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P06104

- UBC2_YEAST

UniProt

P06104 - UBC2_YEAST

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Protein

Ubiquitin-conjugating enzyme E2 2

Gene
RAD6, UBC2, YGL058W
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Catalyzes the covalent attachment of ubiquitin to other proteins. In association with the E3 enzyme BRE1 and LGE1, it plays a role in transcription regulation by catalyzing the monoubiquitination of histone H2B to form H2BK123ub1. H2BK123ub1 gives a specific tag for epigenetic transcriptional activation, elongation by RNA polymerase II, telomeric silencing, and is also a prerequisite for H3K4me and H3K79me formation. In association with the E3 enzyme RAD18, it catalyzes the monoubiquitination of POL30 'Lys-164', involved in postreplication repair of UV-damaged DNA. The RAD6/UBC2-RAD18 complex is also involved in prevention of spontaneous mutations caused by 7,8-dihydro-8-oxoguanine. In association with the E3 enzyme UBR1, is involved in N-end rule-dependent protein degradation. Also involved in sporulation.17 Publications

Catalytic activityi

ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei88 – 881Glycyl thioester intermediate

GO - Molecular functioni

  1. acid-amino acid ligase activity Source: InterPro
  2. ATP binding Source: UniProtKB-KW
  3. protein binding Source: IntAct
  4. ubiquitin-protein transferase activity Source: SGD

GO - Biological processi

  1. ATP catabolic process Source: GOC
  2. chromatin silencing at telomere Source: SGD
  3. DNA-templated transcription, termination Source: SGD
  4. double-strand break repair via homologous recombination Source: SGD
  5. ER-associated ubiquitin-dependent protein catabolic process Source: SGD
  6. error-free postreplication DNA repair Source: SGD
  7. error-free translesion synthesis Source: SGD
  8. error-prone translesion synthesis Source: SGD
  9. histone monoubiquitination Source: SGD
  10. meiotic DNA double-strand break formation Source: SGD
  11. mitotic G1 DNA damage checkpoint Source: SGD
  12. protein monoubiquitination Source: SGD
  13. protein polyubiquitination Source: SGD
  14. protein ubiquitination involved in ubiquitin-dependent protein catabolic process Source: SGD
  15. regulation of dipeptide transport Source: SGD
  16. sporulation resulting in formation of a cellular spore Source: UniProtKB-KW
  17. transcription from RNA polymerase II promoter Source: SGD
  18. ubiquitin-dependent protein catabolic process via the N-end rule pathway Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Ligase

Keywords - Biological processi

DNA damage, DNA repair, Sporulation, Transcription, Transcription regulation, Ubl conjugation pathway

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-30566-MONOMER.
ReactomeiREACT_189060. Antigen processing: Ubiquitination & Proteasome degradation.
UniPathwayiUPA00143.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-conjugating enzyme E2 2 (EC:6.3.2.19)
Alternative name(s):
Radiation sensitivity protein 6
Ubiquitin carrier protein UBC2
Ubiquitin-protein ligase UBC2
Gene namesi
Name:RAD6
Synonyms:UBC2
Ordered Locus Names:YGL058W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome VII

Organism-specific databases

CYGDiYGL058w.
SGDiS000003026. RAD6.

Subcellular locationi

Cytoplasm. Nucleus 3 Publications

GO - Cellular componenti

  1. cytoplasm Source: SGD
  2. nucleus Source: SGD
  3. Rad6-Rad18 complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi1 – 99Missing: Prevents H3K4me3 formation. 2 Publications
Mutagenesisi88 – 881C → A or V: Loss of activity. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 172172Ubiquitin-conjugating enzyme E2 2PRO_0000082540Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei120 – 1201Phosphoserine; by SGV12 Publications

Post-translational modificationi

The N-terminus is blocked.

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiP06104.
PeptideAtlasiP06104.

Expressioni

Inductioni

Up-regulated by UV radiations and during meiosis.1 Publication

Gene expression databases

GenevestigatoriP06104.

