Reviewed, UniProtKB/Swiss-Prot Q9W420 (SPT6H_DROME)

Names and origin

Protein names

Recommended name:
    Transcription elongation factor SPT6

Gene names

Name:	Spt6
ORF Names:	CG12225

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	1831 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Acts to stimulate transcriptional elongation by RNA polymerase II By similarity.
Subunit structure	Self associates. Interacts with RNA polymerase II. Interacts with the FACT complex, which is composed of dre4/Spt16 and Ssrp/Ssrp1. Interacts with the exosome, a complex with 3'-5' exoribonuclease activity which is composed of at least Csl4, Dis3, Mtr3, Rrp4, Rrp6, Rrp40, Rrp42, Rrp46 and Ski6. Interacts with the DRB sensitivity-inducing factor complex (the DSIF complex), which is composed of Spt4 and Spt5. Ref.7 Ref.8
Subcellular location	Nucleus. Note: Recruited to sites of active transcription where it colocalizes with the elongating form of RNA polymerase II. Ref.7 Ref.8 Ref.5 Ref.6
Sequence similarities	Belongs to the SPT6 family. Contains 1 S1 motif domain. Contains 1 SH2 domain.
Sequence caution	The sequence AAF14115.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Domain	Coiled coil
PTM	Phosphoprotein
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	RNA elongation Ref.7 Non-traceable author statement. Source: FlyBase regulation of transcription from RNA polymerase II promoter Inferred from electronic annotation. Source: InterPro transcription from RNA polymerase II promoter Ref.5 Inferred from expression pattern. Source: UniProtKB
Cellular component	nuclear exosome (RNase complex) Ref.7 Inferred from physical interaction. Source: FlyBase polytene chromosome interband Ref.5 Inferred from direct assay. Source: UniProtKB polytene chromosome puff Ref.5 Ref.6 Ref.8 Inferred from direct assay. Source: UniProtKB transcription elongation factor complex Ref.8 Inferred from physical interaction. Source: UniProtKB
Molecular function	RNA binding Inferred from electronic annotation. Source: InterPro hydrolase activity, acting on ester bonds Inferred from electronic annotation. Source: InterPro protein binding Inferred from electronic annotation. Source: InterPro transcription elongation regulator activity Ref.7 Non-traceable author statement. Source: FlyBase
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1831	1831	Transcription elongation factor SPT6		PRO_0000072170
Regions
	Domain	1217 – 1286	70	S1 motif
	Domain	1329 – 1440	112	SH2 1
	Coiled coil	7 – 59	53	Potential
	Coiled coil	467 – 494	28	Potential
	Compositional bias	6 – 245	240	Asp/Glu-rich
	Compositional bias	489 – 512	24	Glu-rich
	Compositional bias	1552 – 1682	131	Ser-rich
	Compositional bias	1675 – 1702	28	Gly-rich
	Compositional bias	1771 – 1783	13	Poly-Gly
Amino acid modifications
	Modified residue	34	1	Phosphoserine Ref.10
	Modified residue	36	1	Phosphoserine Ref.10
	Modified residue	37	1	Phosphoserine Ref.10
	Modified residue	66	1	Phosphoserine Ref.10
	Modified residue	70	1	Phosphoserine Ref.10
	Modified residue	75	1	Phosphoserine Ref.10
	Modified residue	124	1	Phosphoserine Ref.9
	Modified residue	151	1	Phosphoserine Ref.10
	Modified residue	156	1	Phosphoserine Ref.10
	Modified residue	159	1	Phosphoserine Ref.10
	Modified residue	171	1	Phosphothreonine Ref.10
