RPB4_DROME
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 03-AUG-2022, entry version 153.
DE RecName: Full=DNA-directed RNA polymerase II subunit Rpb4 {ECO:0000303|PubMed:19921261};
GN Name=Rpb4 {ECO:0000303|PubMed:19921261, ECO:0000312|FlyBase:FBgn0263757};
GN ORFNames=CG43662 {ECO:0000312|FlyBase:FBgn0263757};
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: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., Komonyi O.,
RA Cserpan I., Lebedeva L., Nabirochkina E., Udvardy A., 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., 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: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., 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:AAY51562.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=Berkeley;
RA Stapleton M., Carlson J.W., Chavez C., Frise E., George R.A., Pacleb J.M.,
RA 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 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 of
CC DNA into RNA using the four ribonucleoside triphosphates as substrates.
CC 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}. Chromosome
CC {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 Name=A;
CC IsoId=Q7KSD8-2; Sequence=External;
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 embryos,
CC decreases sharply in L1 larvae and then remains low throughout larval
CC development. {ECO:0000269|PubMed:19921261}.
CC -!- INDUCTION: Under heat shock conditions, up-regulated in early larvae
CC and then expression levels appear to return to normal during the L2/L3
CC and pupal stages. In second instar larvae, down-regulated 1 hr after
CC starvation and then remains low until at least 4 hr after nutritional
CC starvation. {ECO:0000269|PubMed:19921261}.
CC -!- MISCELLANEOUS: This protein is produced by a bicistronic gene which
CC also produces the Ada2a protein by alternative splicing
CC (PubMed:19921261). 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 III for
CC 5S and tRNA genes (Probable). {ECO:0000269|PubMed:19921261,
CC 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 AlphaFoldDB; Q9VEA5; -.
DR SMR; Q9VEA5; -.
DR BioGRID; 2593107; 2.
DR IntAct; Q9VEA5; 4.
DR STRING; 7227.FBpp0302530; -.
DR PaxDb; Q9VEA5; -.
DR DNASU; 14462484; -.
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 VEuPathDB; VectorBase:FBgn0263757; -.
DR eggNOG; KOG2351; Eukaryota.
DR GeneTree; ENSGT00390000004912; -.
DR HOGENOM; CLU_110332_2_1_1; -.
DR OMA; AQLGTLC; -.
DR PhylomeDB; Q9VEA5; -.
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 BioGRID-ORCS; 14462484; 1 hit in 1 CRISPR screen.
DR GenomeRNAi; 14462484; -.
DR Proteomes; UP000000803; Chromosome 3R.
DR Bgee; FBgn0263757; Expressed in Malpighian tubule and 15 other tissues.
DR Genevisible; Q9VEA5; DM.
DR GO; GO:0000932; C:P-body; IBA:GO_Central.
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:0000166; F:nucleotide binding; IEA:InterPro.
DR GO; GO:0031369; F:translation initiation factor binding; IBA:GO_Central.
DR GO; GO:0031990; P:mRNA export from nucleus in response to heat stress; IBA:GO_Central.
DR GO; GO:0000288; P:nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay; IBA:GO_Central.
DR GO; GO:0045948; P:positive regulation of translational initiation; IBA:GO_Central.
DR GO; GO:0034402; P:recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex; IBA:GO_Central.
DR GO; GO:0006366; P:transcription by RNA polymerase II; IDA:UniProtKB.
DR GO; GO:0006367; P:transcription initiation from RNA polymerase II promoter; IBA:GO_Central.
DR Gene3D; 1.20.1250.40; -; 1.
DR InterPro; IPR010997; HRDC-like_sf.
DR InterPro; IPR006590; RNA_pol_Rpb4/RPC9_core.
DR InterPro; IPR045222; Rpb4-like.
DR InterPro; IPR005574; Rpb4/RPC9.
DR InterPro; IPR038324; Rpb4/RPC9_sf.
DR PANTHER; PTHR21297; PTHR21297; 1.
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; DNA-directed RNA polymerase; Nucleus;
KW Reference proteome; Transcription.
FT CHAIN 1..139
FT /note="DNA-directed RNA polymerase II subunit Rpb4"
FT /id="PRO_0000283732"
FT CONFLICT 124..126
FT /note="LRQ -> ARE (in Ref. 1; AAN88031/AAN88032)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 139 AA; 16212 MW; F7541C9A08C23CB1 CRC64;
MSFMNPVDMV DEDAADLQFP KEFENAETLL ISEVHMLLDH RKRQNESADE EQEFSEVFMK
TYAYTDSFRK FKNKETIMSA RSLLMQKKLH KFELAALGNL CPEAPEEAKA LIPSLEGRFE
DEELRQILDD IGTKRSLQY
