAA47752. Ref.2 | ||||||||||||||||||||||||||
Secondary structure | |||||||||||||||||||||||||||||
Helix Strand Turn | |||||||||||||||||||||||||||||
| Beta strand | 84 – 87 | 4 | |||||||||||||||||||||||||||
| Helix | 94 – 102 | 9 | |||||||||||||||||||||||||||
| Turn | 103 – 105 | 3 | |||||||||||||||||||||||||||
| Beta strand | 112 – 116 | 5 | |||||||||||||||||||||||||||
| Turn | 118 – 120 | 3 | |||||||||||||||||||||||||||
| Beta strand | 123 – 129 | 7 | |||||||||||||||||||||||||||
| Helix | 134 – 143 | 10 | |||||||||||||||||||||||||||
| Helix | 144 – 146 | 3 | |||||||||||||||||||||||||||
| Beta strand | 149 – 151 | 3 | |||||||||||||||||||||||||||
| Beta strand | 155 – 158 | 4 | |||||||||||||||||||||||||||
| Helix | 161 – 170 | 10 | |||||||||||||||||||||||||||
Sequences
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References
| « Hide 'large scale' references | |
| [1] | "Human pre-mRNA cleavage factor Im is related to spliceosomal SR proteins and can be reconstituted in vitro from recombinant subunits." Rueegsegger U., Blank D., Keller W. Mol. Cell 1:243-253(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), PROTEIN SEQUENCE OF 125-138 AND 162-168, FUNCTION, IDENTIFICATION IN THE CLEAVAGE FACTOR IM COMPLEX, SUBCELLULAR LOCATION. Tissue: Leukemia. |
| [2] | Fleischhauer K.L. Submitted (JUN-1995) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM 1). Tissue: Leukemia. |
| [3] | "Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. Sugano S.Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Spleen. |
| [4] | Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S. Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Heart. |
| [5] | Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. Venter J.C.Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. |
| [6] | "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 2 AND 3). Tissue: Kidney. |
| [7] | "Purification and characterization of human cleavage factor Im involved in the 3' end processing of messenger RNA precursors." Rueegsegger U., Beyer K., Keller W. J. Biol. Chem. 271:6107-6113(1996) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, IDENTIFICATION IN A CLEAVAGE FACTOR IM COMPLEX. |
| [8] | "A mechanism for the regulation of pre-mRNA 3' processing by human cleavage factor Im." Brown K.M., Gilmartin G.M. Mol. Cell 12:1467-1476(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION. |
| [9] | "Distinct sequence motifs within the 68-kDa subunit of cleavage factor Im mediate RNA binding, protein-protein interactions, and subcellular localization." Dettwiler S., Aringhieri C., Cardinale S., Keller W., Barabino S.M. J. Biol. Chem. 279:35788-35797(2004) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN A CLEAVAGE FACTOR IM COMPLEX, INTERACTION WITH NUDT21/CPSF5; SFRS3; SFRS7 AND TRA2B, RNA-BINDING, MUTAGENESIS OF GLY-86 AND ASN-87, SUBCELLULAR LOCATION. |
| [10] | "Association of polyadenylation cleavage factor I with U1 snRNP." Awasthi S., Alwine J.C. RNA 9:1400-1409(2003) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN A CLEAVAGE FACTOR IM COMPLEX, INTERACTION WITH NUDT21/CPSF5 AND SNRNP70. |
| [11] | "Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis." Cantin G.T., Yi W., Lu B., Park S.K., Xu T., Lee J.-D., Yates J.R. III J. Proteome Res. 7:1346-1351(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-404, MASS SPECTROMETRY. Tissue: Cervix carcinoma. |
| [12] | "A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. Tissue: Cervix carcinoma. |
| [13] | "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions." Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K. Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-407, MASS SPECTROMETRY. Tissue: Leukemic T-cell. |
| [14] | "Evidence that cleavage factor Im is a heterotetrameric protein complex controlling alternative polyadenylation." Kim S., Yamamoto J., Chen Y., Aida M., Wada T., Handa H., Yamaguchi Y. Genes Cells 15:1003-1013(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBUNIT, SUBCELLULAR LOCATION. |
| [15] | "Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. |
| [16] | "Crystal structure of a human cleavage factor CFI(m)25/CFI(m)68/RNA complex provides an insight into poly(A) site recognition and RNA looping." Yang Q., Coseno M., Gilmartin G.M., Doublie S. Structure 19:368-377(2011) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF 13-235 IN COMPLEX WITH NUDT21/CPSF5 AND RNA, FUNCTION, SUBUNIT, MUTAGENESIS OF TYR-84; 90-TRP-TRP-91; ASP-94; GLU-111; PHE-126 AND LEU-128. |
| + | Additional computationally mapped references. |
Cross-references
Sequence databases | |||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| EMBL GenBank DDBJ | X67336 Genomic DNA. Translation: CAA47751.1. X67337 mRNA. Translation: CAA47752.1. AK223568 mRNA. Translation: BAD97288.1. AK292024 mRNA. Translation: BAF84713.1. CH471054 Genomic DNA. Translation: EAW97215.1. BC000714 mRNA. Translation: AAH00714.1. BC005000 mRNA. Translation: AAH05000.1. | ||||||||||||||||||||||||||||||||||||
