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UniProtKB/Swiss-Prot entry P04052


[Entry info] [Name and origin] [References] [Comments] [Cross-references] [Keywords] [Features] [Sequence] [Tools]

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Entry information
Entry name RPB1_DROME
Primary accession number P04052
Secondary accession number Q9VYX6
Integrated into Swiss-Prot on November 1, 1986
Sequence was last modified on June 1, 2001 (Sequence version 4)
Annotations were last modified on    November 4, 2008 (Entry version 96)
Name and origin of the protein
Protein name DNA-directed RNA polymerase II subunit RPB1
Synonyms RNA polymerase II subunit B1
EC 2.7.7.6
DNA-directed RNA polymerase III largest subunit
Gene name
Name: RpII215
ORFNames: CG1554
From
Drosophila melanogaster (Fruit fly) [TaxID: 7227] 
Taxonomy Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora.
Protein existence 1: Evidence at protein level;
References
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
DOI=10.1007/BF00339727; PubMed=2496296 [NCBI, ExPASy, EBI, Israel, Japan]
Jokerst R.S., Weeks J.R., Zehring W.A., Greenleaf A.L.;
"Analysis of the gene encoding the largest subunit of RNA polymerase II in Drosophila.";
Mol. Gen. Genet. 215:266-275(1989).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=Berkeley;
DOI=10.1126/science.287.5461.2185; PubMed=10731132 [NCBI, ExPASy, EBI, Israel, Japan]
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.;
"The genome sequence of Drosophila melanogaster.";
Science 287:2185-2195(2000).
[3]
GENOME REANNOTATION.
PubMed=12537572 [NCBI, ExPASy, EBI, Israel, Japan]
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.;
"Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.";
Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
[4]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-27.
PubMed=3025586 [NCBI, ExPASy, EBI, Israel, Japan]
Searles L.L., Greenleaf A.L., Kemp W.E., Voelker R.A.;
"Sites of P element insertion and structures of P element deletions in the 5' region of Drosophila melanogaster RpII215.";
Mol. Cell. Biol. 6:3312-3319(1986).
[5]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-472.
DOI=10.1016/0092-8674(85)90118-7; PubMed=2992806 [NCBI, ExPASy, EBI, Israel, Japan]
Biggs J., Searles L.L., Greenleaf A.L.;
"Structure of the eukaryotic transcription apparatus: features of the gene for the largest subunit of Drosophila RNA polymerase II.";
Cell 42:611-621(1985).
[6]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 778-827.
DOI=10.1007/BF00287104; PubMed=8552047 [NCBI, ExPASy, EBI, Israel, Japan]
Petersen G., Song D., Hugle-Dorr B., Oldenburg I., Bautz E.K.;
"Mapping of linear epitopes recognized by monoclonal antibodies with gene-fragment phage display libraries.";
Mol. Gen. Genet. 249:425-431(1995).
[7]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1441-1887.
PubMed=3122024 [NCBI, ExPASy, EBI, Israel, Japan]
Allison L.A., Wong J.K.-C., Fitzpatrick V.D., Moyle M., Ingles C.J.;
"The C-terminal domain of the largest subunit of RNA polymerase II of Saccharomyces cerevisiae, Drosophila melanogaster, and mammals: a conserved structure with an essential function.";
Mol. Cell. Biol. 8:321-329(1988).
Comments
  • FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. 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. RPB1 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template. At the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing (By similarity).
  • CATALYTIC ACTIVITY: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
  • SUBUNIT: Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits (By similarity).
  • INTERACTION:
    P36958:RpII15; NbExp=1; IntAct=EBI-173525, EBI-167046;
  • SUBCELLULAR LOCATION: Nucleus (By similarity).
  • PTM: The tandem 7 residues repeats in the C-terminal domain (CTD) can be highly phosphorylated. The phosphorylation activates Pol II. Phosphorylation occurs mainly at residues 'Ser-2' and 'Ser-5' of the heptapepdtide repeat. The phosphorylation state is believed to result from the balanced action of site-specific CTD kinases and phosphataes, and a "CTD code" that specifies the position of Pol II within the transcription cycle has been proposed.
  • MISCELLANEOUS: The binding of ribonucleoside triphosphate to the RNA polymerase II transcribing complex probably involves a two-step mechanism. The initial binding seems to occur at the entry (E) site and involves a magnesium ion temporarily coordinated by three conserved aspartate residues of the two largest RNA Pol II subunits. The ribonucleoside triphosphate is transferred by a rotation to the nucelotide addition (A) site for pairing with the template DNA. The catalytic A site involves three conserved aspartate residues of the RNA Pol II largest subunit which permanently coordinate a second magnesium ion.
  • SIMILARITY: Belongs to the RNA polymerase beta' chain family.
  • SIMILARITY: Contains 1 C2H2-type zinc finger.
Copyright
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms. Distributed under the Creative Commons Attribution-NoDerivs License.
Cross-references
Sequence databases
EMBL
M27431; AAA28868.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AE014298; AAF48057.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
M14203; AAA28864.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
