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   09-DEC-2015, entry version 110.
DE   RecName: Full=DNA-directed RNA polymerase II 16 kDa polypeptide;
DE            EC=2.7.7.6;
DE   AltName: Full=RNA polymerase II accessory factor rpb4;
GN   Name=Rpb4; ORFNames=CG33520;
OS   Drosophila melanogaster (Fruit fly).
OC   Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta;
OC   Pterygota; Neoptera; Endopterygota; 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).
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   -!- CATALYTIC ACTIVITY: Nucleoside triphosphate + RNA(n) = diphosphate
CC       + RNA(n+1). {ECO:0000305}.
CC   -!- SUBUNIT: RNA polymerase II consists of 12 different subunits.
CC       {ECO:0000250|UniProtKB:O15514}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:12482983}.
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   -!- MISCELLANEOUS: Three distinct zinc-containing RNA polymerases are
CC       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. {ECO:0000305}.
CC   -!- SIMILARITY: Belongs to the eukaryotic RPB4 RNA polymerase subunit
CC       family. {ECO:0000255}.
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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   UniGene; Dm.13710; -.
DR   ProteinModelPortal; Q9VEA5; -.
DR   SMR; Q9VEA5; 11-138.
DR   IntAct; Q9VEA5; 3.
DR   MINT; MINT-764159; -.
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; QTMRKFQ; -.
DR   OrthoDB; EOG7RFTK1; -.
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-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   GenomeRNAi; 14462484; -.
DR   NextBio; 847197; -.
DR   Proteomes; UP000000803; Chromosome 3R.
DR   Bgee; Q9VEA5; -.
DR   Genevisible; Q9VEA5; DM.
DR   GO; GO:0005665; C:DNA-directed RNA polymerase II, core complex; IDA:UniProtKB.
DR   GO; GO:0005700; C:polytene chromosome; IDA:FlyBase.
DR   GO; GO:0005705; C:polytene chromosome interband; IDA:FlyBase.
DR   GO; GO:0003899; F:DNA-directed RNA polymerase activity; IDA:UniProtKB.
DR   GO; GO:0000166; F:nucleotide binding; IEA:InterPro.
DR   GO; GO:0007095; P:mitotic G2 DNA damage checkpoint; IGI:FlyBase.
DR   GO; GO:0022008; P:neurogenesis; IMP:FlyBase.
DR   GO; GO:0006366; P:transcription from RNA polymerase II promoter; IDA:UniProtKB.
DR   InterPro; IPR010997; HRDC-like.
DR   InterPro; IPR005574; RNA_pol_II_Rpb4.
DR   InterPro; IPR006590; RNA_pol_II_Rpb4_core.
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; Complete proteome; DNA-directed RNA polymerase;
KW   Nucleotidyltransferase; Nucleus; Reference proteome; Transcription;
KW   Transferase.
FT   CHAIN         1    139       DNA-directed RNA polymerase II 16 kDa
FT                                polypeptide.
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
//