YJR029W Summary Help

Systematic Name YJR029W
Feature Type transposable_element_gene
Description Retrotransposon TYA Gag and TYB Pol genes; transcribed/translated as one unit; polyprotein is processed to make a nucleocapsid-like protein (Gag), reverse transcriptase (RT), protease (PR), and integrase (IN); similar to retroviral genes (1, 2 and see Summary Paragraph)
Chromosomal Location
ChrX:478344 to 483612 | ORF Map | GBrowse
Gbrowse
Gene Ontology Annotations All YJR029W GO evidence and references
  View Computational GO annotations for YJR029W
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 14 genes
Resources
Large-scale survey
null
Resources
12 total interaction(s) for 9 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 10
  • Affinity Capture-RNA: 1
  • Co-purification: 1

Resources
Expression Summary
histogram
Resources
Length (a.a.) 1,755
Molecular Weight (Da) 198,616
Isoelectric Point (pI) 8.5
Localization
Phosphorylation PhosphoGRID
Structure
Homologs
sequence information
ChrX:478344 to 483612 | ORF Map | GBrowse
This feature contains embedded feature(s): YJR028W
This feature is contained within: YJRWTy1-2
SGD ORF map
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Relative
Coordinates
Chromosomal
Coordinates
Most Recent Updates
Coordinates Sequence
CDS 1..1301 478344..479644 2011-02-03 1996-07-31
Plus 1 translational frameshift 1302..1302 479645..479645 2011-02-03 1996-07-31
CDS 1303..5269 479646..483612 2011-02-03 1996-07-31
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
Resources
External Links All Associated Seq | E.C. | Entrez Gene | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000003790
SUMMARY PARAGRAPH for YJR029W

About yeast retrotransposons...

Ty elements (transposon-yeast) are DNA sequences that move from one chromosomal site to another via an RNA intermediate (3). The DNA segment is transcribed into RNA, then reverse-transcribed into cDNA which is reinserted into the nuclear genome, usually at a different site. The original retrotransposon stays in place, and the new retrotransposon takes with it copies of any adjacent genes or regions that may have been duplicated during the process, making transposition a major source of gene expansion during genome evolution. The insertion event can also influence genomic evolution by disrupting coding or transcriptional control elements, or by promoting chromosomal rearrangements via homologous recombination (1).

There are approximately 50 retrotransposons in the yeast genome, comprising 5 types (Ty1 through Ty5), which represent two distinct groups of eukaryotic LTR-retrotransposons known as Ty1-copia (Pseudoviridae) and Ty3-gypsy (Metaviridae) elements. Ty1, Ty2, Ty4, and Ty5 are all Ty1-copia retrotransposons, whereas the Ty3 retrotransposons are the only representatives of the Ty3-gypsy group (1). Individual types can vary greatly in copy number and also in sequence, indicating different episodes of element amplification and subsequent divergence over time. Transposition is a nonrandom process, and insertion hotspots vary with Ty element type (4). Ty1, Ty2, Ty3 and Ty4 elements tend to integrate near tRNAs or other genes transcribed by RNA polymerase III (5, 6, 1), and Ty5 elements preferentially integrate into heterochromatin at telomeres and silent mating loci (7).

All five types of Ty elements share the same basic structure, consisting of TYA and TYB open reading frames (analogous to the retroviral gag and pol genes) flanked by long terminal repeats (LTRs) (1). TYA encodes structural proteins of the virus-like particle (VLP), where reverse transcription takes place. TYB encodes a polyprotein with protease (PR), integrase (IN), reverse transcriptase (RT) and ribonuclease H (RH) catalytic domains, all of which are essential for retrotransposition (2).

Ty elements are transcribed from their genomic DNA by the host cell's RNA polymerase II, producing RNAs that serve as both genomic RNA and mRNA. The mRNAs have caps and polyadenylated tails, and are translated on cytoplasmic ribosomes. After translation, the RNAs are packaged into virus-like particles (VLPs) in the cytoplasm and are reverse-transcribed by the self-encoded reverse transcriptase (RT) into double-stranded cDNAs (8). The replication cycle is completed by the movement of the cDNA back into the nucleus where it is inserted into new chromosomal sites by the retrotransposon-encoded integrase (9).

Last updated: 2007-03-26 Contact SGD

References cited on this page View Complete Literature Guide for YJR029W
1) Kim JM, et al.  (1998) Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res 8(5):464-78
2) Lesage P and Todeschini AL  (2005) Happy together: the life and times of Ty retrotransposons and their hosts. Cytogenet Genome Res 110(1-4):70-90
3) Roeder GS and Fink GR  (1982) Movement of yeast transposable elements by gene conversion. Proc Natl Acad Sci U S A 79(18):5621-5
4) Natsoulis G, et al.  (1989) Ty1 transposition in Saccharomyces cerevisiae is nonrandom. Genetics 123(2):269-79
5) Chalker DL and Sandmeyer SB  (1992) Ty3 integrates within the region of RNA polymerase III transcription initiation. Genes Dev 6(1):117-28
6) Devine SE and Boeke JD  (1996) Integration of the yeast retrotransposon Ty1 is targeted to regions upstream of genes transcribed by RNA polymerase III. Genes Dev 10(5):620-33
7) Xie W, et al.  (2001) Targeting of the yeast Ty5 retrotransposon to silent chromatin is mediated by interactions between integrase and Sir4p. Mol Cell Biol 21(19):6606-14
8) Roth JF  (2000) The yeast Ty virus-like particles. Yeast 16(9):785-95
9) Perlman PS and Boeke JD  (2004) Molecular biology. Ring around the retroelement. Science 303(5655):182-4