Interactioni

Subunit structurei

Forms a heterodimer complexes with the E3 enzymes BRE1, RAD18 and UBR1. Interacts also with UBR2, RTF1, PAF1 and the RNA polymerase II hyperphosphorylated form. The interaction with RNA polymerase II is BRE1- and PAF1-dependent.6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
BRE1Q074574EBI-19722,EBI-31563
RAD18P108624EBI-19722,EBI-14659
UBR1P198123EBI-19722,EBI-19909
UBR2Q079636EBI-19722,EBI-34338

Protein-protein interaction databases

BioGridi33189. 368 interactions.
DIPiDIP-1555N.
IntActiP06104. 13 interactions.
MINTiMINT-394584.
STRINGi4932.YGL058W.

Structurei

Secondary structure

1
172
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 1815
Beta strandi24 – 296
Beta strandi32 – 4110
Turni47 – 504
Beta strandi52 – 587
Turni61 – 655
Beta strandi69 – 746
Beta strandi85 – 873
Helixi90 – 923
Turni93 – 953
Helixi102 – 11312
Helixi124 – 1329
Helixi134 – 15219

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AYZX-ray2.60A/B/C1-172[»]
ProteinModelPortaliP06104.
SMRiP06104. Positions 2-154.

Miscellaneous databases

EvolutionaryTraceiP06104.

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi150 – 17223Asp/Glu-rich (acidic tail)Add
BLAST

Domaini

The acidic-tail domain of UBC2 mediates interaction with UBR1 and UBR2, and thus is important for polyubiquitination of histones. This domain is also important for sporulation.

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG5078.
GeneTreeiENSGT00730000110565.
HOGENOMiHOG000233454.
KOiK10573.
OMAiETVENSW.
OrthoDBiEOG7SBP18.

Family and domain databases

Gene3Di3.10.110.10. 1 hit.
InterProiIPR000608. UBQ-conjugat_E2.
IPR023313. UBQ-conjugating_AS.
IPR016135. UBQ-conjugating_enzyme/RWD.
[Graphical view]
PfamiPF00179. UQ_con. 1 hit.
[Graphical view]
SUPFAMiSSF54495. SSF54495. 1 hit.
PROSITEiPS00183. UBIQUITIN_CONJUGAT_1. 1 hit.
PS50127. UBIQUITIN_CONJUGAT_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P06104-1 [UniParc]FASTAAdd to Basket

« Hide

MSTPARRRLM RDFKRMKEDA PPGVSASPLP DNVMVWNAMI IGPADTPYED    50
GTFRLLLEFD EEYPNKPPHV KFLSEMFHPN VYANGEICLD ILQNRWTPTY 100
DVASILTSIQ SLFNDPNPAS PANVEAATLF KDHKSQYVKR VKETVEKSWE 150
DDMDDMDDDD DDDDDDDDDE AD 172
Length:172
Mass (Da):19,706
Last modified:January 1, 1988 - v1
Checksum:i5F568DC28ABBD60F
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
K02962 Genomic DNA. Translation: AAA34952.1.
Z72580 Genomic DNA. Translation: CAA96761.1.
BK006941 Genomic DNA. Translation: DAA08044.1.
PIRiA21906.
RefSeqiNP_011457.1. NM_001180923.1.

Genome annotation databases

EnsemblFungiiYGL058W; YGL058W; YGL058W.
GeneIDi852822.
KEGGisce:YGL058W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
K02962 Genomic DNA. Translation: AAA34952.1 .
Z72580 Genomic DNA. Translation: CAA96761.1 .
BK006941 Genomic DNA. Translation: DAA08044.1 .
PIRi A21906.
RefSeqi NP_011457.1. NM_001180923.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1AYZ X-ray 2.60 A/B/C 1-172 [» ]
ProteinModelPortali P06104.
SMRi P06104. Positions 2-154.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 33189. 368 interactions.
DIPi DIP-1555N.
IntActi P06104. 13 interactions.
MINTi MINT-394584.
STRINGi 4932.YGL058W.

