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Protein

Cleavage and polyadenylation specificity factor subunit 6

Gene

Cpsf6

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

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. CPSF6 enhances NUDT21/CPSF5 binding to 5'-UGUA-3' elements localized upstream of pA signals and promotes RNA looping, and hence activates directly the mRNA 3'-processing machinery. Plays a role in mRNA export.By similarity

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionRNA-binding
Biological processmRNA processing

Names & Taxonomyi

Protein namesi
Recommended name:
Cleavage and polyadenylation specificity factor subunit 6By similarity
Gene namesi
Name:Cpsf6Imported
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 10

Organism-specific databases

MGIiMGI:1913948 Cpsf6

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000815221 – 551Cleavage and polyadenylation specificity factor subunit 6Add BLAST551

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei404PhosphothreonineBy similarity1
Modified residuei407PhosphothreonineBy similarity1

Post-translational modificationi

Phosphorylated. Phosphorylated in the Arg/Ser-rich domain by SRPK1, in vitro.By similarity
Symmetrically dimethylated on arginine residues by PRMT5 in a WDR77- and CLNS1A-dependent manner. Asymmetrically dimethylated on arginine residues by PRMT1.By similarity
Symmetrically dimethylated on arginine residues in the GAR motif by PRMT5 in a WDR77- and CLNS1A-dependent manner. Asymmetrically dimethylated on arginine residues in the GAR motif by PRMT1.By similarity

Keywords - PTMi

Methylation, Phosphoprotein

Proteomic databases

EPDiQ6NVF9
MaxQBiQ6NVF9
PaxDbiQ6NVF9
PRIDEiQ6NVF9

PTM databases

iPTMnetiQ6NVF9
PhosphoSitePlusiQ6NVF9

Expressioni

Tissue specificityi

Expressed in testis (PubMed:18032416). Expressed in male germ cells (at protein level) (PubMed:18032416).1 Publication

Inductioni

Up-regulated during spermatogenesis (PubMed:18032416).1 Publication

Gene expression databases

BgeeiENSMUSG00000055531 Expressed in 247 organ(s), highest expression level in pes
CleanExiMM_CPSF6
ExpressionAtlasiQ6NVF9 baseline and differential
GenevisibleiQ6NVF9 MM

Interactioni

Subunit structurei

Component of the cleavage factor Im (CFIm) complex which is an heterotetramer composed of two subunits of NUDT21/CPSF5 and two subunits of CPSF6 or CPSF7 or an heterodimer of CPSF6 and CPSF7. The cleavage factor Im (CFIm) complex associates with the CPSF and CSTF complexes to promote the assembly of the core mRNA 3'-processing machinery. Associates with the exon junction complex (EJC). Associates with the 80S ribosome particle. Interacts (via the RRM domain) with NUDT21/CPSF5; this interaction is direct and enhances binding to RNA. Interacts (via Arg/Ser-rich domain) with FIP1L1 (preferentially via unphosphorylated form and Arg/Glu/Asp-rich region); this interaction mediates, at least in part, the interaction between the CFIm and CPSF complexes and may be inhibited by CPSF6 hyper-phosphorylation. Interacts (via N-terminus) with NXF1; this interaction is direct. Interacts with SRSF3. Interacts with SRSF7. Interacts with SNRNP70. Interacts with TRA2B/SFRS10. Interacts with UPF1. Interacts with UPF3B. Interacts with VIRMA.By similarity

Protein-protein interaction databases

BioGridi240650, 6 interactors
DIPiDIP-49394N
IntActiQ6NVF9, 4 interactors
MINTiQ6NVF9
STRINGi10090.ENSMUSP00000068408

Structurei

3D structure databases

ProteinModelPortaliQ6NVF9
SMRiQ6NVF9
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini81 – 161RRMPROSITE-ProRule annotationAdd BLAST81

