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Protein

Cleavage and polyadenylation specificity factor subunit 4

Gene

CPSF4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition. CPSF4 binds RNA polymers with a preference for poly(U).2 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri35 – 61C3H1-type 1PROSITE-ProRule annotationAdd BLAST27
Zinc fingeri62 – 89C3H1-type 2PROSITE-ProRule annotationAdd BLAST28
Zinc fingeri90 – 117C3H1-type 3PROSITE-ProRule annotationAdd BLAST28
Zinc fingeri118 – 142C3H1-type 4PROSITE-ProRule annotationAdd BLAST25
Zinc fingeri143 – 169C3H1-type 5PROSITE-ProRule annotationAdd BLAST27
Zinc fingeri243 – 260CCHC-typePROSITE-ProRule annotationAdd BLAST18

GO - Molecular functioni

  • endoribonuclease activity Source: GO_Central
  • poly(A) RNA binding Source: UniProtKB
  • RNA binding Source: GO_Central
  • zinc ion binding Source: InterPro

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Host-virus interaction, mRNA processing

Keywords - Ligandi

Metal-binding, RNA-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-109688. Cleavage of Growing Transcript in the Termination Region.
R-HSA-159231. Transport of Mature mRNA Derived from an Intronless Transcript.
R-HSA-168315. Inhibition of Host mRNA Processing and RNA Silencing.
R-HSA-6784531. tRNA processing in the nucleus.
R-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72187. mRNA 3'-end processing.
R-HSA-77595. Processing of Intronless Pre-mRNAs.

Names & Taxonomyi

Protein namesi
Recommended name:
Cleavage and polyadenylation specificity factor subunit 4
Alternative name(s):
Cleavage and polyadenylation specificity factor 30 kDa subunit
Short name:
CPSF 30 kDa subunit
NS1 effector domain-binding protein 1
Short name:
Neb-1
No arches homolog
Gene namesi
Name:CPSF4
Synonyms:CPSF30, NAR, NEB1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 7

Organism-specific databases

HGNCiHGNC:2327. CPSF4.

Subcellular locationi

GO - Cellular componenti

  • mRNA cleavage and polyadenylation specificity factor complex Source: UniProtKB
  • nucleoplasm Source: Reactome
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi10898.
OpenTargetsiENSG00000160917.
PharmGKBiPA26844.

Polymorphism and mutation databases

BioMutaiCPSF4.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000744021 – 269Cleavage and polyadenylation specificity factor subunit 4Add BLAST269

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei200PhosphoserineCombined sources1
Modified residuei202PhosphoserineCombined sources1
Modified residuei212PhosphoserineCombined sources1
Modified residuei267PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiO95639.
MaxQBiO95639.
PaxDbiO95639.
PeptideAtlasiO95639.
PRIDEiO95639.

PTM databases

iPTMnetiO95639.
PhosphoSitePlusiO95639.

Expressioni

Gene expression databases

BgeeiENSG00000160917.
CleanExiHS_CPSF4.
ExpressionAtlasiO95639. baseline and differential.
GenevisibleiO95639. HS.

Organism-specific databases

HPAiHPA049094.
HPA066470.

Interactioni

Subunit structurei

Component of the cleavage and polyadenylation specificity factor (CPSF) complex, composed of CPSF1, CPSF2, CPSF3, CPSF4 and FIP1L1. Interacts with FIP1L1. Association with influenza A virus NS1 blocks processing of pre-mRNAs, thereby preventing nuclear export of host cell mRNAs.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
MEOX2A4D1273EBI-725860,EBI-10172134

Protein-protein interaction databases

BioGridi116104. 29 interactors.
DIPiDIP-48675N.
IntActiO95639. 18 interactors.
MINTiMINT-1429837.
STRINGi9606.ENSP00000292476.

Structurei

Secondary structure

1269
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi69 – 72Combined sources4
Helixi79 – 81Combined sources3
Beta strandi82 – 85Combined sources4
Turni90 – 92Combined sources3
Helixi97 – 102Combined sources6
Beta strandi111 – 113Combined sources3
Beta strandi122 – 125Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2D9NNMR-A61-126[»]
2RHKX-ray1.95C/D61-121[»]
ProteinModelPortaliO95639.
SMRiO95639.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO95639.

