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Q03494

- YD22B_YEAST

UniProt

Q03494 - YD22B_YEAST

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Protein

Transposon Ty2-DR2 Gag-Pol polyprotein

Gene

TY2B-DR2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Protein inferred from homologyi

Functioni

Capsid protein (CA) is the structural component of the virus-like particle (VLP), forming the shell that encapsulates the retrotransposons dimeric RNA genome. The particles are assembled from trimer-clustered units and there are holes in the capsid shells that allow for the diffusion of macromolecules. CA has also nucleocapsid-like chaperone activity, promoting primer tRNA(i)-Met annealing to the multipartite primer-binding site (PBS), dimerization of Ty2 RNA and initiation of reverse transcription (By similarity).By similarity
The aspartyl protease (PR) mediates the proteolytic cleavages of the Gag and Gag-Pol polyproteins after assembly of the VLP.By similarity
Reverse transcriptase/ribonuclease H (RT) is a multifunctional enzyme that catalyzes the conversion of the retro-elements RNA genome into dsDNA within the VLP. The enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes during plus-strand synthesis and hydrolyzes RNA primers. The conversion leads to a linear dsDNA copy of the retrotransposon that includes long terminal repeats (LTRs) at both ends (By similarity).By similarity
Integrase (IN) targets the VLP to the nucleus, where a subparticle preintegration complex (PIC) containing at least integrase and the newly synthesized dsDNA copy of the retrotransposon must transit the nuclear membrane. Once in the nucleus, integrase performs the integration of the dsDNA into the host genome (By similarity).By similarity

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Endonucleolytic cleavage to 5'-phosphomonoester.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei397 – 3982Cleavage; by Ty2 proteaseBy similarity
Active sitei457 – 4571For protease activity; shared with dimeric partnerBy similarity
Sitei578 – 5792Cleavage; by Ty2 proteaseBy similarity
Metal bindingi667 – 6671Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation
Metal bindingi732 – 7321Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation
Sitei1232 – 12332Cleavage; by Ty2 proteaseBy similarity
Metal bindingi1361 – 13611Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
Metal bindingi1442 – 14421Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
Metal bindingi1443 – 14431Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation
Metal bindingi1625 – 16251Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation
Metal bindingi1667 – 16671Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation
Metal bindingi1700 – 17001Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation

GO - Molecular functioni

  1. aspartic-type endopeptidase activity Source: UniProtKB-KW
  2. ATP binding Source: UniProtKB-KW
  3. DNA binding Source: UniProtKB-KW
  4. DNA-directed DNA polymerase activity Source: SGD
  5. metal ion binding Source: UniProtKB-KW
  6. peptidase activity Source: SGD
  7. ribonuclease activity Source: SGD
  8. RNA binding Source: SGD
  9. RNA-directed DNA polymerase activity Source: SGD
  10. RNA-DNA hybrid ribonuclease activity Source: UniProtKB-EC

GO - Biological processi

  1. DNA-dependent DNA replication Source: GOC
  2. DNA integration Source: UniProtKB-KW
  3. DNA recombination Source: UniProtKB-KW
  4. RNA-dependent DNA replication Source: GOC
  5. RNA phosphodiester bond hydrolysis Source: GOC
  6. transposition, RNA-mediated Source: SGD
  7. viral release from host cell Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Aspartyl protease, DNA-directed DNA polymerase, Endonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Protease, RNA-directed DNA polymerase, Transferase

Keywords - Biological processi

DNA integration, DNA recombination, Transposition, Virion maturation, Virus exit from host cell

Keywords - Ligandi

ATP-binding, DNA-binding, Magnesium, Metal-binding, Nucleotide-binding, RNA-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Transposon Ty2-DR2 Gag-Pol polyprotein
Alternative name(s):
TY2A-TY2B
Transposon Ty2 TYA-TYB polyprotein
Cleaved into the following 4 chains:
Capsid protein
Short name:
CA
Ty2 protease (EC:3.4.23.-)
Short name:
PR
Integrase
Short name:
IN
Reverse transcriptase/ribonuclease H (EC:2.7.7.49, EC:2.7.7.7, EC:3.1.26.4)
Short name:
RT
Short name:
RT-RH
Gene namesi
Name:TY2B-DR2
Synonyms:YDRWTy2-2 POL
Ordered Locus Names:YDR210W-B
ORF Names:YD8142A.09
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome IV

Organism-specific databases

SGDiS000007393. YDR210W-B.

