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O95639 (CPSF4_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 119. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:CPSF4
Synonyms:CPSF30, NAR, NEB1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length269 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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). Ref.7 Ref.9

Subunit structure

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. Ref.8 Ref.9 Ref.13

Subcellular location

Nucleus.

Sequence similarities

Belongs to the CPSF4/YTH1 family.

Contains 5 C3H1-type zinc fingers.

Contains 1 CCHC-type zinc finger.

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: O95639-1)

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: O95639-2)

The sequence of this isoform differs from the canonical sequence as follows:
     191-215: Missing.
Note: No experimental confirmation available.
Isoform 3 (identifier: O95639-3)

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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 269269Cleavage and polyadenylation specificity factor subunit 4
PRO_0000074402

Regions

Zinc finger35 – 6127C3H1-type 1
Zinc finger62 – 8928C3H1-type 2
Zinc finger90 – 11728C3H1-type 3
Zinc finger118 – 14225C3H1-type 4
Zinc finger143 – 16927C3H1-type 5
Zinc finger243 – 26018CCHC-type

Amino acid modifications

Modified residue2021Phosphoserine Ref.10 Ref.12
Modified residue2121Phosphoserine Ref.10 Ref.12 Ref.15

Natural variations

Alternative sequence191 – 21626Missing in isoform 3.
VSP_008602
Alternative sequence191 – 21525Missing in isoform 2.
VSP_008601

Secondary structure

.............. 269
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified May 1, 1999. Version 1.
Checksum: 49444E3EB840464A

FASTA26930,255
        10         20         30         40         50         60 
MQEIIASVDH IKFDLEIAVE QQLGAQPLPF PGMDKSGAAV CEFFLKAACG KGGMCPFRHI 

        70         80         90        100        110        120 
SGEKTVVCKH WLRGLCKKGD QCEFLHEYDM TKMPECYFYS KFGECSNKEC PFLHIDPESK 

       130        140        150        160        170        180 
IKDCPWYDRG FCKHGPLCRH RHTRRVICVN YLVGFCPEGP SCKFMHPRFE LPMGTTEQPP 

       190        200        210        220        230        240 
LPQQTQPPAK QSNNPPLQRS SSLIQLTSQN SSPNQQRTPQ VIGVMQSQNS SAGNRGPRPL 

       250        260 
EQVTCYKCGE KGHYANRCTK GHLAFLSGQ 

« Hide

Isoform 2 [UniParc].

Checksum: 0DF72BE36CF97106
Show »

FASTA24427,547
Isoform 3 [UniParc].

Checksum: 3535FE5A0D525C8F
Show »

FASTA24327,419

References

« Hide 'large scale' references
[1]"Assignment of the human homolog of the zebrafish essential gene no arches to 7q22.1."
Kawakami K., Gaiano N., Grosshans D., Scherer S., Tsui L.-C., Hopkins N.
Submitted (NOV-1996) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
[2]"Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
Halleck A., Ebert L., Mkoundinya M., Schick M., Eisenstein S., Neubert P., Kstrang K., Schatten R., Shen B., Henze S., Mar W., Korn B., Zuo D., Hu Y., LaBaer J.
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
[3]SeattleSNPs variation discovery resource
Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]"Human chromosome 7: DNA sequence and biology."
Scherer S.W., Cheung J., MacDonald J.R., Osborne L.R., Nakabayashi K., Herbrick J.-A., Carson A.R., Parker-Katiraee L., Skaug J., Khaja R., Zhang J., Hudek A.K., Li M., Haddad M., Duggan G.E., Fernandez B.A., Kanematsu E., Gentles S. expand/collapse author list , Christopoulos C.C., Choufani S., Kwasnicka D., Zheng X.H., Lai Z., Nusskern D.R., Zhang Q., Gu Z., Lu F., Zeesman S., Nowaczyk M.J., Teshima I., Chitayat D., Shuman C., Weksberg R., Zackai E.H., Grebe T.A., Cox S.R., Kirkpatrick S.J., Rahman N., Friedman J.M., Heng H.H.Q., Pelicci P.G., Lo-Coco F., Belloni E., Shaffer L.G., Pober B., Morton C.C., Gusella J.F., Bruns G.A.P., Korf B.R., Quade B.J., Ligon A.H., Ferguson H., Higgins A.W., Leach N.T., Herrick S.R., Lemyre E., Farra C.G., Kim H.-G., Summers A.M., Gripp K.W., Roberts W., Szatmari P., Winsor E.J.T., Grzeschik K.-H., Teebi A., Minassian B.A., Kere J., Armengol L., Pujana M.A., Estivill X., Wilson M.D., Koop B.F., Tosi S., Moore G.E., Boright A.P., Zlotorynski E., Kerem B., Kroisel P.M., Petek E., Oscier D.G., Mould S.J., Doehner H., Doehner K., Rommens J.M., Vincent J.B., Venter J.C., Li P.W., Mural R.J., Adams M.D., Tsui L.-C.
Science 300:767-772(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[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. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-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: Eye and PNS.
[7]"The 30-kD subunit of mammalian cleavage and polyadenylation specificity factor and its yeast homolog are RNA-binding zinc finger proteins."
Barabino S.M.L., Huebner W., Jenny A., Minvielle-Sebastia L., Keller W.
Genes Dev. 11:1703-1716(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[8]"Influenza virus NS1 protein interacts with the cellular 30 kDa subunit of CPSF and inhibits 3'end formation of cellular pre-mRNAs."
Nemeroff M.E., Barabino S.M.L., Li Y., Keller W., Krug R.M.
Mol. Cell 1:991-1000(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH INFLUENZA A VIRUS NS1 PROTEIN.
[9]"Human Fip1 is a subunit of CPSF that binds to U-rich RNA elements and stimulates poly(A) polymerase."
Kaufmann I., Martin G., Friedlein A., Langen H., Keller W.
EMBO J. 23:616-626(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN PRE-MRNA 3'-END PROCESSING, IDENTIFICATION IN THE CPSF COMPLEX, INTERACTION WITH FIP1L1.
[10]"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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-202 AND SER-212, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[11]"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[12]"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 SER-202 AND SER-212, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Leukemic T-cell.
[13]"The poly A polymerase Star-PAP controls 3'-end cleavage by promoting CPSF interaction and specificity toward the pre-mRNA."
Laishram R.S., Anderson R.A.
EMBO J. 29:4132-4145(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN THE CPSF COMPLEX.
[14]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[15]"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-212, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[16]"Solution structure of CCCH-type zinc-finger domain 2 in cleavage and polyadenylation specificity factor."
RIKEN structural genomics initiative (RSGI)
Submitted (JUN-2006) to the PDB data bank
Cited for: STRUCTURE BY NMR OF 61-126.
+Additional computationally mapped references.