Family & Domainsi

Sequence similaritiesi

Belongs to the CPSF4/YTH1 family.Curated
Contains 5 C3H1-type zinc fingers.PROSITE-ProRule annotation
Contains 1 CCHC-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri35 – 61C3H1-type 1PROSITE-ProRule annotationAdd BLAST27
Zinc fingeri62 – 89C3H1-type 2PROSITE-ProRule annotationAdd BLAST28
Zinc fingeri90 – 117C3H1-type 3PROSITE-ProRule annotationAdd BLAST28
Zinc fingeri118 – 142C3H1-type 4PROSITE-ProRule annotationAdd BLAST25
Zinc fingeri143 – 169C3H1-type 5PROSITE-ProRule annotationAdd BLAST27
Zinc fingeri243 – 260CCHC-typePROSITE-ProRule annotationAdd BLAST18

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1040. Eukaryota.
COG5084. LUCA.
GeneTreeiENSGT00390000009627.
HOGENOMiHOG000212457.
HOVERGENiHBG051108.
InParanoidiO95639.
KOiK14404.
OMAiANKCTKG.
OrthoDBiEOG091G0JUF.
PhylomeDBiO95639.
TreeFamiTF314871.

Family and domain databases

Gene3Di4.10.1000.10. 2 hits.
4.10.60.10. 1 hit.
InterProiIPR000571. Znf_CCCH.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00642. zf-CCCH. 1 hit.
PF00098. zf-CCHC. 1 hit.
[Graphical view]
SMARTiSM00343. ZnF_C2HC. 1 hit.
SM00356. ZnF_C3H1. 5 hits.
[Graphical view]
SUPFAMiSSF57756. SSF57756. 1 hit.
SSF90229. SSF90229. 2 hits.
PROSITEiPS50103. ZF_C3H1. 5 hits.
PS50158. ZF_CCHC. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: O95639-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MQEIIASVDH IKFDLEIAVE QQLGAQPLPF PGMDKSGAAV CEFFLKAACG
60 70 80 90 100
KGGMCPFRHI SGEKTVVCKH WLRGLCKKGD QCEFLHEYDM TKMPECYFYS
110 120 130 140 150
KFGECSNKEC PFLHIDPESK IKDCPWYDRG FCKHGPLCRH RHTRRVICVN
160 170 180 190 200
YLVGFCPEGP SCKFMHPRFE LPMGTTEQPP LPQQTQPPAK QSNNPPLQRS
210 220 230 240 250
SSLIQLTSQN SSPNQQRTPQ VIGVMQSQNS SAGNRGPRPL EQVTCYKCGE
260
KGHYANRCTK GHLAFLSGQ
Length:269
Mass (Da):30,255
Last modified:May 1, 1999 - v1
Checksum:i49444E3EB840464A
GO
Isoform 2 (identifier: O95639-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     191-215: Missing.

Note: No experimental confirmation available.
Show »
Length:244
Mass (Da):27,547
Checksum:i0DF72BE36CF97106
GO
Isoform 3 (identifier: O95639-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     191-216: Missing.

Note: May be due to a competing acceptor splice site. No experimental confirmation available.
Show »
Length:243
Mass (Da):27,419
Checksum:i3535FE5A0D525C8F
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_008602191 – 216Missing in isoform 3. 1 PublicationAdd BLAST26
Alternative sequenceiVSP_008601191 – 215Missing in isoform 2. 1 PublicationAdd BLAST25

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U79569 mRNA. Translation: AAD00321.1.
CR542161 mRNA. Translation: CAG46958.1.
EF191081 Genomic DNA. Translation: ABN05292.1.
CH236956 Genomic DNA. Translation: EAL23878.1.
CH471091 Genomic DNA. Translation: EAW76667.1.
CH471091 Genomic DNA. Translation: EAW76668.1.
BC003101 mRNA. Translation: AAH03101.1.
BC050738 mRNA. Translation: AAH50738.1.
CCDSiCCDS47652.1. [O95639-2]
CCDS5664.1. [O95639-1]
RefSeqiNP_001075028.1. NM_001081559.2. [O95639-2]
NP_001305089.1. NM_001318160.1. [O95639-3]
NP_001305090.1. NM_001318161.1.
NP_001305091.1. NM_001318162.1.
NP_006684.1. NM_006693.3. [O95639-1]
UniGeneiHs.489287.