Subcellular locationi

Cytoplasm. Nucleus By similarity

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-KW
  2. nucleus Source: SGD
  3. retrotransposon nucleocapsid Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 17701770Transposon Ty2-DR2 Gag-Pol polyproteinPRO_0000279292Add
BLAST
Chaini1 – 397397Capsid proteinBy similarityPRO_0000279293Add
BLAST
Chaini398 – 578181Ty2 proteaseBy similarityPRO_0000279294Add
BLAST
Chaini579 – 1232654IntegraseBy similarityPRO_0000279295Add
BLAST
Chaini1233 – 1770538Reverse transcriptase/ribonuclease HBy similarityPRO_0000279296Add
BLAST

Post-translational modificationi

Initially, virus-like particles (VLPs) are composed of the structural unprocessed proteins Gag and Gag-Pol, and contain also the host initiator methionine tRNA (tRNA(i)-Met) which serves as a primer for minus-strand DNA synthesis, and a dimer of genomic Ty RNA. Processing of the polyproteins occurs within the particle and proceeds by an ordered pathway, called maturation. First, the protease (PR) is released by autocatalytic cleavage of the Gag-Pol polyprotein, and this cleavage is a prerequisite for subsequent processing at the remaining sites to release the mature structural and catalytic proteins. Maturation takes place prior to the RT reaction and is required to produce transposition-competent VLPs (By similarity).By similarity

Expressioni

Gene expression databases

GenevestigatoriQ03494.

Interactioni

Subunit structurei

The capsid protein forms a homotrimer, from which the VLPs are assembled. The protease is a homodimer, whose active site consists of two apposed aspartic acid residues (By similarity).By similarity

Protein-protein interaction databases

BioGridi32261. 4 interactions.
IntActiQ03494. 2 interactions.

Structurei

3D structure databases

ProteinModelPortaliQ03494.
SMRiQ03494. Positions 632-833.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini656 – 831176Integrase catalyticPROSITE-ProRule annotationAdd
BLAST
Domaini1353 – 1491139Reverse transcriptase Ty1/copia-typeAdd
BLAST
Domaini1625 – 1767143RNase H Ty1/copia-typeAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni295 – 397103RNA-bindingBy similarityAdd
BLAST
Regioni579 – 63658Integrase-type zinc finger-likeAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi1193 – 122735Bipartite nuclear localization signalBy similarityAdd
BLAST

Domaini

The C-terminal RNA-binding region of CA is sufficient for all its nucleocapsid-like chaperone activities.By similarity
Integrase core domain contains the D-x(n)-D-x(35)-E motif, named for the phylogenetically conserved glutamic acid and aspartic acid residues and the invariant 35 amino acid spacing between the second and third acidic residues. Each acidic residue of the D,D(35)E motif is independently essential for the 3'-processing and strand transfer activities of purified integrase protein (By similarity).By similarity

Sequence similaritiesi

Contains 1 integrase catalytic domain.PROSITE-ProRule annotation
Contains 1 peptidase A11 domain.Curated

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00730000111602.
HOGENOMiHOG000280731.
InParanoidiQ03494.
OrthoDBiEOG7TJ3S3.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
InterProiIPR025724. GAG-pre-integrase_dom.
IPR001584. Integrase_cat-core.
IPR015820. Retrotransposon_Ty1A_N.
IPR012337. RNaseH-like_dom.
IPR013103. RVT_2.
[Graphical view]
PfamiPF13976. gag_pre-integrs. 1 hit.
PF00665. rve. 1 hit.
PF07727. RVT_2. 1 hit.
PF01021. TYA. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS50994. INTEGRASE. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by ribosomal frameshifting. Align

Note: The Gag-Pol polyprotein is generated by a +1 ribosomal frameshift.

Isoform Transposon Ty2-DR2 Gag-Pol polyprotein (identifier: Q03494-1) [UniParc]FASTAAdd to Basket

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.