	Modified residue	173	1	Phosphoserine Ref.10
	Modified residue	1661	1	Phosphoserine Ref.10
	Modified residue	1664	1	Phosphoserine Ref.10
	Modified residue	1815	1	Phosphoserine Ref.10
Experimental info
	Sequence conflict	1194	1	L → I in AAF14114. Ref.1
	Sequence conflict	1194	1	L → I in AAF14115. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Q9W420-1 [UniParc]. Last modified May 1, 2000. Version 1. Checksum: 005FC78C83EF744D	FASTA	1,831	208,599
	10 20 30 40 50 60 MAEFLDSEAE ESEEEEELDV NERKRLKKLK AAVSDSSEEE EDDEERLREE LKDLIDDNPI 70 80 90 100 110 120 EEDDGSGYDS DGVGSGKKRK KHEDDDLDDR LEDDDYDLIE ENLGVKVERR KRFKRLRRIH 130 140 150 160 170 180 DNESDGEEQH VDEGLVREQI AEQLFDENDE SIGHRSERSH READDYDDVD TESDADDFIV 190 200 210 220 230 240 DDNGRPIAEK KKKRRPIFTD ASLQEGQDIF GVDFDYDDFS KYEEDDYEDD SEGDEYDEDL 250 260 270 280 290 300 GVGDDTRVKK KKALKKKVVK KTIFDIYEPS ELKRGHFTDM DNEIRKTDIP ERMQLREVPV 310 320 330 340 350 360 TPVPEGSDEL DLEAEWIYKY AFCKHTVSEQ EKPESREKMR KPPTTVNKIK QTLEFIRNQQ 370 380 390 400 410 420 LEVPFIAFYR KEYVKPELNI DDLWKVYYYD GIWCQLNERK RKLKVLFEKM RQFQLDTLCA 430 440 450 460 470 480 DTDQPVPDDV RLILDSDFER LADVQSMEEL KDVHMYFLLN YSHELPRMQA EQRRKAIQER 490 500 510 520 530 540 REAKARRQAA AAENGDDAAE AIVVPEPEDD DDPELIDYQL KQASNSSPYA VFRKAGICGF 550 560 570 580 590 600 AKHFGLTPEQ YAENLRDNYQ RNEITQESIG PTELAKQYLS PRFMTTDEVI HAAKYVVARQ 610 620 630 640 650 660 LAQEPLLRKT MREVYFDRAR INIRPTKNGM VLIDENSPVY SMKYVAKKPV SDLFGDQFIK 670 680 690 700 710 720 LMMAEEEKLL EITFLEEFEG NACANGTPGD YVEESKALYQ LDQFAKHVQE WNKLRAECVQ 730 740 750 760 770 780 LALQKWVIPD LIKELRSTLH EEAQQFVLRS CTGKLYKWLK VAPYKPQLPP DFGYEEWSTL 790 800 810 820 830 840 RGIRVLGLAY DPDHSVAAFC AVTTVEGDIS DYLRLPNILK RKNSYNLEEK AQKLADLRKL 850 860 870 880 890 900 SDFIKMKKPH IVVIGAESRD AQNIQADIKE ILHELETSEQ FPPIEVEIID NELAKIYANS 910 920 930 940 950 960 KKGESDFKEY PPLLKQAASL ARKMQDPLVE YSQLCDADDE ILCLRYHPLQ ERVPREQLLE 970 980 990 1000 1010 1020 QLSLQFINRT SEVGLDINLM VQNSRTINLL QYICGLGPRK GQALLKLLKQ SNQRLENRTQ 1030 1040 1050 1060 1070 1080 LVTVCHLGPR VFINCSGFIK IDTSSLGDST EAYVEVLDGS RVHPETYEWA RKMAIDAMEY 1090 1100 1110 1120 1130 1140 DDEETNPAGA LEEILESPER LKDLDLDAFA VELERQGFGS KSITLYDIRN ELSCLYKDYR 1150 1160 1170 1180 1190 1200 TPYTKPSAEE LFDMLTKETP DSFYVGKCVT AMVTGFTYRR PQGDQLDSAN PVRLDSNESW 1210 1220 1230 1240 1250 1260 QCPFCHKDDF PELSEVWNHF DANACPGQPS GVRVRLENGL PGFIHIKNLS DRQVRNPEER 1270 1280 1290 1300 1310 1320 VRVSQMIHVR IIKIDIDRFS VECSSRTADL KDVNNEWRPR RDNYYDYVTE EQDNRKVSDA 1330 1340 1350 1360 1370 1380 KARALKRKIY ARRVIAHPSF FNKSYAEVVA MLAEADQGEV ALRPSSKSKD HLTATWKVAD 1390 1400 1410 1420 1430 1440 DIFQHIDVRE EGKENDFSLG RSLWIGTEEF EDLDEIIARH IMPMALAARE LIQYKYYKPN 1450 1460 1470 1480 1490 1500 MVTGDENERD VMEKLLREEK ANDPKKIHYF FTASRAMPGK FLLSYLPKTK VRHEYVTVMP 1510 1520 1530 1540 1550 1560 EGYRFRGQIF DTVNSLLRWF KEHWLDPTAT PASASASNLT PLHLMRPPPT ISSSSQTSLG 1570 1580 1590 1600 1610 1620 PQAPYSVTGS VTGGTPRSGI SSAVGGGGSS AYSITQSITG YGTSGSSAPG AGVSSSHYGS 1630 1640 1650 1660 1670 1680 SSTPSFGAIN TPYTPSGQTP FMTPYTPHAS QTPRYGHNVP SPSSQSSSSQ RHHYGSSSGT 1690 1700 1710 1720 1730 1740 GSTPRYHDMG GGGGGGVGGG GGSNAYSMQP HHQQRAKENL DWQLANDAWA RRRPQQHQSH 1750 1760 1770 1780 1790 1800 QSYHAQQQHH HSQQQPHMGM SMNMGITMSL GRGTGGGGGG GYGSTPVNDY STGGGHNRGM 1810 1820 1830 SSKASVRSTP RTNASPHSMN LGDATPLYDE N

