CPSF4_DROME
ID CPSF4_DROME Reviewed; 296 AA.
AC Q9VPT8; A0JQ42; Q24081;
DT 01-MAY-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 159.
DE RecName: Full=Cleavage and polyadenylation specificity factor subunit 4 {ECO:0000250|UniProtKB:O95639};
DE EC=3.1.-.- {ECO:0000269|PubMed:8943320};
DE AltName: Full=Cleavage and polyadenylation specificity factor 30 kDa subunit {ECO:0000250|UniProtKB:O95639};
DE AltName: Full=Protein clipper {ECO:0000312|EMBL:AAF51453.1};
GN Name=Clp;
GN Synonyms=CPSF30 {ECO:0000312|FlyBase:FBgn0015621},
GN Ssb-c6a {ECO:0000312|EMBL:AAA67954.1}; ORFNames=CG3642;
OS Drosophila melanogaster (Fruit fly).
OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea;
OC Drosophilidae; Drosophila; Sophophora.
OX NCBI_TaxID=7227;
RN [1] {ECO:0000312|EMBL:AAA67954.1}
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=Canton-S {ECO:0000312|EMBL:AAA67954.1};
RC TISSUE=Ovary {ECO:0000312|EMBL:AAA67954.1};
RX PubMed=8206370; DOI=10.1016/0378-1119(94)90093-0;
RA Stroumbakis N.D., Li Z., Tolias P.P.;
RT "RNA- and single-stranded DNA-binding (SSB) proteins expressed during
RT Drosophila melanogaster oogenesis: a homolog of bacterial and eukaryotic
RT mitochondrial SSBs.";
RL Gene 143:171-177(1994).
RN [2] {ECO:0000312|EMBL:AAF51453.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Berkeley;
RX PubMed=10731132; DOI=10.1126/science.287.5461.2185;
RA Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
RA Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
RA George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
RA Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., Brandon R.C.,
RA Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C.,
RA Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A.,
RA An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A.,
RA Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V.,
RA Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J.,
RA Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E.,
RA Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B.,
RA Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I.,
RA Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C.,
RA Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S.,
RA Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M.,
RA Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
RA Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D.,
RA Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F.,
RA Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D.,
RA Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A.,
RA Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C.,
RA McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C.,
RA Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L.,
RA Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R.,
RA Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V.,
RA Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F.,
RA Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
RA Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R.,
RA Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y.,
RA Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T.,
RA Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S.,
RA Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W.,
RA Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M.,
RA Venter J.C.;
RT "The genome sequence of Drosophila melanogaster.";
RL Science 287:2185-2195(2000).
RN [3] {ECO:0000312|EMBL:AAF51453.1}
RP GENOME REANNOTATION.
RC STRAIN=Berkeley;
RX PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
RA Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
RA Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
RA Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
RA Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
RA Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M.,
RA Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E.;
RT "Annotation of the Drosophila melanogaster euchromatic genome: a systematic
RT review.";
RL Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
RN [4] {ECO:0000312|EMBL:ABE01239.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=Berkeley;
RA Stapleton M., Carlson J., Chavez C., Frise E., George R., Kapadia B.,
RA Pacleb J., Park S., Wan K., Yu C., Celniker S.;
RL Submitted (MAR-2006) to the EMBL/GenBank/DDBJ databases.
RN [5] {ECO:0000305}
RP FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, AND DOMAIN.
RC TISSUE=Ovary {ECO:0000269|PubMed:8943320};
RX PubMed=8943320; DOI=10.1128/mcb.16.12.6661;
RA Bai C., Tolias P.P.;
RT "Cleavage of RNA hairpins mediated by a developmentally regulated CCCH zinc
RT finger protein.";
RL Mol. Cell. Biol. 16:6661-6667(1996).
RN [6] {ECO:0000305}
RP FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE,
RP AND DOMAIN.
RX PubMed=9512528; DOI=10.1093/nar/26.7.1597;
RA Bai C., Tolias P.P.;
RT "Drosophila clipper/CPSF 30K is a post-transcriptionally regulated nuclear
RT protein that binds RNA containing GC clusters.";
RL Nucleic Acids Res. 26:1597-1604(1998).