« Hide

        10         20         30         40         50
MESQQLHQNP HSQHGSAYAS VTSKEVPSNQ DPLAVSASNL PEFDRDSTKV
60 70 80 90 100
NSQEETTPGT SAVPENHHHV SPQPASVPPP QNGQYQQHGM MTPNKAMASN
110 120 130 140 150
WAHYQQPSMM TCSHYQTSPA YYQPDPHYPL PQYIPPLSTS SPDPIDSQDQ
160 170 180 190 200
HSEVPQAKTK VRNNVLPPHT LTSEENFSTW VKFYIRFLKN SNLGDIIPND
210 220 230 240 250
QGEIKRQMTY EEHAYIYNTF QAFAPFHLLP TWVKQILEIN YSDILTVLCK
260 270 280 290 300
SVSKMQTNNQ ELKDWIALAN LEYNGSTSAD TFEITVSTII QRLKENNINV
310 320 330 340 350
SDRLACQLIL KGLSGDFKYL RNQYRTKTNM KLSQLFAEIQ LIYDENKIMN
360 370 380 390 400
LNKPSQYKQH SEYKNVSRTS PNTTNTKVTT RNYHRTNSSK PRAAKAHNIA
410 420 430 440 450
TSSKFSRVNS DHINESTVSS QYLSDDNELS LGQQQKESKP TRTIDSNDEL
460 470 480 490 500
PDHLLIDSGA SQTLVRSAHY LHHATPNSEI NIVDAQKQDI PINAIGNLHF
510 520 530 540 550
NFQNGTKTSI KALHTPNIAY DLLSLSELAN QNITACFTRN TLERSDGTVL
560 570 580 590 600
APIVKHGDFY WLSKKYLIPS HISKLTINNV NKSKSVNKYP YPLIHRMLGH
610 620 630 640 650
ANFRSIQKSL KKNAVTYLKE SDIEWSNAST YQCPDCLIGK STKHRHVKGS
660 670 680 690 700
RLKYQESYEP FQYLHTDIFG PVHHLPKSAP SYFISFTDEK TRFQWVYPLH
710 720 730 740 750
DRREESILNV FTSILAFIKN QFNARVLVIQ MDRGSEYTNK TLHKFFTNRG
760 770 780 790 800
ITACYTTTAD SRAHGVAERL NRTLLNDCRT LLHCSGLPNH LWFSAVEFST
810 820 830 840 850
IIRNSLVSPK NDKSARQHAG LAGLDITTIL PFGQPVIVNN HNPDSKIHPR
860 870 880 890 900
GIPGYALHPS RNSYGYIIYL PSLKKTVDTT NYVILQNNQT KLDQFDYDTL
910 920 930 940 950
TFDDDLNRLT AHNQSFIEQN ETEQSYDQNT ESDHDYQSEI EINSDPLVND
960 970 980 990 1000
FSSQSLNPLQ LDKEPVQKVR APKEVDADIS EYNILPSTIR SRTPHIINKE
1010 1020 1030 1040 1050
STEMGGTIES DTTSPRHSST FTARNQKRPG SPNDMIDLTS QDRVNYGLEN
1060 1070 1080 1090 1100
IKTTRLGGTE EPYIQRNSDT NIKYRTTNST PSIDDRSSNS ESTTPIISIE
1110 1120 1130 1140 1150
TKAVCDNTPS IDTDPPEYRS SDHATPNIMP DKSSKNVTAD SILDDLPLPD
1160 1170 1180 1190 1200
LTHKSPTDTS DVAKDIPHIH SRQTNSSLGG MDDSNVLTTT KSKKRSLEDN
1210 1220 1230 1240 1250
ETEIEVSRDT WNNKNMRSLE PPRSKKRINL IAAIKGVKSI KPVRTTLRYD
1260 1270 1280 1290 1300
EAITYNKDNK EKDRYVEAYH KEISQLLKMN TWDTNKYYDR NDIDPKKVIN
1310 1320 1330 1340 1350
SMFIFNKKRD GTHKARFVAR GDIQHPDTYD SDMQSNTVHH YALMTSLSIA
1360 1370 1380 1390 1400
LDNDYYITQL DISSAYLYAD IKEELYIRPP PHLGLNDKLL RLRKSLYGLK
1410 1420 1430 1440 1450
QSGANWYETI KSYLINCCDM QEVRGWSCVF KNSQVTICLF VDDMILFSKD
1460 1470 1480 1490 1500
LNANKKIITT LKKQYDTKII NLGEGDNEIQ YDILGLEIKY QRSKYMKLGM
1510 1520 1530 1540 1550
EKSLTEKLPK LNVPLNPKGK KLRAPGQPGH YIDQDELEID EDEYKEKVHE
1560 1570 1580 1590 1600
MQKLIGLASY VGYKFRFDLL YYINTLAQHI LFPSRQVLDM TYELIQFMWD
1610 1620 1630 1640 1650
TRDKQLIWHK NKPTKPDNKL VAISDASYGN QPYYKSQIGN IFLLNGKVIG
1660 1670 1680 1690 1700
GKSTKASLTC TSTTEAEIHA VSEAIPLLNN LSHLVQELNK KPIIKGLLTD
1710 1720 1730 1740 1750
SRSTISIIKS TNEEKFRNRF FGTKAMRLRD EVSGNNLYVY YIETKKNIAD
1760 1770
VMTKPLPIKT FKLLTNKWIH

