Reviewed, UniProtKB/Swiss-Prot P36958 (RPB9_DROME)

Names and origin

Protein names

Recommended name:
    DNA-directed RNA polymerase II subunit RPB9
      Short name=RNA polymerase II subunit B9
Alternative name(s):
    DNA-directed RNA polymerase II 15.1 kDa polypeptide

Gene names

Name:	RpII15
ORF Names:	CG3284

Organism

Drosophila melanogaster (Fruit fly) [Complete proteome]

Taxonomic identifier

7227 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Arthropoda › Hexapoda › Insecta › Pterygota › Neoptera › Endopterygota › Diptera › Brachycera › Muscomorpha › Ephydroidea › Drosophilidae › Drosophila › Sophophora

Protein attributes

Sequence length	129 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB9 is part of the upper jaw surrounding the central large cleft and thought to grab the incoming DNA template By similarity.
Subunit structure	Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits By similarity.
Subcellular location	Nucleus By similarity.
Developmental stage	Expressed both maternally and zygotically throughout development. Ref.1
Sequence similarities	Belongs to the archaeal rpoM/eukaryotic RPA12/RPB9/RPC11 RNA polymerase family. Contains 1 TFIIS-type zinc finger.

Ontologies

Keywords
Biological process	Transcription
Cellular component	DNA-directed RNA polymerase Nucleus
Domain	Zinc-finger
Ligand	Metal-binding Zinc
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	regulation of transcription Inferred from electronic annotation. Source: InterPro transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro DNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct transcription regulator activity Inferred from electronic annotation. Source: InterPro zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
MED6	Q8MSX2	1	EBI-167046,EBI-194467
RpII215	P04052	1	EBI-167046,EBI-173525

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 129	129	DNA-directed RNA polymerase II subunit RPB9		PRO_0000121470
Regions
	Zinc finger	21 – 46	26	C4-type By similarity
	Zinc finger	86 – 128	43	TFIIS-type
Sites
	Metal binding	21	1	Zinc 1 By similarity
	Metal binding	24	1	Zinc 1 By similarity
	Metal binding	43	1	Zinc 1 By similarity
	Metal binding	46	1	Zinc 1 By similarity
	Metal binding	90	1	Zinc 2 By similarity
	Metal binding	93	1	Zinc 2 By similarity
	Metal binding	118	1	Zinc 2 By similarity
	Metal binding	123	1	Zinc 2 By similarity
Experimental info
	Sequence conflict	51 – 53	3	EAD → KTN in AAB21674. Ref.1
	Sequence conflict	100	1	F → S in AAB29028. Ref.2
	Sequence conflict	102	1	Q → K in AAB21674. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P36958-1 [UniParc]. Last modified November 8, 2005. Version 2. Checksum: B96CAB2022752DB3	FASTA	129	15,098
	10 20 30 40 50 60 MTTAFDAAHT EGPGFVGIRF CQECNNMLYP KEDKENKILL YACRNCDYKQ EADSNCIYVN 70 80 90 100 110 120 KIMHEIDELT HIVPDVISDP TLPRTEDHAC PKCSHREAVF FQAQTRRAEE EMRLYYVCTN QNCTHRWTE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The RNA polymerase II 15-kilodalton subunit is essential for viability in Drosophila melanogaster." Harrison D.A., Mortin M.A., Corces V.G. Mol. Cell. Biol. 12:928-935(1992) [PubMed: 1545824] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], DEVELOPMENTAL STAGE.
[2]	"RPII15 codes for the M(r) 15,000 subunit 9 of Drosophila melanogaster RNA polymerase II." Liu Z., Kontermann R.E., Schulze R.A., Petersen G., Bautz E.K. FEBS Lett. 335:73-75(1993) [PubMed: 8243669] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"The genome sequence of Drosophila melanogaster." Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F., George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N., Sutton G.G., Wortman J.R., Yandell M.D. , Zhang Q., Chen L.X., Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E., Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B., Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I., Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C., Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S., Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M., Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M., Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D., Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F., Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D., Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A., Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C., McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C., Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L., Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R., Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V., Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F., Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J., Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R., Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y., Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T., Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S., Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W., Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M., Venter J.C. Science 287:2185-2195(2000) [PubMed: 10731132] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Berkeley.
[4]	"Annotation of the Drosophila melanogaster euchromatic genome: a systematic review." Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S., Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E., Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P., Bettencourt B.R., Celniker S.E., de Grey A.D.N.J. , Drysdale R.A., Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M., Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E. Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002) [PubMed: 12537572] [Abstract] Cited for: GENOME REANNOTATION.

Cross-references

Sequence databases
EMBLGenBankDDBJ	S88139 Genomic DNA. Translation: AAB21674.1. S66940 Genomic DNA. Translation: AAB29028.2. AE014297 Genomic DNA. Translation: AAF55045.1.
PIR	S39445.
RefSeq	NP_731898.1.
UniGene	Dm.11852
3D structure databases
HSSP	HSSP built from PDB template 1I3Q based on UniProtKB P27999.
ModBase	Search...
Protein-protein interaction databases
IntAct	P36958. 3 interactions.
Genome annotation databases
Ensembl	FBgn0004855. Drosophila melanogaster. [Contig view]
GeneID	41741.
KEGG	dme:Dmel_CG3284.
NMPDR	fig|7227.3.peg.12746.
Organism-specific databases
FlyBase	FBgn0004855. RpII15.
Phylogenomic databases
HOGENOM	P36958.
OMA	P36958. REAVFFQ.
Gene expression databases
ArrayExpress	P36958.
GermOnline	CG3284. Drosophila melanogaster.
Family and domain databases
InterPro	IPR019761. DNA-dir_RNA_pol-M_15_CS. IPR001529. DNA-dir_RNA_pol_M/15kDsu. IPR001222. Znf_TFIIS. [Graphical view]
Pfam	PF02150. RNA_POL_M_15KD. 1 hit. PF01096. TFIIS_C. 1 hit. [Graphical view]
SMART	SM00661. RPOL9. 1 hit. SM00440. ZnF_C2C2. 1 hit. [Graphical view]
PROSITE	PS01030. RNA_POL_M_15KD. 1 hit. PS00466. ZF_TFIIS_1. 1 hit. PS51133. ZF_TFIIS_2. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	825340.

Entry information

Entry name

RPB9_DROME

Accession

Primary (citable) accession number: P36958
Secondary accession number(s): Q9VFK8

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 1, 1994
Last sequence update:	November 8, 2005
Last modified:	June 16, 2009
This is version 78 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Drosophila annotation project