RN [7] {ECO:0000305}
RP IDENTIFICATION IN THE CPSF COMPLEX.
RX PubMed=19450530; DOI=10.1016/j.molcel.2009.04.024;
RA Sullivan K.D., Steiniger M., Marzluff W.F.;
RT "A core complex of CPSF73, CPSF100, and Symplekin may form two different
RT cleavage factors for processing of poly(A) and histone mRNAs.";
RL Mol. Cell 34:322-332(2009).
CC -!- FUNCTION: Component of the cleavage and polyadenylation specificity
CC factor (CPSF) complex that plays a key role in pre-mRNA 3'-end
CC formation, recognizing the AAUAAA signal sequence and interacting with
CC poly(A) polymerase and other factors to bring about cleavage and
CC poly(A) addition. Has endonuclease activity. Binds RNA polymers with a
CC preference for G- and/or C-rich clusters. Binds single-stranded DNA
CC non-specifically. {ECO:0000269|PubMed:8943320,
CC ECO:0000269|PubMed:9512528}.
CC -!- SUBUNIT: Component of the cleavage and polyadenylation specificity
CC factor (CPSF) complex, composed of at least Clp, Cpsf73, Cpsf100 and
CC Cpsf160. {ECO:0000269|PubMed:19450530}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:9512528}.
CC -!- TISSUE SPECIFICITY: During oogenesis, expression is detected in the
CC germarium, in nurse cells, in the oocyte, and in the somatically
CC derived follicular epithelial cells (at protein level). At oogenesis
CC stage 12, nurse cells degenerate and their content is transferred into
CC the oocyte. In larvae, expressed in all organs and disks (at protein
CC level). In the larval salivary gland, expression is initially confined
CC to cells at the anterior end but later expands throughout the entire
CC gland (at protein level). {ECO:0000269|PubMed:8943320,
CC ECO:0000269|PubMed:9512528}.
CC -!- DEVELOPMENTAL STAGE: Expressed both maternally and zygotically. During
CC embryogenesis expressed only at transcript level. Expressed in larvae
CC (at protein level), pupae and adults. Initial embryonic expression is
CC maternally derived, then gradually decreases until third-instar larvae
CC when there is a burst of zygotic expression. Most of the female
CC expression is ovarian (at protein level). {ECO:0000269|PubMed:8943320,
CC ECO:0000269|PubMed:9512528}.
CC -!- DOMAIN: The N-terminal region containing the five C3H1-type zinc
CC fingers is essential for endonuclease activity.
CC {ECO:0000269|PubMed:8943320}.
CC -!- DOMAIN: The C-terminal region containing the two CCHC-type zinc fingers
CC confers a binding preference for RNAs that contain G- and/or C-rich
CC clusters. {ECO:0000269|PubMed:9512528}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ABK57069.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; U26549; AAA67954.1; -; mRNA.
DR EMBL; AE014134; AAF51453.1; -; Genomic_DNA.
DR EMBL; BT025009; ABE01239.1; -; mRNA.
DR EMBL; BT029412; ABK57069.1; ALT_INIT; mRNA.
DR RefSeq; NP_477156.1; NM_057808.2.
DR AlphaFoldDB; Q9VPT8; -.
DR BioGRID; 59513; 19.
DR IntAct; Q9VPT8; 11.
DR STRING; 7227.FBpp0077676; -.
DR PaxDb; Q9VPT8; -.
DR DNASU; 33259; -.
DR EnsemblMetazoa; FBtr0078011; FBpp0077676; FBgn0015621.
DR GeneID; 33259; -.
DR KEGG; dme:Dmel_CG3642; -.
DR UCSC; CG3642-RA; d. melanogaster.
DR CTD; 33259; -.
DR FlyBase; FBgn0015621; Clp.
DR VEuPathDB; VectorBase:FBgn0015621; -.
DR eggNOG; KOG1040; Eukaryota.
DR GeneTree; ENSGT00940000155520; -.
DR HOGENOM; CLU_024513_0_1_1; -.