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Characterization of Drosophila SPT6 homolog." Chiang P.-W. Submitted (NOV-1998) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
[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.
[4]	"A Drosophila full-length cDNA resource." Stapleton M., Carlson J.W., Brokstein P., Yu C., Champe M., George R.A., Guarin H., Kronmiller B., Pacleb J.M., Park S., Wan K.H., Rubin G.M., Celniker S.E. Genome Biol. 3:RESEARCH0080.1-RESEARCH0080.8(2002) [PubMed: 12537569] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 400-1831. Strain: Berkeley. Tissue: Embryo.
[5]	"Spt5 and spt6 are associated with active transcription and have characteristics of general elongation factors in D. melanogaster." Kaplan C.D., Morris J.R., Wu C.-T., Winston F. Genes Dev. 14:2623-2634(2000) [PubMed: 11040216] [Abstract] Cited for: SUBCELLULAR LOCATION.
[6]	"High-resolution localization of Drosophila Spt5 and Spt6 at heat shock genes in vivo: roles in promoter proximal pausing and transcription elongation." Andrulis E.D., Guzman E., Doering P., Werner J., Lis J.T. Genes Dev. 14:2635-2649(2000) [PubMed: 11040217] [Abstract] Cited for: SUBCELLULAR LOCATION.
[7]	"The RNA processing exosome is linked to elongating RNA polymerase II in Drosophila." Andrulis E.D., Werner J., Nazarian A., Erdjument-Bromage H., Tempst P., Lis J.T. Nature 420:837-841(2002) [PubMed: 12490954] [Abstract] Cited for: SELF-ASSOCIATION, INTERACTION WITH SPT5 AND THE EXOSOME COMPLEX, SUBCELLULAR LOCATION.
[8]	"Tracking FACT and the RNA polymerase II elongation complex through chromatin in vivo." Saunders A., Werner J., Andrulis E.D., Nakayama T., Hirose S., Reinberg D., Lis J.T. Science 301:1094-1096(2003) [PubMed: 12934007] [Abstract] Cited for: INTERACTION WITH SPT5; RNA POLYMERASE II AND THE FACT COMPLEX, SUBCELLULAR LOCATION.
[9]	"An integrated chemical, mass spectrometric and computational strategy for (quantitative) phosphoproteomics: application to Drosophila melanogaster Kc167 cells." Bodenmiller B., Mueller L.N., Pedrioli P.G.A., Pflieger D., Juenger M.A., Eng J.K., Aebersold R., Tao W.A. Mol. Biosyst. 3:275-286(2007) [PubMed: 17372656] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-124, MASS SPECTROMETRY.
[10]	"Phosphoproteome analysis of Drosophila melanogaster embryos." Zhai B., Villen J., Beausoleil S.A., Mintseris J., Gygi S.P. J. Proteome Res. 7:1675-1682(2008) [PubMed: 18327897] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-34; SER-36; SER-37; SER-66; SER-70; SER-75; SER-151; SER-156; SER-159; THR-171; SER-173; SER-1661; SER-1664 AND SER-1815, MASS SPECTROMETRY. Tissue: Embryo.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AF104400 mRNA. Translation: AAF14114.1. AF104401 Genomic DNA. Translation: AAF14115.1. Sequence problems. AE014298 Genomic DNA. Translation: AAF46140.1. AY052030 mRNA. Translation: AAK93454.1. Different initiation.
RefSeq	NP_651962.2.
UniGene	Dm.7373
3D structure databases
HSSP	HSSP built from PDB template 5RXN based on UniProtKB P00268.
ModBase	Search...
Proteomic databases
PRIDE	Q9W420.
Genome annotation databases
Ensembl	FBgn0028982. Drosophila melanogaster. [Contig view]
GeneID	44000.
KEGG	dme:Dmel_CG12225.
NMPDR	fig|7227.3.peg.16696.
Organism-specific databases
FlyBase	FBgn0028982. Spt6.
Phylogenomic databases
HOGENOM	Q9W420.
OMA	Q9W420. QHFEVPF.
Gene expression databases
ArrayExpress	Q9W420.
GermOnline	CG12225. Drosophila melanogaster.
Family and domain databases
InterPro	IPR012340. NA-bd_OB-fold. IPR003029. Rbsml_prot_S1_RNA-bd_dom. IPR006641. Resolv_RNaseH-like. IPR000980. SH2. IPR017072. TF_Spt6. [Graphical view]
Gene3D	G3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.
Pfam	PF00575. S1. 1 hit. [Graphical view]
PIRSF	PIRSF036947. Spt6. 1 hit.
SMART	SM00252. SH2. 2 hits. SM00732. YqgFc. 1 hit. [Graphical view]
PROSITE	PS50126. S1. 1 hit. PS50001. SH2. False negative. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	836551.

Entry information

Entry name

SPT6H_DROME

Accession

Primary (citable) accession number: Q9W420
Secondary accession number(s): Q960J2, Q9U8B5, Q9U8B6

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 22, 2005
Last sequence update:	May 1, 2000
Last modified:	June 16, 2009
This is version 64 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Drosophila annotation project