RPB9_DROME
ID RPB9_DROME Reviewed; 129 AA.
AC P36958; Q9VFK8;
DT 01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
DT 08-NOV-2005, sequence version 2.
DT 03-AUG-2022, entry version 174.
DE RecName: Full=DNA-directed RNA polymerase II subunit RPB9;
DE Short=RNA polymerase II subunit B9;
DE AltName: Full=DNA-directed RNA polymerase II 15.1 kDa polypeptide;
GN Name=RpII15; ORFNames=CG3284;
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]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND DEVELOPMENTAL STAGE.
RX PubMed=1545824; DOI=10.1128/mcb.12.3.928-935.1992;
RA Harrison D.A., Mortin M.A., Corces V.G.;
RT "The RNA polymerase II 15-kilodalton subunit is essential for viability in
RT Drosophila melanogaster.";
RL Mol. Cell. Biol. 12:928-935(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=8243669; DOI=10.1016/0014-5793(93)80442-w;
RA Liu Z., Kontermann R.E., Schulze R.A., Petersen G., Bautz E.K.;
RT "RPII15 codes for the M(r) 15,000 subunit 9 of Drosophila melanogaster RNA
RT polymerase II.";
RL FEBS Lett. 335:73-75(1993).
RN [3]
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 [4]
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).
CC -!- FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of
CC DNA into RNA using the four ribonucleoside triphosphates as substrates.
CC Component of RNA polymerase II which synthesizes mRNA precursors and
CC many functional non-coding RNAs. Pol II is the central component of the
CC basal RNA polymerase II transcription machinery. It is composed of
CC mobile elements that move relative to each other. RPB9 is part of the
CC upper jaw surrounding the central large cleft and thought to grab the
CC incoming DNA template (By similarity). {ECO:0000250}.
CC -!- SUBUNIT: Component of the RNA polymerase II (Pol II) complex consisting
CC of 12 subunits. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus
CC {ECO:0000250|UniProtKB:P32529}.
CC -!- DEVELOPMENTAL STAGE: Expressed both maternally and zygotically
CC throughout development. {ECO:0000269|PubMed:1545824}.
CC -!- SIMILARITY: Belongs to the archaeal RpoM/eukaryotic RPA12/RPB9/RPC11
CC RNA polymerase family. {ECO:0000305}.
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DR EMBL; S88139; AAB21674.1; -; Genomic_DNA.
DR EMBL; S66940; AAB29028.2; -; Genomic_DNA.
DR EMBL; AE014297; AAF55045.1; -; Genomic_DNA.
DR PIR; S39445; S39445.
DR RefSeq; NP_001247099.1; NM_001260170.2.
DR RefSeq; NP_001287326.1; NM_001300397.1.
DR RefSeq; NP_731898.1; NM_169575.3.
DR AlphaFoldDB; P36958; -.
DR SMR; P36958; -.
DR IntAct; P36958; 3.
DR STRING; 7227.FBpp0082384; -.
DR PaxDb; P36958; -.
DR PRIDE; P36958; -.
DR DNASU; 41741; -.
DR EnsemblMetazoa; FBtr0082925; FBpp0082384; FBgn0004855.
DR EnsemblMetazoa; FBtr0309995; FBpp0301701; FBgn0004855.
DR EnsemblMetazoa; FBtr0346348; FBpp0312065; FBgn0004855.
DR GeneID; 41741; -.
DR KEGG; dme:Dmel_CG3284; -.
DR CTD; 41741; -.
DR FlyBase; FBgn0004855; RpII15.
DR VEuPathDB; VectorBase:FBgn0004855; -.
DR eggNOG; KOG2691; Eukaryota.
DR GeneTree; ENSGT00550000075063; -.
DR HOGENOM; CLU_093932_0_1_1; -.
DR InParanoid; P36958; -.
DR OMA; CRDCNNM; -.
DR OrthoDB; 1421187at2759; -.
DR PhylomeDB; P36958; -.
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 SignaLink; P36958; -.
DR BioGRID-ORCS; 41741; 0 hits in 1 CRISPR screen.
DR GenomeRNAi; 41741; -.
DR PRO; PR:P36958; -.
DR Proteomes; UP000000803; Chromosome 3R.
DR Bgee; FBgn0004855; Expressed in egg cell and 23 other tissues.
DR ExpressionAtlas; P36958; baseline and differential.
DR Genevisible; P36958; DM.
DR GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:FlyBase.
DR GO; GO:0005665; C:RNA polymerase II, core complex; IDA:FlyBase.
DR GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0001193; P:maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter; IBA:GO_Central.
DR GO; GO:0000278; P:mitotic cell cycle; HMP:FlyBase.
DR GO; GO:0006379; P:mRNA cleavage; IEA:InterPro.
DR GO; GO:0006366; P:transcription by RNA polymerase II; ISS:FlyBase.
DR GO; GO:0006367; P:transcription initiation from RNA polymerase II promoter; IBA:GO_Central.
DR GO; GO:0006283; P:transcription-coupled nucleotide-excision repair; IBA:GO_Central.
DR CDD; cd10508; Zn-ribbon_RPB9; 1.
DR InterPro; IPR019761; DNA-dir_RNA_pol-M_15_CS.
DR InterPro; IPR001529; DNA-dir_RNA_pol_M/15kDasu.
DR InterPro; IPR012164; Rpa12/Rpb9/Rpc10/TFS.
DR InterPro; IPR034012; Zn_ribbon_RPB9_C.
DR InterPro; IPR001222; Znf_TFIIS.
DR PANTHER; PTHR11239; PTHR11239; 1.
DR Pfam; PF02150; RNA_POL_M_15KD; 1.
DR Pfam; PF01096; TFIIS_C; 1.
DR PIRSF; PIRSF005586; RNApol_RpoM; 1.
DR SMART; SM00661; RPOL9; 1.
DR SMART; SM00440; ZnF_C2C2; 1.
DR PROSITE; PS01030; RNA_POL_M_15KD; 1.
DR PROSITE; PS00466; ZF_TFIIS_1; 1.
DR PROSITE; PS51133; ZF_TFIIS_2; 1.
PE 2: Evidence at transcript level;
KW DNA-directed RNA polymerase; Metal-binding; Nucleus; Reference proteome;
KW Transcription; Zinc; Zinc-finger.
FT CHAIN 1..129
FT /note="DNA-directed RNA polymerase II subunit RPB9"
FT /id="PRO_0000121470"
FT ZN_FING 21..46
FT /note="C4-type"
FT /evidence="ECO:0000255"
FT ZN_FING 86..128
FT /note="TFIIS-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00472"
FT BINDING 21
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P27999"
FT BINDING 24
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P27999"
FT BINDING 43
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P27999"
FT BINDING 46
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P27999"
FT BINDING 90
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00472"
FT BINDING 93
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00472"
FT BINDING 118
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00472"
FT BINDING 123
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00472"
FT CONFLICT 51..53
FT /note="EAD -> KTN (in Ref. 1; AAB21674)"
FT /evidence="ECO:0000305"
FT CONFLICT 100
FT /note="F -> S (in Ref. 2; AAB29028)"
FT /evidence="ECO:0000305"
FT CONFLICT 102
FT /note="Q -> K (in Ref. 1; AAB21674)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 129 AA; 15098 MW; B96CAB2022752DB3 CRC64;
MTTAFDAAHT EGPGFVGIRF CQECNNMLYP KEDKENKILL YACRNCDYKQ EADSNCIYVN
KIMHEIDELT HIVPDVISDP TLPRTEDHAC PKCSHREAVF FQAQTRRAEE EMRLYYVCTN
QNCTHRWTE