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 213Necessary for interaction with NXF1By similarityAdd BLAST213
Regioni81 – 161Necessary for interaction with NUDT21/CPSF5By similarityAdd BLAST81
Regioni81 – 161Necessary for nuclear paraspeckles localizationBy similarityAdd BLAST81
Regioni404 – 551Sufficient for nuclear speckle localizationBy similarityAdd BLAST148
Regioni405 – 551Necessary for RNA-bindingBy similarityAdd BLAST147
Regioni481 – 551Necessary for interaction with SRSF3, SRSF7 and TRA2B/SFRS10By similarityAdd BLAST71
Regioni490 – 551Arg/Ser-rich domainBy similarityAdd BLAST62
Regioni510 – 551Sufficient for nuclear targetingBy similarityAdd BLAST42

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi202 – 206GARBy similarity5

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi208 – 398Pro-richAdd BLAST191
Compositional biasi490 – 551Arg-richAdd BLAST62

Domaini

Contains an Arg/Ser-rich domain composed of arginine-serine dipeptide repeats within the C-terminal region that is necessary and sufficient for activating mRNA 3'-processing and alternative polyadenylation (APA).By similarity

Sequence similaritiesi

Belongs to the RRM CPSF6/7 family.Curated

Phylogenomic databases

eggNOGiKOG4849 Eukaryota
ENOG410Y0H0 LUCA
GeneTreeiENSGT00730000110905
HOGENOMiHOG000111137
InParanoidiQ6NVF9
KOiK14398
PhylomeDBiQ6NVF9
TreeFamiTF316430

Family and domain databases

Gene3Di3.30.70.330, 1 hit
InterProiView protein in InterPro
IPR034769 CPSF6
IPR034772 CPSF6/7
IPR012677 Nucleotide-bd_a/b_plait_sf
IPR035979 RBD_domain_sf
IPR000504 RRM_dom
PANTHERiPTHR23204 PTHR23204, 1 hit
PTHR23204:SF3 PTHR23204:SF3, 1 hit
PfamiView protein in Pfam
PF00076 RRM_1, 1 hit
SMARTiView protein in SMART
SM00360 RRM, 1 hit
SUPFAMiSSF54928 SSF54928, 1 hit
PROSITEiView protein in PROSITE
PS50102 RRM, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 5 potential isoforms that are computationally mapped.Show allAlign All

Q6NVF9-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MADGVDHIDI YADVGEEFNQ EAEYGGHDQI DLYDDVISPS ANNGDAPEDR
60 70 80 90 100
DYMDTLPPTV GDDVGKGAAP NVVYTYTGKR IALYIGNLTW WTTDEDLTEA
110 120 130 140 150
VHSLGVNDIL EIKFFENRAN GQSKGFALVG VGSEASSKKL MDLLPKRELH
160 170 180 190 200
GQSPVVTPCN KQFLSQFEMQ SRKTTQSGQM SGEGKAGPPG GGSRAAFPQG
210 220 230 240 250
GRGRGRFPGA VPGGDRFPGP AGPGGPPPPF PAGQTPPRPP LGPPGPPGPP
260 270 280 290 300
GPPPPGQVLP PPLAGPPNRG DRPPPPVLFP GQPFGQPPLG PLPPGPPPPV
310 320 330 340 350
PGYGPPPGPP PPQQGPPPPP GPFPPRPPGP LGPPLTLAPP PHLPGPPPGA
360 370 380 390 400
PPPAPHVNPA FFPPPTNSGM PTSDSRGPPP TDPYGRPPPY DRGDYGPPGR
410 420 430 440 450
EMDTARTPLS EAEFEEIMNR NRAISSSAIS RAVSDASAGD YGSAIETLVT
460 470 480 490 500
AISLIKQSKV SADDRCKVLI SSLQDCLHGI ESKSYGSGSR RERSRERDHS
510 520 530 540 550
RSREKSRRHK SRSRDRHDDY YRERSRERER HRDRDRDRDR ERDREREYRH

R
Length:551
Mass (Da):59,153
Last modified:July 5, 2004 - v1
Checksum:iFCE1420FBE7589C8
GO