Note: Produced by +1 ribosomal frameshifting between codon Leu-431 and Gly-432 of the YDR210W-A ORF.

Length:1,770
Mass (Da):202,095
Last modified:March 6, 2007 - v2
Checksum:i8833D6F4FC6CAC68
GO
Isoform Transposon Ty2-DR2 Gag polyprotein (identifier: Q03483-1) [UniParc]FASTAAdd to Basket

The sequence of this isoform can be found in the external entry Q03483.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: Produced by conventional translation.

Length:438
Mass (Da):49,835
GO

Sequence cautioni

The sequence CAA92351.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z68194 Genomic DNA. Translation: CAA92351.1. Sequence problems.
BK006938 Genomic DNA. Translation: DAA12051.1.
PIRiS69950.
RefSeqiNP_058142.3. NM_001184419.3. [Q03494-1]

Genome annotation databases

EnsemblFungiiYDR210W-B; YDR210W-B; YDR210W-B. [Q03494-1]
GeneIDi851793.
KEGGisce:YDR210W-B.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z68194 Genomic DNA. Translation: CAA92351.1 . Sequence problems.
BK006938 Genomic DNA. Translation: DAA12051.1 .
PIRi S69950.
RefSeqi NP_058142.3. NM_001184419.3. [Q03494-1 ]

3D structure databases

ProteinModelPortali Q03494.
SMRi Q03494. Positions 632-833.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 32261. 4 interactions.
IntActi Q03494. 2 interactions.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YDR210W-B ; YDR210W-B ; YDR210W-B . [Q03494-1 ]
GeneIDi 851793.
KEGGi sce:YDR210W-B.

Organism-specific databases

SGDi S000007393. YDR210W-B.

Phylogenomic databases

GeneTreei ENSGT00730000111602.
HOGENOMi HOG000280731.
InParanoidi Q03494.
OrthoDBi EOG7TJ3S3.

Miscellaneous databases

NextBioi 969618.

Gene expression databases

Genevestigatori Q03494.

Family and domain databases

Gene3Di 3.30.420.10. 1 hit.
InterProi IPR025724. GAG-pre-integrase_dom.
IPR001584. Integrase_cat-core.
IPR015820. Retrotransposon_Ty1A_N.
IPR012337. RNaseH-like_dom.
IPR013103. RVT_2.
[Graphical view ]
Pfami PF13976. gag_pre-integrs. 1 hit.
PF00665. rve. 1 hit.
PF07727. RVT_2. 1 hit.
PF01021. TYA. 1 hit.
[Graphical view ]
SUPFAMi SSF53098. SSF53098. 1 hit.
PROSITEi PS50994. INTEGRASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
    Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
    , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
    Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. "Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence."
    Kim J.M., Vanguri S., Boeke J.D., Gabriel A., Voytas D.F.
    Genome Res. 8:464-478(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NOMENCLATURE.
  4. "Happy together: the life and times of Ty retrotransposons and their hosts."
    Lesage P., Todeschini A.L.
    Cytogenet. Genome Res. 110:70-90(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.

Entry informationi

Entry nameiYD22B_YEAST
AccessioniPrimary (citable) accession number: Q03494
Secondary accession number(s): D6VSJ1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 6, 2007
Last sequence update: March 6, 2007
Last modified: October 29, 2014
This is version 92 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Retrotransposons are mobile genetic entities that are able to replicate via an RNA intermediate and a reverse transcription step. In contrast to retroviruses, retrotransposons are non-infectious, lack an envelope and remain intracellular. Ty2 retrotransposons belong to the copia elements (pseudoviridae).

Keywords - Technical termi

Complete proteome, Multifunctional enzyme, Reference proteome, Transposable element

Documents

  1. Peptidase families
    Classification of peptidase families and list of entries
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

External Data

Dasty 3