DR InParanoid; Q9VPT8; -.
DR OMA; NSCKQYV; -.
DR OrthoDB; 1472764at2759; -.
DR PhylomeDB; Q9VPT8; -.
DR Reactome; R-DME-159231; Transport of Mature mRNA Derived from an Intronless Transcript.
DR Reactome; R-DME-72163; mRNA Splicing - Major Pathway.
DR Reactome; R-DME-72187; mRNA 3'-end processing.
DR Reactome; R-DME-73856; RNA Polymerase II Transcription Termination.
DR Reactome; R-DME-77595; Processing of Intronless Pre-mRNAs.
DR SignaLink; Q9VPT8; -.
DR BioGRID-ORCS; 33259; 0 hits in 3 CRISPR screens.
DR GenomeRNAi; 33259; -.
DR PRO; PR:Q9VPT8; -.
DR Proteomes; UP000000803; Chromosome 2L.
DR Bgee; FBgn0015621; Expressed in ovary and 13 other tissues.
DR Genevisible; Q9VPT8; DM.
DR GO; GO:0005847; C:mRNA cleavage and polyadenylation specificity factor complex; ISS:FlyBase.
DR GO; GO:0004521; F:endoribonuclease activity; IDA:FlyBase.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0098789; P:pre-mRNA cleavage required for polyadenylation; ISS:FlyBase.
DR InterPro; IPR045348; CPSF4/Yth1.
DR InterPro; IPR000571; Znf_CCCH.
DR InterPro; IPR036855; Znf_CCCH_sf.
DR InterPro; IPR001878; Znf_CCHC.
DR InterPro; IPR036875; Znf_CCHC_sf.
DR PANTHER; PTHR23102; PTHR23102; 2.
DR Pfam; PF00098; zf-CCHC; 2.
DR SMART; SM00343; ZnF_C2HC; 2.
DR SMART; SM00356; ZnF_C3H1; 5.
DR SUPFAM; SSF57756; SSF57756; 2.
DR SUPFAM; SSF90229; SSF90229; 1.
DR PROSITE; PS50103; ZF_C3H1; 5.
DR PROSITE; PS50158; ZF_CCHC; 2.
PE 1: Evidence at protein level;
KW Developmental protein; Endonuclease; Hydrolase; Metal-binding;
KW mRNA processing; Nuclease; Nucleus; Reference proteome; Repeat;
KW RNA-binding; Zinc; Zinc-finger.
FT CHAIN 1..296
FT /note="Cleavage and polyadenylation specificity factor
FT subunit 4"
FT /id="PRO_0000422156"
FT ZN_FING 35..63
FT /note="C3H1-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00723"
FT ZN_FING 64..91
FT /note="C3H1-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00723"
FT ZN_FING 92..119
FT /note="C3H1-type 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00723"
FT ZN_FING 120..147
FT /note="C3H1-type 4"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00723"
FT ZN_FING 149..171
FT /note="C3H1-type 5"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00723"
FT ZN_FING 189..206
FT /note="CCHC-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00047"
FT ZN_FING 266..283
FT /note="CCHC-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00047"
FT REGION 222..254
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 161
FT /note="G -> A (in Ref. 1; AAA67954)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 296 AA; 33500 MW; 0FE03B60F042FBDB CRC64;
MDILLANVSG LQFKAERDLI EQVGAIPLPF YGMDKSIAAV CNFITRNGQE CDKGSACPFR
HIRGDRTIVC KHWLRGLCKK GDQCEFLHEY DMTKMPECYF YSRFNACHNK ECPFLHIDPQ
SKVKDCPWYK RGFCRHGPHC RHQHLRRVLC MDYLAGFCPE GPSCKHMHPH FELPPLAELG
KDQLHKKLPT CHYCGELGHK ANSCKQYVGS LEHRNNINAM DHSGGHSGGY SGHSGHIEGA
DDMQSNHHSQ PHGPGFVKVP TPLEEITCYK CGNKGHYANK CPKGHLAFLS NQHSHK
