A Transposon-Based Strategy for Sequencing Repetitive DNA in Eukaryotic Genomes

Table 1.

IR-1 Elements inC. elegans

Element no. Chromosome Location Nearest Gene(s) Size (bp) Comment Percent Identity TSD (bp) TSD
R07D5 X intergenic unc-7, R07D5.2 379 full length 99.5 2 AT
F18E3 V intergenic F18E3.1 F18E3.2 379 full length 99.2 2 TA
F08G5 IV intron F08G5.5 379 full length 97.4 2 TA
C17C3 II intron C17C3.12 379 full length 96.6 2 AA
F39B3 X intergenic F39B3, Unknown 400 internal insertion 96.0 2 AA
C04E47 X intergenic C04E7.2, C04E7.3 379 full length 94.5 2 AC
F52H3 II intergenic ZK892.5 F52H3.7 399 truncated, unique  spacer 70.0 2 AT*
F35E12 V — — 392 internal insertion 94.4 2 AC
F22B7 III intergenic F22B7.9, F22B7.10 194 truncated 97.5 2 TT*
ZK849 I — — 1105 internal insertion — 2 TA
F47E1 X intron F47E1.3 112 truncated and  rearranged 82.1 2 TA*
ZC8 X intergenic ZC8.2, ZC8.3 1105 internal insertion — 2 TA
F54D1 IV intergenic F54D1.5, F54D1.6 1083 internal insertion — none
F45E1 X intron F45E1.7 103 internal deletion 99.0 2 CA
F10D11 I intron F10D11.d 173 internal deletion — 2 TA
ZK354 I — — 173 internal deletion — 2 TA
F02E9 I — — 173 internal deletion — 2 TA
C44H4 X intron C44H4.6 102 internal deletion — 2 TG
DH11 II intergenic DH11.1, DH11.2 84 internal deletion 100 2 TA

  • Copies of IR-1 found in the C. elegans genome. Of the 19 elements shown, 14 had BLAST P < 10−25, using the consensus element sequence as the query (Table 2). The remaining five elements (at the bottom) had BLAST P < 10−19. The element number is the same as the corresponding cosmid number for the clone harboring the element. Elements were classified as intergenic if they were between known or predicted genes, or as intron if located within the intron of a known or predicted gene. Percent identity is relative to the reference consensus sequence (Table2). An asterisk (*) next to the target site duplication (TSD) indicates that the element was truncated at one end, and the intact end was used to determine the expected duplication sequence. Elements within regions for which information is not yet available have dashes in the appropriate column. Similar tables are available at our website for this and the other element families (http://www.welch.jhu.edu/~devine/RepDNAdb.html). In the website tables, the element number is hot-linked to the appropriate GenBank record, facilitating rapid information retrieval.

This Article

  1. Genome Res. 7: 551-563

Preprint Server



Current Issue

  1. January 2026, 36 (1)
  1. Current Issue
  1. Alert me to new issues of Genome Research