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Candidate promoter sequences of the solitary genes.

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posted on 28.01.2016, 12:39 by Andrea Degl'Innocenti, Marta Parrilla, Bettina Harr, Meike Teschke

A: detail of the P element showing the sequences used to generate the position-specific weight matrix for homeodomain factor binding sites; on the main sequence, 3'-pointing arrows in salmon show position and orientation of homeodomain factor binding sites as annotated by Vassalli et al.; blue arrows, also 3'-oriented, show emipalindromes identified by EMBOSS Palindrome and used to extend sequences to be added to the matrix; grey boxes mark sequence stretches conserved between the P element and the neighboring Olfr713 (P3) promoter (Conserved P-P3) or between the P and the H element (Conserved P-H); a matrix (depicted on the right, top) was obtained aligning the three extended binding sites on P element and the single extended binding site on H element (identical to the central binding site on P element). B: on the putative promoter of Olfr266 (3'-pointing grey arrow) a homeodomain factor binding site (3'-pointing salmon arrow labelled as HDBS) is predicted; also, sequences conserved in Mammalia Eutheria are found (green boxes); more towards the 3'-end of the putative promoter, SNPs that are present in the wild for Mus musculus domesticus are found in two positions. C: multi-alignments of candidate promoter sequences (5'-3') from different mouse populations for the solitary genes plus (orange box) the non-solitary, reference odorant receptor gene Olfr6 (M50); for Olfr466 two different sequences are presented, one 5' RACE-derived (tagged with [R]) and one based on Plessy et al. (labelled with [P]); B6 stands for C57BL/6J, W stands for consensus of all wild-caught populations, F stands for French population, G stands for German population and I stands for Iranian population; in brown are marked mutant C57BL/6J bases; in violet are highlighted bases differing from consensus; thin vertical lines (light blue) on sequence alignment mark the position of variations in at least some of the 36 non-C57BL/6J laboratory strains, reporting also the fraction of strains carrying the variation (above) and the variation details (below); for Olfr266, sequences boxed in green are conserved in Mammalia Eutheria, and bases in arrowed salmon box (arrow points towards 3') are part of the predicted homeodomain factor binding site.