Human-ovine comparative sequencing of a 250-kb imprinted domain encompassing the callipyge (clpg) locus and identification of six imprinted transcripts: DLK1, DAT, GTL2, PEG11, antiPEG11, and MEG8 - PubMed (original) (raw)
Ovine–human comparative sequence annotation of the callipyge imprinted domain. (Gaps) White bars correspond to the gaps defined by the
BESTFIT
program (GCG Wisconsin Package) in, respectively, the ovine (O) and human (H) sequence when aligning the orthologous sequences between anchorpoints defined as in Results. These gaps are reported in the background in dark grey throughout the rest of the figure. The red bars in the “Gaps: O” line report the limits between adjacent ovine sequence contigs. (Repeats) Reports the positions of repetitive sequences identified with
RepeatMasker
(Smit & Green 2000) in, respectively, the ovine (O) and human (H) sequences, and labeled according to the color code shown at the bottom of the figure. (CpG islands/(G + C) content) The moving average (G + C) content computed using a 200-bp sliding window is shown for the human sequence (H) only, as the profiles were virtually identical in both species; the red line corresponds to 50% average (G + C) content. CpG islands defined according to Gardiner-Garden and Frommer (1987) and Larsen et al. (1992) are represented as yellow bars for the ovine (O) and human (H) sequences respectively. (Similarity) Similarity profile obtained by sliding a 100-bp window through the
BESTFIT
alignment and plotting the corresponding percent identity between the two species (H and O). The bottom line corresponds to 50% identity, and the red line to 80% identity. (ESTs) Genomic sequences aligned with at least one human (H) or bovine (O) EST when performing high-stringency
BLAST
searches with the corresponding repeat-masked genomic sequence against dbEST, are indicated by the thick yellow lines. The thin yellow lines connect noncontiguous genomic sequences which are either matching contiguous segments of the same EST (corresponding therefore to introns), or matching different ESTs belonging to the same cDNA clone. (
GENSCAN
“+”) (
GENSCAN
“−”) output of the
GENSCAN
software (Burge and Karlin 1997) applied to the “+” and “−” strand respectively. Predicted transcription start sites and polyadenylation signals are symbolized by white and ▸, respectively. Exons are shown as green (“+” strand) or red (“−” strand) boxes, respectively. Conserved exons with a “forward–backward” probability value ≥ 0.9 in at least one of the two species are shown in bright colors; other exons in darker colors. The positions of three previously-described microsatellite markers (Berghmans et al. 2001): MULGE6, BULGE33, and BMS1561 are marked by blue asterisks on top of the sequence alignment. The position of the identified and confirmed genes or transcripts (DLK1, DAT, GTL2, PEG11, antiPEG11, and MEG8) are shown at the bottom of the sequence alignment.