Web resources

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_001075028.1. NM_001081559.1.
NP_006684.1. NM_006693.2.
UniGeneHs.489287.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2D9NNMR-A61-126[»]
2RHKX-ray1.95C/D61-121[»]
ProteinModelPortalO95639.
SMRO95639. Positions 38-168.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid116104. 9 interactions.
DIPDIP-48675N.
IntActO95639. 7 interactions.
MINTMINT-1429837.
STRING9606.ENSP00000292476.

PTM databases

PhosphoSiteO95639.

Proteomic databases

PaxDbO95639.
PRIDEO95639.

Protocols and materials databases

DNASU10898.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000292476; ENSP00000292476; ENSG00000160917. [O95639-1]
ENST00000436336; ENSP00000395311; ENSG00000160917. [O95639-2]
GeneID10898.
KEGGhsa:10898.
UCSCuc003uqi.3. human. [O95639-2]
uc003uqj.3. human. [O95639-1]
uc003uqk.3. human. [O95639-3]

Organism-specific databases

CTD10898.
GeneCardsGC07P099036.
HGNCHGNC:2327. CPSF4.
HPAHPA049094.
MIM603052. gene.
neXtProtNX_O95639.
PharmGKBPA26844.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG5084.
HOGENOMHOG000212457.
HOVERGENHBG051108.
InParanoidO95639.
KOK14404.
OMAPLDQVTC.
OrthoDBEOG7XH6QD.
PhylomeDBO95639.
TreeFamTF314871.

Enzyme and pathway databases

ReactomeREACT_116125. Disease.

Gene expression databases

ArrayExpressO95639.
BgeeO95639.
CleanExHS_CPSF4.
GenevestigatorO95639.

Family and domain databases

Gene3D4.10.1000.10. 2 hits.
4.10.60.10. 1 hit.
InterProIPR000571. Znf_CCCH.
IPR001878. Znf_CCHC.
[Graphical view]
PfamPF00642. zf-CCCH. 2 hits.
PF00098. zf-CCHC. 1 hit.
[Graphical view]
SMARTSM00343. ZnF_C2HC. 1 hit.
SM00356. ZnF_C3H1. 5 hits.
[Graphical view]
SUPFAMSSF57756. SSF57756. 1 hit.
PROSITEPS50103. ZF_C3H1. 5 hits.
PS50158. ZF_CCHC. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceO95639.
GeneWikiCPSF4.
GenomeRNAi10898.
NextBio41385.
PROO95639.
SOURCESearch...

Entry information

Entry nameCPSF4_HUMAN
AccessionPrimary (citable) accession number: O95639
Secondary accession number(s): D6W5S8 expand/collapse secondary AC list , Q6FGE6, Q86TF8, Q9BTW6
Entry history
Integrated into UniProtKB/Swiss-Prot: October 24, 2003
Last sequence update: May 1, 1999
Last modified: April 16, 2014
This is version 119 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 7

Human chromosome 7: entries, gene names and cross-references to MIM