ID   RPB4_DROME              Reviewed;         139 AA.
AC   Q9VEA5; Q4V3P8; Q8I0A4;
DT   03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT   03-APR-2007, sequence version 5.
DT   05-JUN-2019, entry version 137.
DE   RecName: Full=DNA-directed RNA polymerase II subunit Rpb4 {ECO:0000303|PubMed:19921261};
GN   Name=Rpb4 {ECO:0000303|PubMed:19921261,
GN   ECO:0000312|FlyBase:FBgn0263757};
GN   ORFNames=CG43662 {ECO:0000312|FlyBase:FBgn0263757};
OS   Drosophila melanogaster (Fruit fly).
OC   Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta;
OC   Pterygota; Neoptera; Holometabola; Diptera; Brachycera; Muscomorpha;
OC   Ephydroidea; Drosophilidae; Drosophila; Sophophora.
OX   NCBI_TaxID=7227;
RN   [1] {ECO:0000305, ECO:0000312|EMBL:AAN88031.1}
RP   NUCLEOTIDE SEQUENCE [MRNA], AND SUBCELLULAR LOCATION.
RX   PubMed=12482983; DOI=10.1128/MCB.23.1.306-321.2003;
RA   Muratoglu S., Georgieva S., Papai G., Scheer E., Enunlu I.,
RA   Komonyi O., Cserpan I., Lebedeva L., Nabirochkina E., Udvardy A.,
RA   Tora L., Boros I.;
RT   "Two different Drosophila ADA2 homologues are present in distinct GCN5
RT   histone acetyltransferase-containing complexes.";
RL   Mol. Cell. Biol. 23:306-321(2003).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Berkeley {ECO:0000269|PubMed:10731132};
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.,
RA   Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D.,
RA   Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G.,
RA   Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D.,
RA   Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M.,
RA   Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S.,
RA   Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P.,
RA   Burtis K.C., Busam D.A., Butler H., Cadieu E., Center A., Chandra I.,
RA   Cherry J.M., Cawley S., Dahlke C., Davenport L.B., Davies P.,
RA   de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I., Dietz S.M.,
RA   Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C., Dunn P.,
RA   Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S., Fleischmann W.,
RA   Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M., Glasser K.,
RA   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.,
RA   Hostin D., Houston K.A., Howland T.J., Wei M.-H., Ibegwam C.,
RA   Jalali M., Kalush F., Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A.,
RA   Kimmel B.E., Kodira C.D., Kraft C.L., Kravitz S., Kulp D., Lai Z.,
RA   Lasko P., Lei Y., Levitsky A.A., Li J.H., Li Z., Liang Y., Lin X.,
RA   Liu X., Mattei B., McIntosh T.C., McLeod M.P., McPherson D.,
RA   Merkulov G., Milshina N.V., Mobarry C., Morris J., Moshrefi A.,
RA   Mount S.M., Moy M., Murphy B., Murphy L., Muzny D.M., Nelson D.L.,
RA   Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R., Pacleb J.M.,
RA   Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V., Reese M.G.,
RA   Reinert K., Remington K., Saunders R.D.C., Scheeler F., Shen H.,
RA   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.,
RA   Svirskas R., Tector C., Turner R., Venter E., Wang A.H., Wang X.,
RA   Wang Z.-Y., Wassarman D.A., Weinstock G.M., Weissenbach J.,
RA   Williams S.M., Woodage T., Worley K.C., Wu D., Yang S., Yao Q.A.,
RA   Ye J., Yeh R.-F., Zaveri J.S., Zhan M., Zhang G., Zhao Q., Zheng L.,
RA   Zheng X.H., Zhong F.N., Zhong W., Zhou X., Zhu S.C., Zhu X.,
RA   Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M., Venter J.C.;
RT   "The genome sequence of Drosophila melanogaster.";
RL   Science 287:2185-2195(2000).
RN   [3] {ECO:0000305}
RP   GENOME REANNOTATION, AND ALTERNATIVE SPLICING.
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.,
RA   Stapleton M., Yamada C., Ashburner M., Gelbart W.M., Rubin G.M.,
RA   Lewis S.E.;
RT   "Annotation of the Drosophila melanogaster euchromatic genome: a
RT   systematic review.";
RL   Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
RN   [4] {ECO:0000312|EMBL:AAY51562.1}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=Berkeley;
RA   Stapleton M., Carlson J.W., Chavez C., Frise E., George R.A.,
RA   Pacleb J.M., Park S., Wan K.H., Yu C., Celniker S.E.;
RL   Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases.
RN   [5]
RP   FUNCTION.