Genome annotation databases

EnsembliENST00000292476; ENSP00000292476; ENSG00000160917. [O95639-1]
ENST00000436336; ENSP00000395311; ENSG00000160917. [O95639-2]
GeneIDi10898.
KEGGihsa:10898.
UCSCiuc003uqi.4. human. [O95639-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Web resourcesi

SeattleSNPs

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U79569 mRNA. Translation: AAD00321.1.
CR542161 mRNA. Translation: CAG46958.1.
EF191081 Genomic DNA. Translation: ABN05292.1.
CH236956 Genomic DNA. Translation: EAL23878.1.
CH471091 Genomic DNA. Translation: EAW76667.1.
CH471091 Genomic DNA. Translation: EAW76668.1.
BC003101 mRNA. Translation: AAH03101.1.
BC050738 mRNA. Translation: AAH50738.1.
CCDSiCCDS47652.1. [O95639-2]
CCDS5664.1. [O95639-1]
RefSeqiNP_001075028.1. NM_001081559.2. [O95639-2]
NP_001305089.1. NM_001318160.1. [O95639-3]
NP_001305090.1. NM_001318161.1.
NP_001305091.1. NM_001318162.1.
NP_006684.1. NM_006693.3. [O95639-1]
UniGeneiHs.489287.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2D9NNMR-A61-126[»]
2RHKX-ray1.95C/D61-121[»]
ProteinModelPortaliO95639.
SMRiO95639.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116104. 29 interactors.
DIPiDIP-48675N.
IntActiO95639. 18 interactors.
MINTiMINT-1429837.
STRINGi9606.ENSP00000292476.

PTM databases

iPTMnetiO95639.
PhosphoSitePlusiO95639.

Polymorphism and mutation databases

BioMutaiCPSF4.

Proteomic databases

EPDiO95639.
MaxQBiO95639.
PaxDbiO95639.
PeptideAtlasiO95639.
PRIDEiO95639.

Protocols and materials databases

DNASUi10898.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000292476; ENSP00000292476; ENSG00000160917. [O95639-1]
ENST00000436336; ENSP00000395311; ENSG00000160917. [O95639-2]
GeneIDi10898.
KEGGihsa:10898.
UCSCiuc003uqi.4. human. [O95639-1]

Organism-specific databases

CTDi10898.
DisGeNETi10898.
GeneCardsiCPSF4.
HGNCiHGNC:2327. CPSF4.
HPAiHPA049094.
HPA066470.
MIMi603052. gene.
neXtProtiNX_O95639.
OpenTargetsiENSG00000160917.
PharmGKBiPA26844.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1040. Eukaryota.
COG5084. LUCA.
GeneTreeiENSGT00390000009627.
HOGENOMiHOG000212457.
HOVERGENiHBG051108.
InParanoidiO95639.
KOiK14404.
OMAiANKCTKG.
OrthoDBiEOG091G0JUF.
PhylomeDBiO95639.
TreeFamiTF314871.

Enzyme and pathway databases

ReactomeiR-HSA-109688. Cleavage of Growing Transcript in the Termination Region.
R-HSA-159231. Transport of Mature mRNA Derived from an Intronless Transcript.
R-HSA-168315. Inhibition of Host mRNA Processing and RNA Silencing.
R-HSA-6784531. tRNA processing in the nucleus.
R-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72187. mRNA 3'-end processing.
R-HSA-77595. Processing of Intronless Pre-mRNAs.

Miscellaneous databases

EvolutionaryTraceiO95639.
GeneWikiiCPSF4.
GenomeRNAii10898.
PROiO95639.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000160917.
CleanExiHS_CPSF4.
ExpressionAtlasiO95639. baseline and differential.
GenevisibleiO95639. HS.

Family and domain databases

Gene3Di4.10.1000.10. 2 hits.
4.10.60.10. 1 hit.
InterProiIPR000571. Znf_CCCH.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00642. zf-CCCH. 1 hit.
PF00098. zf-CCHC. 1 hit.
[Graphical view]
SMARTiSM00343. ZnF_C2HC. 1 hit.
SM00356. ZnF_C3H1. 5 hits.
[Graphical view]
SUPFAMiSSF57756. SSF57756. 1 hit.
SSF90229. SSF90229. 2 hits.
PROSITEiPS50103. ZF_C3H1. 5 hits.
PS50158. ZF_CCHC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCPSF4_HUMAN
AccessioniPrimary (citable) accession number: O95639
Secondary accession number(s): D6W5S8
, Q6FGE6, Q86TF8, Q9BTW6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 24, 2003
Last sequence update: May 1, 1999
Last modified: November 2, 2016
This is version 145 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 7
    Human chromosome 7: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.