Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Cleavage and polyadenylation specificity factor subunit 4

Gene

Clp

Organism
Drosophila melanogaster (Fruit fly)
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 plays 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. Has endonuclease activity. Binds RNA polymers with a preference for G- and/or C-rich clusters. Binds single-stranded DNA non-specifically.2 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri35 – 6329C3H1-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri64 – 9128C3H1-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri92 – 11928C3H1-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri120 – 14728C3H1-type 4PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri149 – 17123C3H1-type 5PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri189 – 20618CCHC-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri266 – 28318CCHC-type 2PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • endoribonuclease activity Source: FlyBase
  • RNA binding Source: UniProtKB-KW
  • zinc ion binding Source: InterPro

GO - Biological processi

  • mRNA cleavage Source: FlyBase
  • mRNA polyadenylation Source: FlyBase
  • neurogenesis Source: FlyBase
  • RNA phosphodiester bond hydrolysis, endonucleolytic Source: GOC
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein, Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

mRNA processing

Keywords - Ligandi

Metal-binding, RNA-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Cleavage and polyadenylation specificity factor subunit 4By similarity (EC:3.1.-.-1 Publication)
Alternative name(s):
Cleavage and polyadenylation specificity factor 30 kDa subunitBy similarity
Protein clipperImported
Gene namesi
Name:Clp
Synonyms:CPSF30Imported, Ssb-c6aImported
ORF Names:CG3642
OrganismiDrosophila melanogaster (Fruit fly)
Taxonomic identifieri7227 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaArthropodaHexapodaInsectaPterygotaNeopteraEndopterygotaDipteraBrachyceraMuscomorphaEphydroideaDrosophilidaeDrosophilaSophophora
Proteomesi
  • UP000000803 Componenti: Chromosome 2L

Organism-specific databases

FlyBaseiFBgn0015621. Clp.

Subcellular locationi

  • Nucleus 1 Publication

GO - Cellular componenti

  • mRNA cleavage and polyadenylation specificity factor complex Source: FlyBase
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 296296Cleavage and polyadenylation specificity factor subunit 4PRO_0000422156Add
BLAST

Proteomic databases

PaxDbiQ9VPT8.
PRIDEiQ9VPT8.

Expressioni

Tissue specificityi

During oogenesis, expression is detected in the germarium, in nurse cells, in the oocyte, and in the somatically derived follicular epithelial cells (at protein level). At oogenesis stage 12, nurse cells degenerate and their content is transferred into the oocyte. In larvae, expressed in all organs and disks (at protein level). In the larval salivary gland, expression is initially confined to cells at the anterior end but later expands throughout the entire gland (at protein level).2 Publications

Developmental stagei

Expressed both maternally and zygotically. During embryogenesis expressed only at transcript level. Expressed in larvae (at protein level), pupae and adults. Initial embryonic expression is maternally derived, then gradually decreases until third-instar larvae when there is a burst of zygotic expression. Most of the female expression is ovarian (at protein level).2 Publications

Gene expression databases

GenevisibleiQ9VPT8. DM.

Interactioni

Subunit structurei

Component of the cleavage and polyadenylation specificity factor (CPSF) complex, composed of at least Clp, Cpsf73, Cpsf100 and Cpsf160.1 Publication

Protein-protein interaction databases

BioGridi59513. 18 interactions.
IntActiQ9VPT8. 3 interactions.
MINTiMINT-341478.
STRINGi7227.FBpp0077676.

Structurei

3D structure databases

ProteinModelPortaliQ9VPT8.
SMRiQ9VPT8. Positions 64-128.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domaini

The N-terminal region containing the five C3H1-type zinc fingers is essential for endonuclease activity.1 Publication
The C-terminal region containing the two CCHC-type zinc fingers confers a binding preference for RNAs that contain G-and/or C-rich clusters.1 Publication

Sequence similaritiesi

Contains 5 C3H1-type zinc fingers.PROSITE-ProRule annotation
Contains 2 CCHC-type zinc fingers.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri35 – 6329C3H1-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri64 – 9128C3H1-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri92 – 11928C3H1-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri120 – 14728C3H1-type 4PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri149 – 17123C3H1-type 5PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri189 – 20618CCHC-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri266 – 28318CCHC-type 2PROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1040. Eukaryota.
COG5084. LUCA.
GeneTreeiENSGT00390000009627.
InParanoidiQ9VPT8.
KOiK14404.
OMAiANKCTKG.
OrthoDBiEOG7XH6QD.
PhylomeDBiQ9VPT8.

Family and domain databases

Gene3Di4.10.1000.10. 1 hit.
4.10.60.10. 2 hits.
InterProiIPR000571. Znf_CCCH.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00098. zf-CCHC. 2 hits.
[Graphical view]
SMARTiSM00343. ZnF_C2HC. 2 hits.
SM00356. ZnF_C3H1. 5 hits.
[Graphical view]
SUPFAMiSSF57756. SSF57756. 2 hits.
SSF90229. SSF90229. 1 hit.
PROSITEiPS50103. ZF_C3H1. 5 hits.
PS50158. ZF_CCHC. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9VPT8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDILLANVSG LQFKAERDLI EQVGAIPLPF YGMDKSIAAV CNFITRNGQE
60 70 80 90 100
CDKGSACPFR HIRGDRTIVC KHWLRGLCKK GDQCEFLHEY DMTKMPECYF
110 120 130 140 150
YSRFNACHNK ECPFLHIDPQ SKVKDCPWYK RGFCRHGPHC RHQHLRRVLC
160 170 180 190 200
MDYLAGFCPE GPSCKHMHPH FELPPLAELG KDQLHKKLPT CHYCGELGHK
210 220 230 240 250
ANSCKQYVGS LEHRNNINAM DHSGGHSGGY SGHSGHIEGA DDMQSNHHSQ
260 270 280 290
PHGPGFVKVP TPLEEITCYK CGNKGHYANK CPKGHLAFLS NQHSHK
Length:296
Mass (Da):33,500
Last modified:May 1, 2000 - v1
Checksum:i0FE03B60F042FBDB
GO