RX   PubMed=12697829; DOI=10.1128/MCB.23.9.3305-3319.2003;
RA   Kusch T., Guelman S., Abmayr S.M., Workman J.L.;
RT   "Two Drosophila Ada2 homologues function in different multiprotein
RT   complexes.";
RL   Mol. Cell. Biol. 23:3305-3319(2003).
RN   [6]
RP   SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE, AND INDUCTION BY HEAT
RP   SHOCK.
RX   PubMed=19921261; DOI=10.1007/s00438-009-0499-6;
RA   Pankotai T., Ujfaludi Z., Vamos E., Suri K., Boros I.M.;
RT   "The dissociable RPB4 subunit of RNA Pol II has vital functions in
RT   Drosophila.";
RL   Mol. Genet. Genomics 283:89-97(2010).
CC   -!- FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription
CC       of DNA into RNA using the four ribonucleoside triphosphates as
CC       substrates. Associates with POLR2G. {ECO:0000269|PubMed:12482983,
CC       ECO:0000269|PubMed:12697829}.
CC   -!- SUBUNIT: RNA polymerase II consists of 12 different subunits.
CC       {ECO:0000250|UniProtKB:O15514}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:12482983}.
CC       Chromosome {ECO:0000269|PubMed:19921261}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=5;
CC       Name=D {ECO:0000269|PubMed:10731132};
CC         IsoId=Q9VEA5-1; Sequence=Displayed;
CC       Name=B;
CC         IsoId=Q7KSD8-1; Sequence=External;
CC         Note=No experimental confirmation available. {ECO:0000305};
CC       Name=A;
CC         IsoId=Q7KSD8-2; Sequence=External;
CC         Note=No experimental confirmation available. {ECO:0000305};
CC       Name=C {ECO:0000269|PubMed:12482983}; Synonyms=ADA2A-SV2
CC       {ECO:0000269|PubMed:12482983};
CC         IsoId=Q7KSD8-3; Sequence=External;
CC       Name=E {ECO:0000269|PubMed:12482983}; Synonyms=ADA2A-SV1
CC       {ECO:0000269|PubMed:12482983};
CC         IsoId=Q7KSD8-4; Sequence=External;
CC   -!- DEVELOPMENTAL STAGE: During development expression peaks in
CC       embryos, decreases sharply in L1 larvae and then remains low
CC       throughout larval development. {ECO:0000269|PubMed:19921261}.
CC   -!- INDUCTION: Under heat shock conditions, up-regulated in early
CC       larvae and then expression levels appear to return to normal
CC       during the L2/L3 and pupal stages. In second instar larvae, down-
CC       regulated 1 hr after starvation and then remains low until at
CC       least 4 hr after nutritional starvation.
CC       {ECO:0000269|PubMed:19921261}.
CC   -!- MISCELLANEOUS: This protein is produced by a bicistronic gene
CC       which also produces the Ada2a protein by alternative splicing
CC       (PubMed:19921261). Three distinct zinc-containing RNA polymerases
CC       are found in eukaryotic nuclei: polymerase I for the ribosomal RNA
CC       precursor, polymerase II for the mRNA precursor, and polymerase
CC       III for 5S and tRNA genes (Probable).
CC       {ECO:0000269|PubMed:19921261, ECO:0000305}.
CC   -!- SIMILARITY: Belongs to the eukaryotic RPB4 RNA polymerase subunit
CC       family. {ECO:0000255}.
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; AF544019; AAN88031.1; -; mRNA.
DR   EMBL; AF544020; AAN88032.1; -; mRNA.
DR   EMBL; AE014297; AAF55522.5; -; Genomic_DNA.
DR   EMBL; BT022168; AAY51562.1; -; mRNA.
DR   EMBL; BT023308; AAY55724.1; -; mRNA.
DR   EMBL; BT023309; AAY55725.1; -; mRNA.
DR   RefSeq; NP_001014633.2; NM_001014633.3. [Q9VEA5-1]
DR   SMR; Q9VEA5; -.
DR   BioGrid; 2593107; 8.
DR   IntAct; Q9VEA5; 4.
DR   STRING; 7227.FBpp0302530; -.
DR   PaxDb; Q9VEA5; -.
DR   PRIDE; Q9VEA5; -.
DR   EnsemblMetazoa; FBtr0310379; FBpp0302530; FBgn0263757. [Q9VEA5-1]
DR   GeneID; 14462484; -.
DR   KEGG; dme:Dmel_CG43662; -.
DR   UCSC; CG33520-RA; d. melanogaster. [Q9VEA5-1]
DR   CTD; 14462484; -.
