Reviewed, UniProtKB/Swiss-Prot Q12391 (YN11A_YEAST)

Names and origin

Protein names

Recommended name:
    Transposon Ty1-NL1 Gag polyprotein
Alternative name(s):
    Gag-p49
    Transposon Ty1 protein A
      Short name=TY1A
      Short name=TYA
    p58
Cleaved into the following 2 chains:
    1- Recommended name:
            Capsid protein
                Short name=CA
        Alternative name(s):
            Gag-p45
            p54
    2- Recommended name:
            Gag-p4

Gene names

Name:	TY1A-NL1
Synonyms:	YNLCTy1-1 GAG
Ordered Locus Names:	YNL284C-A
ORF Names:	N0569

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	440 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at transcript level.

General annotation (Comments)

Function	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 Ty1 RNA and initiation of reverse transcription By similarity.
Subunit structure	Homotrimer By similarity.
Subcellular location	Cytoplasm By similarity.
Induction	Ty1-NL1 is a weakly expressed element. Induced under amino acid starvation conditions by GCN4. Ref.3
Domain	The C-terminal RNA-binding region of CA is sufficient for all its nucleocapsid-like chaperone activities By similarity.
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. Ty1 retrotransposons belong to the copia elements (pseudoviridae).

Ontologies

Keywords
Cellular component	Cytoplasm
Coding sequence diversity	Ribosomal frameshifting
Ligand	RNA-binding
Technical term	Complete proteome Transposable element
Gene Ontology (GO)
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	RNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by ribosomal frameshifting. [Align] [Select]

Note: The Gag-Pol polyprotein is generated by a +1 ribosomal frameshift. The ratio of Gag:Gag-Pol varies between 20:1 and 5:1 (By similarity).

Isoform Transposon Ty1-NL1 Gag polyprotein (identifier: Q12391-1)

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.

Note: Produced by conventional translation.

Isoform Transposon Ty1-NL1 Gag-Pol polyprotein (identifier: Q12112-1)

The sequence of this isoform can be found in the external entry Q12112-1.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: Produced by +1 ribosomal frameshifting between codon Leu-435 and Gly-436 of the YNL284C-A ORF.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 440	440	Transposon Ty1-NL1 Gag polyprotein		PRO_0000279142
	Chain	1 – 401	401	Capsid protein By similarity		PRO_0000279143
	Peptide	402 – 440	39	Gag-p4 By similarity		PRO_0000279144
Regions
	Region	299 – 401	103	RNA-binding By similarity
Sites
	Site	401 – 402	2	Cleavage; by Ty1 protease By similarity

Sequences

	Sequence		Length	Mass (Da)
	Isoform Transposon Ty1-NL1 Gag polyprotein [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 173DE7FDF7C2102A	FASTA	440	49,309
	10 20 30 40 50 60 MESQQLSQHS PISHGSACAS VTSKEVHTNQ DPLDVSASKI QEYDKASTKA NSQQTTTPAS 70 80 90 100 110 120 SAVPENPHHA SPQTAQSHSP QNGPYQQQCM MTQNQANPSG WSFYGRPSMI PYTPYQMSPM 130 140 150 160 170 180 YFPPGPHSQF PQYPSSVGTP LSTPSPESGN TFTDSSSADS DMTSTKKYVR PPPMLTSPND 190 200 210 220 230 240 FLNWVKTYIK FLQNSNLGDI IPTATRKAVR QMTDDELTFL CHTFQLFAPS QFLPTWVKDI 250 260 270 280 290 300 LSADYTDIMK ILSKSINKMQ SDTQEVNDIT TLATLHYNGS TPADAFEAEV TNILDRLNNN 310 320 330 340 350 360 GIPINNKVAC QFIMRGLSGE YKFLRYARHR YIHMTVADLF SDIHSMYEEQ QESKRNKSTY 370 380 390 400 410 420 RRNPSDEKKD SRTYTNTTKP KSITRNSQKP NNSQSRTARA HNVSTSNNSS GPDNDLIRGS 430 440 TTEPIQLKNK HDLHLRPGTY
	Isoform Transposon Ty1-NL1 Gag-Pol polyprotein. See Q12112.	FASTA	–	–

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications." Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J. , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J. Nature 387:93-98(1997) [PubMed: 9169873] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[2]	"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: 9582191] [Abstract] Cited for: NOMENCLATURE.
[3]	"Differential effects of chromatin and Gcn4 on the 50-fold range of expression among individual yeast Ty1 retrotransposons." Morillon A., Benard L., Springer M., Lesage P. Mol. Cell. Biol. 22:2078-2088(2002) [PubMed: 11884596] [Abstract] Cited for: INDUCTION.
[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: 16093660] [Abstract] Cited for: REVIEW.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	Z71560 Genomic DNA. Translation: CAA96197.1. Z71561 Genomic DNA. Translation: CAA96202.1.
PIR	S69970.
RefSeq	NP_058179.1.
3D structure databases
ModBase	Search...
Genome annotation databases
Ensembl	YNL284C-A; YNL284C-A; YNL284C-A; Saccharomyces cerevisiae. [Genome view]
GeneID	855434.
KEGG	sce:YNL284C-A.
NMPDR	fig|4932.3.peg.5178.
Organism-specific databases
CYGD	YNL284c-a.
SGD	S000007386. YNL284C-A.
Phylogenomic databases
HOGENOM	HBG204345.
OrthoDB	EOG9869VW.
Gene expression databases
Genevestigator	Q12391.
Family and domain databases
InterPro	IPR015820. Retrotransposon_Ty1A_N. [Graphical view]
Pfam	PF01021. TYA. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	979315.

Entry information

Entry name

YN11A_YEAST

Accession

Primary (citable) accession number: Q12391

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 6, 2007
Last sequence update:	November 1, 1996
Last modified:	December 15, 2009
This is version 51 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)