P36958 (RPB9_DROME) Reviewed, UniProtKB/Swiss-Prot

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)

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.
Protein existence	Evidence at transcript 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 Reference proteome
Gene Ontology (GO)
Biological process	mitosis Inferred from mutant phenotype. Source: FlyBase mitotic cell cycle G2/M transition DNA damage checkpoint Inferred from genetic interaction. Source: FlyBase
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 zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

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 Potential
	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 [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. Strain: Berkeley.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	S88139 Genomic DNA. Translation: AAB21674.1. S66940 Genomic DNA. Translation: AAB29028.2. AE014297 Genomic DNA. Translation: AAF55045.1.
PIR	S39445.
RefSeq	NP_731898.1. NM_169575.1.
UniGene	Dm.11852.
3D structure databases
ProteinModelPortal	P36958.
SMR	P36958. Positions 16-129.
ModBase	Search...
Protein-protein interaction databases
IntAct	P36958. 3 interactions.
STRING	P36958.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblMetazoa	FBtr0082925; FBpp0082384; FBgn0004855.
GeneID	41741.
KEGG	dme:Dmel_CG3284.
NMPDR	fig|7227.3.peg.12746.
Organism-specific databases
CTD	41741.
FlyBase	FBgn0004855. RpII15.
Phylogenomic databases
eggNOG	inNOG08102.
GeneTree	EMGT00050000010609.
InParanoid	P36958.
OMA	REAVFFQ.
OrthoDB	EOG4D51F3.
PhylomeDB	P36958.
Gene expression databases
Bgee	P36958.
GermOnline	CG3284. Drosophila melanogaster.
Family and domain databases
InterPro	IPR019761. DNA-dir_RNA_pol-M_15_CS. IPR001529. DNA-dir_RNA_pol_M/15kDasu. IPR012164. DNA-dir_RNApol_C11. IPR001222. Znf_TFIIS. [Graphical view]
KO	K03017.
Pfam	PF02150. RNA_POL_M_15KD. 1 hit. PF01096. TFIIS_C. 1 hit. [Graphical view]
PIRSF	PIRSF005586. RNApol_RpoM. 1 hit.
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
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:	January 25, 2012
This is version 99 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Drosophila annotation project