M11798; AAA28863.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
M19537; AAA28827.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
PIR S04457; RNFF2L.
RefSeq NP_511124.1; -.
UniGene Dm.2925
3D structure databases
HSSP P04050; 1K83. [HSSP ENTRY / PDB]
ModBase P04052.
Protein-protein interaction databases
DIP DIP:22282N; -.
IntAct P04052; -.
Enzyme and pathway databases
BioCyc DMEL-XXX-02:DMEL-XXX-02-001503-MON; -.
Organism-specific databases
FlyBase FBgn0003277; RpII215.
Gene expression databases
ArrayExpress P04052; -.
GermOnline CG1554; Drosophila melanogaster.
Ontologies
GO
GO:0005703; Cellular component: polytene chromosome puff (inferred from direct assay from FlyBase).
GO:0005515; Molecular function: protein binding (inferred from physical interaction from IntAct).
QuickGo view.
Family and domain databases
InterPro IPR000722; RNA_pol_A.
IPR000684; RNA_pol_II_repeat_euk.
IPR006592; RNA_pol_N.
IPR007080; RNA_pol_Rpb1_1.
IPR007066; RNA_pol_Rpb1_3.
IPR007083; RNA_pol_Rpb1_4.
IPR007081; RNA_pol_Rpb1_5.
IPR007075; RNA_pol_Rpb1_6.
IPR007073; RNA_pol_Rpb1_7.
Graphical view of domain structure.
Gene3D G3DSA:2.40.40.30; RNA_pol_A; 1.
G3DSA:3.90.1120.10; RNA_pol_Rpb1_1; 1.
G3DSA:3.30.1360.90; RNA_pol_Rpb1_7; 1.
Pfam PF04997; RNA_pol_Rpb1_1; 1.
PF00623; RNA_pol_Rpb1_2; 1.
PF04983; RNA_pol_Rpb1_3; 1.
PF05000; RNA_pol_Rpb1_4; 1.
PF04998; RNA_pol_Rpb1_5; 1.
PF04992; RNA_pol_Rpb1_6; 1.
PF04990; RNA_pol_Rpb1_7; 1.
PF05001; RNA_pol_Rpb1_R; 18.
Pfam graphical view of domain structure.
SMART SM00663; RPOLA_N; 1.
SMART graphical view of domain structure.
PROSITE PS00115; RNA_POL_II_REPEAT; 11.
BLOCKS P04052.
ProtoNet P04052.
Genome annotation databases
Ensembl CG1554; Drosophila melanogaster. [Contig view]
GeneID 32100; -.
KEGG dme:Dmel_CG1554; -.
NMPDR fig|7227.3.peg.17442; -.
Phylogenomic databases
HOGENOM P04052; -.
Other
NextBio 776837; -.
UniRef View cluster of proteins with at least 50% / 90% / 100% identity.
Keywords
Complete proteome; DNA-binding; DNA-directed RNA polymerase; Magnesium; Metal-binding; Nucleotidyltransferase; Nucleus; Phosphoprotein; Repeat; Transcription; Transferase; Zinc; Zinc-finger.
Features
SEVIEWER logo Feature table viewer FT aligner logo Feature aligner
KeyFrom    To Length Description FTId
CHAIN   1   1887  1887     DNA-directed RNA polymerase II subunit RPB1. PRO_0000073937
REPEAT   1579   1585  7     1. 
REPEAT   1586   1592  7     2; approximate. 
REPEAT   1598   1604  7     3. 
REPEAT   1605   1611  7     4. 
REPEAT   1631   1637  7     5. 
REPEAT   1638   1644  7     6. 
REPEAT   1671   1677  7     7. 
REPEAT   1678   1684  7     8. 
REPEAT   1685   1691  7     9. 
REPEAT   1692   1698  7     10. 
REPEAT   1699   1705  7     11. 
REPEAT   1706   1712  7     12. 
REPEAT   1713   1719  7     13. 
REPEAT   1720   1726  7     14. 
REPEAT   1727   1733  7     15. 
REPEAT   1740   1746  7     16. 
REPEAT   1754   1760  7     17. 
REPEAT   1761   1767  7     18. 
REPEAT   1777   1783  7     19. 
REPEAT   1784   1790  7     20. 
REPEAT   1791   1797  7     21. 
REPEAT   1798   1804  7     22. 
REPEAT   1811   1817  7     23. 
REPEAT   1818   1824  7     24; approximate. 
REPEAT   1825   1831  7     25. 
REPEAT   1832   1838  7     26. 
REPEAT   1839   1845  7     27. 
REPEAT   1846   1852  7     28. 
REPEAT   1853   1859  7     29. 
REPEAT   1860   1866  7     30. 
REPEAT   1868   1874  7     31. 
REPEAT   1875   1881  7     32. 
ZN_FING   67     83  17     C2H2-type (By similarity). 
REGION   825    837  13     Bridging helix. 
REGION   1579   1881  303     32 X 7 AA approximate tandem repeats of Y-[ST]-P-[STNVAPGN]-[STGMA]-[PSTR]-[SNAGCQKTLRIMH]. 
METAL   67     67        Zinc 1 (By similarity). 
METAL   70     70        Zinc 1 (By similarity). 
METAL   77     77        Zinc 1 (By similarity). 
METAL   80     80        Zinc 1 (By similarity). 
METAL   107    107        Zinc 2 (By similarity). 
METAL   110    110        Zinc 2 (By similarity). 
METAL   150    150        Zinc 2 (By similarity). 
METAL   176    176        Zinc 2 (By similarity). 
METAL   487    487        Magnesium 1; catalytic (By similarity). 
METAL   487    487        Magnesium 2; shared with RPB2 (By similarity). 
METAL   489    489        Magnesium 1; catalytic (By similarity). 
METAL   489    489        Magnesium 2; shared with RPB2 (By similarity). 
METAL   491    491        Magnesium 1; catalytic (By similarity). 
CONFLICT   319    324        RAMQKS -> GYAKV (in Ref. 5; AAA28863). 
CONFLICT   450    450        F -> G (in Ref. 5; AAA28863). 
CONFLICT   455    458        TLHK -> RCTT (in Ref. 5). 
CONFLICT   463    472        GHRVKVLPWS -> VTGESVASST (in Ref. 5). 
CONFLICT   741    741        R -> H (in Ref. 1; AAA28868). 
CONFLICT   1485   1524        SMLGGAAMFIGGGSTPSMTPPMTPWANCNTPRYFSPPGHV -> I (in Ref. 7; AAA28827). 
CONFLICT   1506   1508        MTP -> ELDSA (in Ref. 1; AAA28868). 
CONFLICT   1887   1887        D -> DVRKGGRG (in Ref. 1; AAA28868). 
Sequence information
Length: 1887 AA [This is the length of the unprocessed precursor] Molecular weight: 209168 Da [This is the MW of the unprocessed precursor] CRC64: 4EC68C7708A167A3 [This is a checksum on the sequence]
        10         20         30         40         50         60 
MSTPTDSKAP LRQVKRVQFG ILSPDEIRRM SVTEGGVQFA ETMEGGRPKL GGLMDPRQGV 