Proteomic databases

PaxDbi P06104.
PeptideAtlasi P06104.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YGL058W ; YGL058W ; YGL058W .
GeneIDi 852822.
KEGGi sce:YGL058W.

Organism-specific databases

CYGDi YGL058w.
SGDi S000003026. RAD6.

Phylogenomic databases

eggNOGi COG5078.
GeneTreei ENSGT00730000110565.
HOGENOMi HOG000233454.
KOi K10573.
OMAi ETVENSW.
OrthoDBi EOG7SBP18.

Enzyme and pathway databases

UniPathwayi UPA00143 .
BioCyci YEAST:G3O-30566-MONOMER.
Reactomei REACT_189060. Antigen processing: Ubiquitination & Proteasome degradation.

Miscellaneous databases

EvolutionaryTracei P06104.
NextBioi 972372.
PROi P06104.

Gene expression databases

Genevestigatori P06104.

Family and domain databases

Gene3Di 3.10.110.10. 1 hit.
InterProi IPR000608. UBQ-conjugat_E2.
IPR023313. UBQ-conjugating_AS.
IPR016135. UBQ-conjugating_enzyme/RWD.
[Graphical view ]
Pfami PF00179. UQ_con. 1 hit.
[Graphical view ]
SUPFAMi SSF54495. SSF54495. 1 hit.
PROSITEi PS00183. UBIQUITIN_CONJUGAT_1. 1 hit.
PS50127. UBIQUITIN_CONJUGAT_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "RAD6 gene of Saccharomyces cerevisiae encodes a protein containing a tract of 13 consecutive aspartates."
    Reynolds P., Weber S., Prakash L.
    Proc. Natl. Acad. Sci. U.S.A. 82:168-172(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The characterization of two new clusters of duplicated genes suggests a 'Lego' organization of the yeast Saccharomyces cerevisiae chromosomes."
    Feuermann M., de Montigny J., Potier S., Souciet J.-L.
    Yeast 13:861-869(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII."
    Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E.
    , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K.
    Nature 387:81-84(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. "The yeast DNA repair gene RAD6 encodes a ubiquitin-conjugating enzyme."
    Jentsch S., McGrath J.P., Varshavsky A.
    Nature 329:131-134(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 77-91, FUNCTION.
  6. "Recombination and mutagenesis in rad6 mutants of Saccharomyces cerevisiae: evidence for multiple functions of the RAD6 gene."
    Montelone B.A., Prakash S., Prakash L.
    Mol. Gen. Genet. 184:410-415(1981) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  7. "Expression of the Saccharomyces cerevisiae DNA repair gene RAD6 that encodes a ubiquitin conjugating enzyme, increases in response to DNA damage and in meiosis but remains constant during the mitotic cell cycle."
    Madura K., Prakash S., Prakash L.
    Nucleic Acids Res. 18:771-778(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
  8. "Mutation of cysteine-88 in the Saccharomyces cerevisiae RAD6 protein abolishes its ubiquitin-conjugating activity and its various biological functions."
    Sung P., Prakash S., Prakash L.
    Proc. Natl. Acad. Sci. U.S.A. 87:2695-2699(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF CYS-88.
  9. "The N-end rule is mediated by the UBC2(RAD6) ubiquitin-conjugating enzyme."
    Dohmen R.J., Madura K., Bartel B., Varshavsky A.
    Proc. Natl. Acad. Sci. U.S.A. 88:7351-7355(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH UBR1.
  10. "Yeast RAD6 encoded ubiquitin conjugating enzyme mediates protein degradation dependent on the N-end-recognizing E3 enzyme."
    Sung P., Berleth E., Pickart C.M., Prakash S., Prakash L.
    EMBO J. 10:2187-2193(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  11. "The extremely conserved amino terminus of RAD6 ubiquitin-conjugating enzyme is essential for amino-end rule-dependent protein degradation."
    Watkins J.F., Sung P., Prakash S., Prakash L.
    Genes Dev. 7:250-261(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH UBR1, MUTAGENESIS OF 1-MET--LEU-9.
  12. "Specific complex formation between yeast RAD6 and RAD18 proteins: a potential mechanism for targeting RAD6 ubiquitin-conjugating activity to DNA damage sites."
    Bailly V., Lamb J., Sung P., Prakash S., Prakash L.
