Artiodactyl retroposons: association with microsatellites and use in SINEmorph detection by PCR.
During a search of polymorphic microsatellites for bovine genome mapping, we found that microsatellites often occur as tails of artiodactyl C-A retroposon elements. In this element, C (85bp) is a tRNA derivative, while A (117bp) is of unknown origin. The A element also occurs as dimer element with a connecting 27bp linker sequence comprising hexanucleotide CACTTT repeats. In 10 clones (45% of those selected deliberately for dinucleotide repeats), the microsatellite motif is associated with the C-A retroposon. In 50% of 44 database artiodactyl C-A sequences, the element also has a microsatellite tail. The microsatellite is usually a simple (CA)n repeat, but in some cases it is an apparent derivative of the linker sequence CACTTT. All but one of 33 database dimer elements have trinucleotide repeat tails (AGC)n, n = 1-9. Microsatellites, retroposons, and their truncated versions (C and/or A) often occur as clusters. We derived the consensus sequence (202bp) of the C-A element, and designed four primers for inter-SINE amplification with the aim of finding SINEmorph polymorphisms. The method is potentially powerful for rapidly producing polymorphic markers for artiodactyl genome mapping.
Kaukinen
J
J
Institute of Biotechnology, University of Helsinki, Finland.
Varvio
S L
SL
D000818:Animals; D001483:Base Sequence; D002417:Cattle; D003001:Cloning, Molecular; D016384:Consensus Sequence; D004251:DNA Transposable Elements / Q000235:genetics*; D004276:DNA, Satellite / Q000235:genetics*; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D012343:RNA, Transfer / Q000235:genetics*; D012194:RNA-Directed DNA Polymerase / Q000378:metabolism
D004251:DNA Transposable Elements; D004276:DNA, Satellite; D012343:RNA, Transfer; D012194:RNA-Directed DNA Polymerase