Reviewed, UniProtKB/Swiss-Prot Q9VEA5 (RPB4_DROME)

Names and origin

Protein names

Recommended name:
    DNA-directed RNA polymerase II 16 kDa polypeptide
    EC=2.7.7.6
Alternative name(s):
    RNA polymerase II accessory factor rpb4

Gene names

Name:	Rpb4
ORF Names:	CG33520

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	139 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. Associates with POLR2G. Ref.5 Ref.1
Catalytic activity	Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
Subunit structure	RNA polymerase II consists of 12 different subunits By similarity. UniProtKB O15514
Subcellular location	Nucleus. Ref.1
Miscellaneous	Three distinct zinc-containing RNA polymerases are found in eukaryotic nuclei: polymerase I for the ribosomal RNA precursor, polymerase II for the mRNA precursor, and polymerase III for 5S and tRNA genes.
Sequence similarities	Belongs to the eukaryotic RPB4 RNA polymerase subunit family.
Sequence caution	The sequence AAF55522.4 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Transcription
Cellular component	DNA-directed RNA polymerase Nucleus
Coding sequence diversity	Alternative splicing
Molecular function	Nucleotidyltransferase Transferase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	regulation of histone acetylation Inferred from direct assay. Source: FlyBase transcription from RNA polymerase II promoter Ref.1 Inferred from direct assay. Source: UniProtKB
Cellular component	DNA-directed RNA polymerase II, core complex Ref.1 Inferred from direct assay. Source: UniProtKB H4/H2A histone acetyltransferase complex Inferred from direct assay. Source: FlyBase polytene chromosome Ref.1 Ref.5 Inferred from direct assay. Source: FlyBase
Molecular function	DNA-directed RNA polymerase activity Ref.1 Inferred from direct assay. Source: UniProtKB nucleotide binding Inferred from electronic annotation. Source: InterPro protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
Bap60	Q9VYG2	1	EBI-83826,EBI-75169
EG:25E8.4	O46070	1	EBI-83826,EBI-122171

Alternative products

This entry describes 5 isoforms produced by alternative splicing. [Align] [Select]

Isoform D Ref.2 (identifier: Q9VEA5-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform A Ref.2 (identifier: Q7KSD8-1)

The sequence of this isoform can be found in the external entry Q7KSD8-1.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: No experimental confirmation available.

Isoform B Ref.2 (identifier: Q7KSD8-2)

The sequence of this isoform can be found in the external entry Q7KSD8-2.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: No experimental confirmation available.

Isoform C Ref.1 (identifier: Q7KSD8-3)

Also known as: ADA2A-SV2;

The sequence of this isoform can be found in the external entry Q7KSD8-3.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Isoform E Ref.1 (identifier: Q7KSD8-4)

Also known as: ADA2A-SV1;

The sequence of this isoform can be found in the external entry Q7KSD8-4.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 139	139	DNA-directed RNA polymerase II 16 kDa polypeptide		PRO_0000283732
Experimental info
	Sequence conflict	124 – 126	3	LRQ → ARE in AAN88031. Ref.1
	Sequence conflict	124 – 126	3	LRQ → ARE in AAN88032. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform D [UniParc]. Last modified April 3, 2007. Version 5. Checksum: F7541C9A08C23CB1	FASTA	139	16,212
	10 20 30 40 50 60 MSFMNPVDMV DEDAADLQFP KEFENAETLL ISEVHMLLDH RKRQNESADE EQEFSEVFMK 70 80 90 100 110 120 TYAYTDSFRK FKNKETIMSA RSLLMQKKLH KFELAALGNL CPEAPEEAKA LIPSLEGRFE 130 DEELRQILDD IGTKRSLQY
	Isoform A. See Q7KSD8.	FASTA	–	–
	Isoform B. See Q7KSD8.	FASTA	–	–
	Isoform C (ADA2A-SV2). See Q7KSD8.	FASTA	–	–
	Isoform E (ADA2A-SV1). See Q7KSD8.	FASTA	–	–

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Two different Drosophila ADA2 homologues are present in distinct GCN5 histone acetyltransferase-containing complexes." Muratoglu S., Georgieva S., Papai G., Scheer E., Enunlu I., Komonyi O., Cserpan I., Lebedeva L., Nabirochkina E., Udvardy A., Tora L., Boros I. Mol. Cell. Biol. 23:306-321(2003) [PubMed: 12482983] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], SUBCELLULAR LOCATION.
[2]	"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.
[3]	"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, ALTERNATIVE SPLICING.
[4]	Stapleton M., Carlson J.W., Chavez C., Frise E., George R.A., Pacleb J.M., Park S., Wan K.H., Yu C., Celniker S.E. Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: Berkeley.
[5]	"Two Drosophila Ada2 homologues function in different multiprotein complexes." Kusch T., Guelman S., Abmayr S.M., Workman J.L. Mol. Cell. Biol. 23:3305-3319(2003) [PubMed: 12697829] [Abstract] Cited for: FUNCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AF544019 mRNA. Translation: AAN88031.1. AF544020 mRNA. Translation: AAN88032.1. AE014297 Genomic DNA. Translation: AAF55522.4. Sequence problems. BT022168 mRNA. Translation: AAY51562.1. BT023308 mRNA. Translation: AAY55724.1. BT023309 mRNA. Translation: AAY55725.1.
RefSeq	NP_001014633.1.
UniGene	Dm.13710
3D structure databases
SMR	Q9VEA5. Positions 11-136.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9VEA5. 22 interactions.
STRING	Q9VEA5.
Proteomic databases
PRIDE	Q9VEA5.
Genome annotation databases
Ensembl	FBtr0083603; FBpp0099661; FBgn0053520; Drosophila melanogaster. [Genome view]
GeneID	326128.
KEGG	dme:Dmel_CG33520.
UCSC	CG33520-RA. d. melanogaster.
Organism-specific databases
CTD	326128.
FlyBase	FBgn0053520. Rpb4.
Enzyme and pathway databases
BRENDA	2.7.7.6. 48.
Family and domain databases
InterPro	IPR005574. RNA_pol_II_Rpb4. IPR006590. RNA_pol_II_Rpb4_core. [Graphical view]
Pfam	PF03874. RNA_pol_Rpb4. 1 hit. [Graphical view]
SMART	SM00657. RPOL4c. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	847197.

Entry information

Entry name

RPB4_DROME

Accession

Primary (citable) accession number: Q9VEA5
Secondary accession number(s): Q4V3P8, Q8I0A4

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 3, 2007
Last sequence update:	April 3, 2007
Last modified:	September 1, 2009
This is version 59 of the entry and version 5 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Drosophila annotation project