    Genes Dev. 8:811-820(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH RAD18 AND UBR1.
  13. "Yeast DNA repair proteins Rad6 and Rad18 form a heterodimer that has ubiquitin conjugating, DNA binding, and ATP hydrolytic activities."
    Bailly V., Lauder S., Prakash S., Prakash L.
    J. Biol. Chem. 272:23360-23365(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH RAD18.
  14. "The ubiquitin-conjugating enzyme Rad6 (Ubc2) is required for silencing in Saccharomyces cerevisiae."
    Huang H., Kahana A., Gottschling D.E., Prakash L., Liebman S.W.
    Mol. Cell. Biol. 17:6693-6699(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  15. "The E2-E3 interaction in the N-end rule pathway: the RING-H2 finger of E3 is required for the synthesis of multiubiquitin chain."
    Xie Y., Varshavsky A.
    EMBO J. 18:6832-6844(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH UBR1 AND UBR2.
  16. "Two RING finger proteins mediate cooperation between ubiquitin-conjugating enzymes in DNA repair."
    Ulrich H.D., Jentsch S.
    EMBO J. 19:3388-3397(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  17. "Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast."
    Sun Z.-W., Allis C.D.
    Nature 418:104-108(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF CYS-88 AND 1-MET--LEU-9.
  18. "RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO."
    Hoege C., Pfander B., Moldovan G.-L., Pyrowolakis G., Jentsch S.
    Nature 419:135-141(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  19. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  20. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  21. "Rad6 plays a role in transcriptional activation through ubiquitylation of histone H2B."
    Kao C.-F., Hillyer C., Tsukuda T., Henry K.W., Berger S.L., Osley M.A.
    Genes Dev. 18:184-195(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  22. "The post-replication repair RAD18 and RAD6 genes are involved in the prevention of spontaneous mutations caused by 7,8-dihydro-8-oxoguanine in Saccharomyces cerevisiae."
    de Padula M., Slezak G., Auffret van Der Kemp P., Boiteux S.
    Nucleic Acids Res. 32:5003-5010(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  23. "The Bur1/Bur2 complex is required for histone H2B monoubiquitination by Rad6/Bre1 and histone methylation by COMPASS."
    Wood A., Schneider J., Dover J., Johnston M., Shilatifard A.
    Mol. Cell 20:589-599(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, PHOSPHORYLATION AT SER-120.
  24. "Histone H2B ubiquitylation is associated with elongating RNA polymerase II."
    Xiao T., Kao C.-F., Krogan N.J., Sun Z.-W., Greenblatt J.F., Osley M.A., Strahl B.D.
    Mol. Cell. Biol. 25:637-651(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH RTF1; PAF1 AND THE RNA POLYMERASE II HYPERPHOSPHORYLATED FORM.
  25. "The error-free component of the RAD6/RAD18 DNA damage tolerance pathway of budding yeast employs sister-strand recombination."
    Zhang H., Lawrence C.W.
    Proc. Natl. Acad. Sci. U.S.A. 102:15954-15959(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  26. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-120, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  27. "Crystal structure of the Saccharomyces cerevisiae ubiquitin-conjugating enzyme Rad6 at 2.6-A resolution."
    Worthylake D.K., Prakash S., Prakash L., Hill C.P.
    J. Biol. Chem. 273:6271-6276(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).

Entry informationi

Entry nameiUBC2_YEAST
AccessioniPrimary (citable) accession number: P06104
Secondary accession number(s): D6VU83
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: January 1, 1988
Last modified: September 3, 2014
This is version 153 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 2770 molecules/cell in log phase SD medium.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome VII
    Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

External Data

Dasty 3

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