        70         80         90        100        110        120 
IDRTSRCQTC AGNMTECPGH FGHIDLAKPV FHIGFITKTI KILRCVCFYC SKMLVSPHNP 

       130        140        150        160        170        180 
KIKEIVMKSR GQPRKRLAYV YDLCKGKTIC EGGEDMDLTK ENQQPDPNKK PGHGGCGHYQ 

       190        200        210        220        230        240 
PSIRRTGLDL TAEWKHQNED SQEKKIVVSA ERVWEILKHI TDEECFILGM DPKYARPDWM 

       250        260        270        280        290        300 
IVTVLPVPPL AVRPAVVMFG AAKNQDDLTH KLSDIIKANN ELRKNEASGA AAHVIQENIK 

       310        320        330        340        350        360 
MLQFHVATLV DNDMPGMPRA MQKSGKPLKA IKARLKGKEG RIRGNLMGKR VDFSARTVIT 

       370        380        390        400        410        420 
PDPNLRIDQV GVPRSIAQNL TFPELVTPFN IDRMQELVRR GNSQYPGAKY IVRDNGERID 

       430        440        450        460        470        480 
LRFHPKSSDL HLQCGYKVER HLRDDDLVIF NRQPTLHKMS MMGHRVKVLP WSTFRMNLSC 