Sequence cautioni

The sequence ABK57069.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti161 – 1611G → A in AAA67954 (PubMed:8206370).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U26549 mRNA. Translation: AAA67954.1.
AE014134 Genomic DNA. Translation: AAF51453.1.
BT025009 mRNA. Translation: ABE01239.1.
BT029412 mRNA. Translation: ABK57069.1. Different initiation.
RefSeqiNP_477156.1. NM_057808.2.
UniGeneiDm.4233.

Genome annotation databases

EnsemblMetazoaiFBtr0078011; FBpp0077676; FBgn0015621.
GeneIDi33259.
KEGGidme:Dmel_CG3642.
UCSCiCG3642-RA. d. melanogaster.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U26549 mRNA. Translation: AAA67954.1.
AE014134 Genomic DNA. Translation: AAF51453.1.
BT025009 mRNA. Translation: ABE01239.1.
BT029412 mRNA. Translation: ABK57069.1. Different initiation.
RefSeqiNP_477156.1. NM_057808.2.
UniGeneiDm.4233.

3D structure databases

ProteinModelPortaliQ9VPT8.
SMRiQ9VPT8. Positions 64-128.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi59513. 18 interactions.
IntActiQ9VPT8. 3 interactions.
MINTiMINT-341478.
STRINGi7227.FBpp0077676.

Proteomic databases

PaxDbiQ9VPT8.
PRIDEiQ9VPT8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiFBtr0078011; FBpp0077676; FBgn0015621.
GeneIDi33259.
KEGGidme:Dmel_CG3642.
UCSCiCG3642-RA. d. melanogaster.

Organism-specific databases

CTDi33259.
FlyBaseiFBgn0015621. Clp.

Phylogenomic databases

eggNOGiKOG1040. Eukaryota.
COG5084. LUCA.
GeneTreeiENSGT00390000009627.
InParanoidiQ9VPT8.
KOiK14404.
OMAiANKCTKG.
OrthoDBiEOG7XH6QD.
PhylomeDBiQ9VPT8.

Miscellaneous databases

GenomeRNAii33259.
NextBioi782702.
PROiQ9VPT8.

Gene expression databases

GenevisibleiQ9VPT8. DM.

Family and domain databases

Gene3Di4.10.1000.10. 1 hit.
4.10.60.10. 2 hits.
InterProiIPR000571. Znf_CCCH.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00098. zf-CCHC. 2 hits.
[Graphical view]
SMARTiSM00343. ZnF_C2HC. 2 hits.
SM00356. ZnF_C3H1. 5 hits.
[Graphical view]
SUPFAMiSSF57756. SSF57756. 2 hits.
SSF90229. SSF90229. 1 hit.
PROSITEiPS50103. ZF_C3H1. 5 hits.
PS50158. ZF_CCHC. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "RNA- and single-stranded DNA-binding (SSB) proteins expressed during Drosophila melanogaster oogenesis: a homolog of bacterial and eukaryotic mitochondrial SSBs."
    Stroumbakis N.D., Li Z., Tolias P.P.
    Gene 143:171-177(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: Canton-SImported.
    Tissue: OvaryImported.
  2. "The genome sequence of Drosophila melanogaster."
    Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F., George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N., Sutton G.G., Wortman J.R., Yandell M.D.
    , Zhang Q., Chen L.X., Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E., Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B., Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I., Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C., Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S., Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M., Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M., Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D., Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F., Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D., Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A., Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C., McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C., Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L., Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R., Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V., Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F., Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J., Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R., Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y., Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T., Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S., Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W., Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M., Venter J.C.
    Science 287:2185-2195(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Berkeley.
  3. Cited for: GENOME REANNOTATION.
    Strain: Berkeley.
  4. Stapleton M., Carlson J., Chavez C., Frise E., George R., Kapadia B., Pacleb J., Park S., Wan K., Yu C., Celniker S.
    Submitted (MAR-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: Berkeley.
  5. "Cleavage of RNA hairpins mediated by a developmentally regulated CCCH zinc finger protein."
    Bai C., Tolias P.P.
    Mol. Cell. Biol. 16:6661-6667(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, DOMAIN.
    Tissue: Ovary1 Publication.
  6. "Drosophila clipper/CPSF 30K is a post-transcriptionally regulated nuclear protein that binds RNA containing GC clusters."
    Bai C., Tolias P.P.
    Nucleic Acids Res. 26:1597-1604(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, DOMAIN.
  7. "A core complex of CPSF73, CPSF100, and Symplekin may form two different cleavage factors for processing of poly(A) and histone mRNAs."
    Sullivan K.D., Steiniger M., Marzluff W.F.
    Mol. Cell 34:322-332(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE CPSF COMPLEX.

Entry informationi

Entry nameiCPSF4_DROME
AccessioniPrimary (citable) accession number: Q9VPT8
Secondary accession number(s): A0JQ42, Q24081
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 2013
Last sequence update: May 1, 2000
Last modified: May 11, 2016
This is version 121 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programDrosophila annotation project

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Drosophila
    Drosophila: entries, gene names and cross-references to FlyBase
  2. 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.