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United States Department of Agriculture

Agricultural Research Service

Title: Identification of Novel Porcine Repeat Elements

Authors
item Wiedmann, Ralph
item Nonneman, Danny
item Keele, John

Submitted to: Plant and Animal Genome VX Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: December 1, 2004
Publication Date: January 15, 2005
Citation: Wiedmann, R.T., Nonneman, D.J., Keele, J.W. Identification of novel porcine repeat elements. Proc., Plant & Animal Genome XIII, San Diego, CA. P528. p. 203. 2005.

Technical Abstract: A comparison of the 220 fully sequenced porcine BACs generated by the Comparative Vertebrate Sequencing Initiative (http://www.nisc.nih.gov/)revealed 60 potential repeat sequences that were not identified by RepeatMasker. Further analyses indicated that these could coalesce into a reduced number of sequences. Two sequences were split because components were not always adjacent. Others were either shortened or lengthened depending on how the frequency of blast hits varied across the sequence. We now have 31 distinct, novel porcine repetitive elements ranging in length from 55 to 912 nucleotides. We are actively characterizing them as SINE's, LINE's or other repeat type. The set of fully sequenced BAC's covers approximately 1% of the entire genome, with an emphasis on areas important to comparative genomics. The observed copy numbers of our novel repeat elements in these BAC's can be generalized as follows: 7 appear less than 30 times, 11 between 30 and 59 times, 5 appear between 60 and 100 times, 4 between 100 and 500 times and 3 repeat elements have copy numbers greater than 1000. Several of the repeat elements were found in the bovine genome and we have examples of two in particular that occur in long homologous stretches of sequence at the same location in both pig and cow, indicating that the repeats predate speciation. Most integration sites are not orthologous between pig and cow, indicating replication post speciation.

Last Modified: 4/19/2014
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