| IPI | IPI00012998. IPI00030654. IPI01025254. | ||||||||||||||||||||||||||||||||||||
| PIR | S57447. | ||||||||||||||||||||||||||||||||||||
| RefSeq | NP_008938.2. NM_007007.2. | ||||||||||||||||||||||||||||||||||||
| UniGene | Hs.369606. | ||||||||||||||||||||||||||||||||||||
3D structure databases | |||||||||||||||||||||||||||||||||||||
| PDBe RCSB PDB PDBj |
| ||||||||||||||||||||||||||||||||||||
| ProteinModelPortal | Q16630. | ||||||||||||||||||||||||||||||||||||
| ModBase | Search... | ||||||||||||||||||||||||||||||||||||
Protein-protein interaction databases | |||||||||||||||||||||||||||||||||||||
| DIP | DIP-34501N. | ||||||||||||||||||||||||||||||||||||
| IntAct | Q16630. 25 interactions. | ||||||||||||||||||||||||||||||||||||
| MINT | MINT-1153789. | ||||||||||||||||||||||||||||||||||||
| STRING | 9606.ENSP00000391774. | ||||||||||||||||||||||||||||||||||||
PTM databases | |||||||||||||||||||||||||||||||||||||
| PhosphoSite | Q16630. | ||||||||||||||||||||||||||||||||||||
Polymorphism databases | |||||||||||||||||||||||||||||||||||||
| DMDM | 88909266. | ||||||||||||||||||||||||||||||||||||
Proteomic databases | |||||||||||||||||||||||||||||||||||||
| PaxDb | Q16630. | ||||||||||||||||||||||||||||||||||||
| PeptideAtlas | Q16630. | ||||||||||||||||||||||||||||||||||||
| PRIDE | Q16630. | ||||||||||||||||||||||||||||||||||||
Protocols and materials databases | |||||||||||||||||||||||||||||||||||||
| DNASU | 11052. | ||||||||||||||||||||||||||||||||||||
| StructuralBiologyKnowledgebase | Search... | ||||||||||||||||||||||||||||||||||||
Genome annotation databases | |||||||||||||||||||||||||||||||||||||
| Ensembl | ENST00000266679; ENSP00000266679; ENSG00000111605. ENST00000435070; ENSP00000391774; ENSG00000111605. | ||||||||||||||||||||||||||||||||||||
| GeneID | 11052. | ||||||||||||||||||||||||||||||||||||
| KEGG | hsa:11052. | ||||||||||||||||||||||||||||||||||||
| UCSC | uc001sut.4. human. uc001suu.4. human. | ||||||||||||||||||||||||||||||||||||
Organism-specific databases | |||||||||||||||||||||||||||||||||||||
| CTD | 11052. | ||||||||||||||||||||||||||||||||||||
| GeneCards | GC12P069633. | ||||||||||||||||||||||||||||||||||||
| HGNC | HGNC:13871. CPSF6. | ||||||||||||||||||||||||||||||||||||
| HPA | HPA039973. | ||||||||||||||||||||||||||||||||||||
| MIM | 604979. gene. | ||||||||||||||||||||||||||||||||||||
| neXtProt | NX_Q16630. | ||||||||||||||||||||||||||||||||||||
| PharmGKB | PA26846. | ||||||||||||||||||||||||||||||||||||
| GenAtlas | Search... | ||||||||||||||||||||||||||||||||||||
Phylogenomic databases | |||||||||||||||||||||||||||||||||||||
| eggNOG | NOG313287. | ||||||||||||||||||||||||||||||||||||
| HOGENOM | HOG000111137. | ||||||||||||||||||||||||||||||||||||
| KO | K14398. | ||||||||||||||||||||||||||||||||||||
| OMA | GKGSAPN. | ||||||||||||||||||||||||||||||||||||
| OrthoDB | EOG432101. | ||||||||||||||||||||||||||||||||||||
Enzyme and pathway databases | |||||||||||||||||||||||||||||||||||||
| Reactome | REACT_116125. Disease. | ||||||||||||||||||||||||||||||||||||
Gene expression databases | |||||||||||||||||||||||||||||||||||||
| ArrayExpress | Q16630. | ||||||||||||||||||||||||||||||||||||
| Bgee | Q16630. | ||||||||||||||||||||||||||||||||||||
| CleanEx | HS_CPSF6. | ||||||||||||||||||||||||||||||||||||
| Genevestigator | Q16630. | ||||||||||||||||||||||||||||||||||||
| GermOnline | ENSG00000111605. Homo sapiens. | ||||||||||||||||||||||||||||||||||||
Family and domain databases | |||||||||||||||||||||||||||||||||||||
| Gene3D | 3.30.70.330. 1 hit. | ||||||||||||||||||||||||||||||||||||
| InterPro | IPR012677. Nucleotide-bd_a/b_plait. IPR000504. RRM_dom. [Graphical view] | ||||||||||||||||||||||||||||||||||||
| SMART | SM00360. RRM. 1 hit. [Graphical view] | ||||||||||||||||||||||||||||||||||||
| PROSITE | PS50102. RRM. 1 hit. [Graphical view] | ||||||||||||||||||||||||||||||||||||
| ProtoNet | Search... | ||||||||||||||||||||||||||||||||||||
Other | |||||||||||||||||||||||||||||||||||||
| GenomeRNAi | 11052. | ||||||||||||||||||||||||||||||||||||
| NextBio | 41995. | ||||||||||||||||||||||||||||||||||||
| SOURCE | Search... | ||||||||||||||||||||||||||||||||||||
Entry information
| Entry name | CPSF6_HUMAN | ||||||||
| Accession | Primary (citable) accession number: Q16630 Secondary accession number(s): A8K7K9 Q9BW18 | ||||||||
| Entry history |
| ||||||||
| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation program | Chordata Protein Annotation Program | ||||||||
| Disclaimer | Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care. | ||||||||
Relevant documents
| Human chromosome 12 Human chromosome 12: entries, gene names and cross-references to MIM |
| MIM cross-references Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot |
| PDB cross-references Index of Protein Data Bank (PDB) cross-references |
| SIMILARITY comments Index of protein domains and families |

Clusters with
