UniProtKB - Q6NWC6 (CPSF6_DANRE)
Protein
Cleavage and polyadenylation specificity factor subunit 6
Gene
cpsf6
Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Functioni
Component of the cleavage factor Im (CFIm) complex that functions as an activator of the pre-mRNA 3'-end cleavage and polyadenylation processing required for the maturation of pre-mRNA into functional mRNAs. CFIm contributes to the recruitment of multiprotein complexes on specific sequences on the pre-mRNA 3'-end, so called cleavage and polyadenylation signals (pA signals). Most pre-mRNAs contain multiple pA signals, resulting in alternative cleavage and polyadenylation (APA) producing mRNAs with variable 3'-end formation. The CFIm complex acts as a key regulator of cleavage and polyadenylation site choice during APA through its binding to 5'-UGUA-3' elements localized in the 3'-untranslated region (UTR) for a huge number of pre-mRNAs. Plays a role in mRNA export.By similarity
GO - Molecular functioni
- mRNA binding Source: UniProtKB
GO - Biological processi
- messenger ribonucleoprotein complex assembly Source: UniProtKB
- mRNA alternative polyadenylation Source: UniProtKB
- mRNA processing Source: UniProtKB-KW
- positive regulation of RNA export from nucleus Source: UniProtKB
- protein heterotetramerization Source: UniProtKB
Keywordsi
Biological process | mRNA processing |
Enzyme and pathway databases
Reactomei | R-DRE-72163, mRNA Splicing - Major Pathway R-DRE-72187, mRNA 3'-end processing R-DRE-73856, RNA Polymerase II Transcription Termination R-DRE-77595, Processing of Intronless Pre-mRNAs |
Names & Taxonomyi
Protein namesi | Recommended name: Cleavage and polyadenylation specificity factor subunit 6By similarity |
Gene namesi | Name:cpsf6By similarity |
Organismi | Danio rerio (Zebrafish) (Brachydanio rerio) |
Taxonomic identifieri | 7955 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Actinopterygii › Neopterygii › Teleostei › Ostariophysi › Cypriniformes › Danionidae › Danioninae › Danio |
Proteomesi |
|
Organism-specific databases
ZFINi | ZDB-GENE-030131-5277, cpsf6 |
Subcellular locationi
Nucleus
- Nucleus By similarity
- nucleoplasm By similarity
- Nucleus speckle By similarity
Other locations
- Cytoplasm By similarity
Note: Shuttles between the nucleus and the cytoplasm.By similarity
Nucleus
- interchromatin granule Source: UniProtKB
- mRNA cleavage factor complex Source: UniProtKB
- nuclear speck Source: UniProtKB
- nucleoplasm Source: UniProtKB
- nucleus Source: UniProtKB
- paraspeckles Source: UniProtKB
- perichromatin fibrils Source: UniProtKB
Other locations
- cytoplasm Source: UniProtKB
Keywords - Cellular componenti
Cytoplasm, NucleusPTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000081525 | 1 – 545 | Cleavage and polyadenylation specificity factor subunit 6Add BLAST | 545 |
Proteomic databases
PaxDbi | Q6NWC6 |
PRIDEi | Q6NWC6 |
Expressioni
Gene expression databases
Bgeei | ENSDARG00000018618, Expressed in gastrula and 39 other tissues |
ExpressionAtlasi | Q6NWC6, baseline and differential |
Interactioni
Subunit structurei
Component of the cleavage factor Im (CFIm) complex.
By similarityProtein-protein interaction databases
STRINGi | 7955.ENSDARP00000076726 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 81 – 161 | RRMPROSITE-ProRule annotationAdd BLAST | 81 |
Compositional bias
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Compositional biasi | 188 – 384 | Pro-richAdd BLAST | 197 | |
Compositional biasi | 484 – 545 | Arg-richAdd BLAST | 62 |
Sequence similaritiesi
Belongs to the RRM CPSF6/7 family.Curated
Phylogenomic databases
eggNOGi | KOG4849, Eukaryota |
GeneTreei | ENSGT00730000110905 |
HOGENOMi | CLU_025289_1_0_1 |
InParanoidi | Q6NWC6 |
OMAi | HPQGGLM |
OrthoDBi | 1016696at2759 |
PhylomeDBi | Q6NWC6 |
TreeFami | TF316430 |
Family and domain databases
Gene3Di | 3.30.70.330, 1 hit |
InterProi | View protein in InterPro IPR034769, CPSF6 IPR034772, CPSF6/7 IPR012677, Nucleotide-bd_a/b_plait_sf IPR035979, RBD_domain_sf IPR000504, RRM_dom |
PANTHERi | PTHR23204, PTHR23204, 1 hit PTHR23204:SF3, PTHR23204:SF3, 1 hit |
Pfami | View protein in Pfam PF00076, RRM_1, 1 hit |
SMARTi | View protein in SMART SM00360, RRM, 1 hit |
SUPFAMi | SSF54928, SSF54928, 1 hit |
PROSITEi | View protein in PROSITE PS50102, RRM, 1 hit |
s (2+)i Sequence
Sequence statusi: Complete.