DR   FlyBase; FBgn0263757; Rpb4.
DR   eggNOG; KOG2351; Eukaryota.
DR   eggNOG; COG5250; LUCA.
DR   GeneTree; ENSGT00390000004912; -.
DR   KO; K03012; -.
DR   OMA; PEFNNAG; -.
DR   Reactome; R-DME-112382; Formation of RNA Pol II elongation complex.
DR   Reactome; R-DME-113418; Formation of the Early Elongation Complex.
DR   Reactome; R-DME-5578749; Transcriptional regulation by small RNAs.
DR   Reactome; R-DME-674695; RNA Polymerase II Pre-transcription Events.
DR   Reactome; R-DME-6781823; Formation of TC-NER Pre-Incision Complex.
DR   Reactome; R-DME-6782135; Dual incision in TC-NER.
DR   Reactome; R-DME-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
DR   Reactome; R-DME-6796648; TP53 Regulates Transcription of DNA Repair Genes.
DR   Reactome; R-DME-6803529; FGFR2 alternative splicing.
DR   Reactome; R-DME-6807505; RNA polymerase II transcribes snRNA genes.
DR   Reactome; R-DME-72086; mRNA Capping.
DR   Reactome; R-DME-72163; mRNA Splicing - Major Pathway.
DR   Reactome; R-DME-72165; mRNA Splicing - Minor Pathway.
DR   Reactome; R-DME-72203; Processing of Capped Intron-Containing Pre-mRNA.
DR   Reactome; R-DME-73776; RNA Polymerase II Promoter Escape.
DR   Reactome; R-DME-73779; RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
DR   Reactome; R-DME-75953; RNA Polymerase II Transcription Initiation.
DR   Reactome; R-DME-75955; RNA Polymerase II Transcription Elongation.
DR   Reactome; R-DME-76042; RNA Polymerase II Transcription Initiation And Promoter Clearance.
DR   Reactome; R-DME-77075; RNA Pol II CTD phosphorylation and interaction with CE.
DR   Reactome; R-DME-9018519; Estrogen-dependent gene expression.
DR   GenomeRNAi; 14462484; -.
DR   Proteomes; UP000000803; Chromosome 3R.
DR   Bgee; FBgn0263757; Expressed in 7 organ(s), highest expression level in head.
DR   Genevisible; Q9VEA5; DM.
DR   GO; GO:0005700; C:polytene chromosome; IDA:FlyBase.
DR   GO; GO:0005705; C:polytene chromosome interband; IDA:FlyBase.
DR   GO; GO:0005703; C:polytene chromosome puff; IDA:UniProtKB.
DR   GO; GO:0005665; C:RNA polymerase II, core complex; IDA:UniProtKB.
DR   GO; GO:0003899; F:DNA-directed 5'-3' RNA polymerase activity; IDA:UniProtKB.
DR   GO; GO:0000166; F:nucleotide binding; IEA:InterPro.
DR   GO; GO:0006352; P:DNA-templated transcription, initiation; IEA:InterPro.
DR   GO; GO:0006366; P:transcription by RNA polymerase II; IDA:UniProtKB.
DR   Gene3D; 1.20.1250.40; -; 1.
DR   InterPro; IPR010997; HRDC-like_sf.
DR   InterPro; IPR006590; RNA_pol_Rpb4/RPC9_core.
DR   InterPro; IPR005574; RPB4/RPC9.
DR   InterPro; IPR038324; Rpb4/RPC9_sf.
DR   Pfam; PF03874; RNA_pol_Rpb4; 1.
DR   SMART; SM00657; RPOL4c; 1.
DR   SUPFAM; SSF47819; SSF47819; 1.
PE   2: Evidence at transcript level;
KW   Alternative splicing; Chromosome; Complete proteome;
KW   DNA-directed RNA polymerase; Nucleus; Reference proteome;
KW   Transcription.
FT   CHAIN         1    139       DNA-directed RNA polymerase II subunit
FT                                Rpb4.
FT                                /FTId=PRO_0000283732.
FT   CONFLICT    124    126       LRQ -> ARE (in Ref. 1; AAN88031/
FT                                AAN88032). {ECO:0000305}.
SQ   SEQUENCE   139 AA;  16212 MW;  F7541C9A08C23CB1 CRC64;
     MSFMNPVDMV DEDAADLQFP KEFENAETLL ISEVHMLLDH RKRQNESADE EQEFSEVFMK
     TYAYTDSFRK FKNKETIMSA RSLLMQKKLH KFELAALGNL CPEAPEEAKA LIPSLEGRFE
     DEELRQILDD IGTKRSLQY
//