Computationally mapped potential isoform sequencesi

There are 5 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
H3BJ30H3BJ30_MOUSE
Cleavage and polyadenylation-specif...
Cpsf6
552Annotation score:
H3BJW3H3BJW3_MOUSE
Cleavage and polyadenylation-specif...
Cpsf6
588Annotation score:
H3BKW0H3BKW0_MOUSE
Cleavage and polyadenylation-specif...
Cpsf6
182Annotation score:
H3BLM9H3BLM9_MOUSE
Cleavage and polyadenylation-specif...
Cpsf6
91Annotation score:
H3BLM1H3BLM1_MOUSE
Cleavage and polyadenylation-specif...
Cpsf6
39Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti95E → K in BAC32898 (PubMed:16141072).Curated1
Sequence conflicti266P → L in BAC32898 (PubMed:16141072).Curated1
Sequence conflicti289L → V in BAC33392 (PubMed:16141072).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK046856 mRNA Translation: BAC32898.1
AK048615 mRNA Translation: BAC33392.1
AK168764 mRNA Translation: BAE40600.1
BC068133 mRNA Translation: AAH68133.1
CCDSiCCDS24193.1
RefSeqiNP_001013409.1, NM_001013391.2
XP_006513921.1, XM_006513858.3
UniGeneiMm.478881
Mm.478884
Mm.479892

Genome annotation databases

EnsembliENSMUST00000069168; ENSMUSP00000068408; ENSMUSG00000055531
ENSMUST00000177145; ENSMUSP00000135136; ENSMUSG00000055531
GeneIDi432508
KEGGimmu:432508
UCSCiuc007hdd.2 mouse

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK046856 mRNA Translation: BAC32898.1
AK048615 mRNA Translation: BAC33392.1
AK168764 mRNA Translation: BAE40600.1
BC068133 mRNA Translation: AAH68133.1
CCDSiCCDS24193.1
RefSeqiNP_001013409.1, NM_001013391.2
XP_006513921.1, XM_006513858.3
UniGeneiMm.478881
Mm.478884
Mm.479892

3D structure databases

ProteinModelPortaliQ6NVF9
SMRiQ6NVF9
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi240650, 6 interactors
DIPiDIP-49394N
IntActiQ6NVF9, 4 interactors
MINTiQ6NVF9
STRINGi10090.ENSMUSP00000068408

PTM databases

iPTMnetiQ6NVF9
PhosphoSitePlusiQ6NVF9

Proteomic databases

EPDiQ6NVF9
MaxQBiQ6NVF9
PaxDbiQ6NVF9
PRIDEiQ6NVF9

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000069168; ENSMUSP00000068408; ENSMUSG00000055531
ENSMUST00000177145; ENSMUSP00000135136; ENSMUSG00000055531
GeneIDi432508
KEGGimmu:432508
UCSCiuc007hdd.2 mouse

Organism-specific databases

CTDi11052
MGIiMGI:1913948 Cpsf6

Phylogenomic databases

eggNOGiKOG4849 Eukaryota
ENOG410Y0H0 LUCA
GeneTreeiENSGT00730000110905
HOGENOMiHOG000111137
InParanoidiQ6NVF9
KOiK14398
PhylomeDBiQ6NVF9
TreeFamiTF316430

Miscellaneous databases

PROiPR:Q6NVF9
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000055531 Expressed in 247 organ(s), highest expression level in pes
CleanExiMM_CPSF6
ExpressionAtlasiQ6NVF9 baseline and differential
GenevisibleiQ6NVF9 MM

Family and domain databases

Gene3Di3.30.70.330, 1 hit
InterProiView protein in InterPro
IPR034769 CPSF6
IPR034772 CPSF6/7
IPR012677 Nucleotide-bd_a/b_plait_sf
IPR035979 RBD_domain_sf
IPR000504 RRM_dom
PANTHERiPTHR23204 PTHR23204, 1 hit
PTHR23204:SF3 PTHR23204:SF3, 1 hit
PfamiView protein in Pfam
PF00076 RRM_1, 1 hit
SMARTiView protein in SMART
SM00360 RRM, 1 hit
SUPFAMiSSF54928 SSF54928, 1 hit
PROSITEiView protein in PROSITE
PS50102 RRM, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiCPSF6_MOUSE
AccessioniPrimary (citable) accession number: Q6NVF9
Secondary accession number(s): Q8BX86, Q8BXI8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 7, 2006
Last sequence update: July 5, 2004
Last modified: September 12, 2018
This is version 128 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
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