This entry describes 2 produced by isoformsialternative splicing. AlignAdd to basketThis entry has 2 described isoforms and 3 potential isoforms that are computationally mapped.Show allAlign All
Isoform 1 (identifier: Q6NWC6-1) [UniParc]FASTAAdd to basket
This isoform has been chosen as the sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. canonicali
10 20 30 40 50
MADGVDHIDI YADVEEEFNQ ESDYPVHDQI DLYDDVISPS ANNGDAPEDR
60 70 80 90 100
DYLDSLPAPG GNEGSKGAPA NVVYTYNGKR IALYIGNLTW WTTDEDLTDA
110 120 130 140 150
IRSIGINDVL EIKFFENRAN GQSKGFALVC VGSDSSSRKL MDLLSKRELH
160 170 180 190 200
GQNPIVTPCN KQSLSQFEMQ SRKSTQSGQM SGEGKAGPPG SGSRGGGFPP
210 220 230 240 250
GKGQRRFPGP PGQGDRFPGP VGPGGPPPHF PGMQGPPRLP SGPPGPLGPP
260 270 280 290 300
GPPPPGQGLP PPLGGPPNRG DRPPPPVLFP GQFGQPPMGP MPPGPPPPGY
310 320 330 340 350
GPPPGPPPPQ QGPPPPGPFP PRPPGPLGPP LGLAPPPHMQ GPPPGGPPPA
360 370 380 390 400
PHVNPAFFPP PGNNMPSSDG RGPPPGDPYG RPPPYDRDFP GGRDMDASRT
410 420 430 440 450
PLSEAEFEEI MNRNRAISSS AISRAVSDAS AADYGSAIET LVTAISLIKQ
460 470 480 490 500
SKVSADDRCK VLISSLQDCL HGIESKSYGS VAGRRERSRE RDHSRSREKS
510 520 530 540
RRHKSRSRDR HEDYYRERSR ERDRHRERDR DRERDRERER EYRHR
Computationally mapped potential isoform sequencesi
There are 3 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basketA0A2R8RIN6 | A0A2R8RIN6_DANRE | Cleavage and polyadenylation specif... | cpsf6 | 571 | Annotation score: | ||
H0WFE8 | H0WFE8_DANRE | Cleavage and polyadenylation-specif... | cpsf6 | 127 | Annotation score: | ||
Q1L8Q3 | Q1L8Q3_DANRE | Cleavage and polyadenylation-specif... | cpsf6 | 117 | Annotation score: |
Alternative sequence
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Alternative sequenceiVSP_017193 | 174 | S → SERRGFDNSHYHKG in isoform 2. 1 Publication | 1 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AY398330 mRNA Translation: AAQ97763.1 BC067642 mRNA Translation: AAH67642.1 |
RefSeqi | NP_001017993.1, NM_001017993.1 [Q6NWC6-2] XP_005164510.1, XM_005164453.3 [Q6NWC6-1] |
Genome annotation databases
Ensembli | ENSDART00000082289; ENSDARP00000076726; ENSDARG00000018618 [Q6NWC6-2] ENSDART00000129521; ENSDARP00000110285; ENSDARG00000018618 [Q6NWC6-1] |
GeneIDi | 327069 |
KEGGi | dre:327069 |
Keywords - Coding sequence diversityi
Alternative splicingSimilar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AY398330 mRNA Translation: AAQ97763.1 BC067642 mRNA Translation: AAH67642.1 |
RefSeqi | NP_001017993.1, NM_001017993.1 [Q6NWC6-2] XP_005164510.1, XM_005164453.3 [Q6NWC6-1] |
3D structure databases
SMRi | Q6NWC6 |
ModBasei | Search... |
Protein-protein interaction databases
STRINGi | 7955.ENSDARP00000076726 |
Proteomic databases
PaxDbi | Q6NWC6 |
PRIDEi | Q6NWC6 |
Genome annotation databases
Ensembli | ENSDART00000082289; ENSDARP00000076726; ENSDARG00000018618 [Q6NWC6-2] ENSDART00000129521; ENSDARP00000110285; ENSDARG00000018618 [Q6NWC6-1] |
GeneIDi | 327069 |
KEGGi | dre:327069 |
Organism-specific databases
CTDi | 11052 |
ZFINi | ZDB-GENE-030131-5277, cpsf6 |
Phylogenomic databases
eggNOGi | KOG4849, Eukaryota |
GeneTreei | ENSGT00730000110905 |
HOGENOMi | CLU_025289_1_0_1 |
InParanoidi | Q6NWC6 |
OMAi | HPQGGLM |
OrthoDBi | 1016696at2759 |
PhylomeDBi | Q6NWC6 |
TreeFami | TF316430 |
Enzyme and pathway databases
Reactomei | R-DRE-72163, mRNA Splicing - Major Pathway R-DRE-72187, mRNA 3'-end processing R-DRE-73856, RNA Polymerase II Transcription Termination R-DRE-77595, Processing of Intronless Pre-mRNAs |
Miscellaneous databases
PROi | PR:Q6NWC6 |
Gene expression databases
Bgeei | ENSDARG00000018618, Expressed in gastrula and 39 other tissues |
ExpressionAtlasi | Q6NWC6, baseline and differential |
Family and domain databases
Gene3Di | 3.30.70.330, 1 hit |
InterProi | View protein in InterPro IPR034769, CPSF6 IPR034772, CPSF6/7 IPR012677, Nucleotide-bd_a/b_plait_sf IPR035979, RBD_domain_sf IPR000504, RRM_dom |
PANTHERi | PTHR23204, PTHR23204, 1 hit PTHR23204:SF3, PTHR23204:SF3, 1 hit |
Pfami | View protein in Pfam PF00076, RRM_1, 1 hit |
SMARTi | View protein in SMART SM00360, RRM, 1 hit |
SUPFAMi | SSF54928, SSF54928, 1 hit |
PROSITEi | View protein in PROSITE PS50102, RRM, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | CPSF6_DANRE | |
Accessioni | Q6NWC6Primary (citable) accession number: Q6NWC6 Secondary accession number(s): Q6TH26 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | February 7, 2006 |
Last sequence update: | July 5, 2004 | |
Last modified: | December 2, 2020 | |
This is version 113 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
Reference proteomeDocuments
- SIMILARITY comments
Index of protein domains and families