       490        500        510        520        530        540 
TSPYNADFDG DEMNLHVPQS METRAEVENI HITPRQIITP QANKPVMGIV QDTLTAVRKM 

       550        560        570        580        590        600 
TKRDVFITRE QVMNLLMFLP TWDAKMPQPC ILKPRPLWTG KQIFSLIIPG NVNMIRTHST 

       610        620        630        640        650        660 
HPDEEDEGPY KWISPGDTKV MVEHGELIMG ILCKKSLGTS AGSLLHICFL ELGHDIAGRF 

       670        680        690        700        710        720 
YGNIQTVINN WLLFEGHSIG IGDTIADPQT YNEIQQAIKK AKDDVINVIQ KAHNMELEPT 

       730        740        750        760        770        780 
PGNTLRQTFE NKVNRILNDA RDKTGGSAKK SLTEYNNLKA MVVSGSKGSN INISQVIACV 

       790        800        810        820        830        840 
GQQNVEGKRI PYGFRKRTLP HFIKDDYGPE SRGFVENSYL AGLTPSEFYF HAMGGREGLI 

       850        860        870        880        890        900 
DTAVKTAETG YIQRRLIKAM ESVMVNYDGT VRNSVGQLIQ LRYGEDGLCG ELVEFQNMPT 

       910        920        930        940        950        960 
VKLSNKSFEK RFKFDWSNER LMKKVFTDDV IKEMTDSSEA IQELEAEWDR LVSDRDSLRQ 

       970        980        990       1000       1010       1020 
IFPNGESKVV LPCNLQRMIW NVQKIFHINK RLPTDLSPIR VIKGVKTLLE RCVIVTGNDR 

      1030       1040       1050       1060       1070       1080 
ISKQANENAT LLFQCLIRST LCTKYVSEEF RLSTEAFEWL VGEIETRFQQ AQANPGEMVG 

      1090       1100       1110       1120       1130       1140 
ALAAQSLGEP ATQMTLNTFH FAGVSSKNVT LGVPRLKEII NISKKPKAPS LTVFLTGGAA 

      1150       1160       1170       1180       1190       1200 
RDAEKAKNVL CRLEHTTLRK VTANTAIYYD PDPQRTVISE DQEFVNVYYE MPDFDPTRIS 

      1210       1220       1230       1240       1250       1260 
PWLLRIELDR KRMTDKKLTM EQIAEKINVG FGEDLNCIFN DDNADKLVLR IRIMNNEENK 

      1270       1280       1290       1300       1310       1320 
FQDEDEAVDK MEDDMFLRCI EANMLSDMTL QGIEAIGKVY MHLPQTDSKK RIVITETGEF 

      1330       1340       1350       1360       1370       1380 
KAIGEWLLET DGTSMMKVLS ERDVDPIRTS SNDICEIFQV LGIEAVRKSV EKEMNAVLQF 

      1390       1400       1410       1420       1430       1440 
YGLYVNYRHL ALLCDVMTAK GHLMAITRHG INRQDTGALM RCSFEETVDV LMDAAAHAET 

      1450       1460       1470       1480       1490       1500 
DPMRGVSENI IMGQLPKMGT GCFDLLLDAE KCRFGIEIPN TLGNSMLGGA AMFIGGGSTP 

      1510       1520       1530       1540       1550       1560 
SMTPPMTPWA NCNTPRYFSP PGHVSAMTPG GPSFSPSAAS DASGMSPSWS PAHPGSSPSS 

      1570       1580       1590       1600       1610       1620 
PGPSMSPYFP ASPSVSPSYS PTSPNYTASS PGGASPNYSP SSPNYSPTSP LYASPRYAST 

      1630       1640       1650       1660       1670       1680 
TPNFNPQSTG YSPSSSGYSP TSPVYSPTVQ FQSSPSFAGS GSNIYSPGNA YSPSSSNYSP 

      1690       1700       1710       1720       1730       1740 
NSPSYSPTSP SYSPSSPSYS PTSPCYSPTS PSYSPTSPNY TPVTPSYSPT SPNYSASPQY 

      1750       1760       1770       1780       1790       1800 
SPASPAYSQT GVKYSPTSPT YSPPSPSYDG SPGSPQYTPG SPQYSPASPK YSPTSPLYSP 

      1810       1820       1830       1840       1850       1860 
SSPQHSPSNQ YSPTGSTYSA TSPRYSPNMS IYSPSSTKYS PTSPTYTPTA RNYSPTSPMY 

      1870       1880 
SPTAPSHYSP TSPAYSPSSP TFEESED 

P04052 in FASTA format

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