—Phylogenetic analysis of LTRs from mys-9 alleles. L designates the left LTR of each indicated allele, and R designates the right LTR. Analysis was based on the 209-bp region common to the left and right LTRs of each element. The phylogram is drawn with midpoint rooting.
—Unrooted consensus tree derived from total sequence set overlaid with SINE insertions. Parsimony analysis was based on 903 bp that included both LTRs and flanking regions for each element. Nodes with >70% support are shown. The bootstrap support is shown below the node and insertions are shown above the node.
—Sequence flanking insertions into mys-9. The first and last 20 bases of sequence in each line is the sequence surrounding the designated inserts. The three bases immediately after the first dash in each line are the first three bases of the insert, and the four bases immediately before the second dash are the last four bases of the insert. ∼ denotes insert sequence that is not shown. Target site duplications are in lowercase. Pyrimidines immediately 5′ of the target site duplication that are believed to be important for SINE insertion mediated by LINE-1 reverse transcriptase/endonuclease are boxed. Purine stretches believed to be important for the same process are underlined in the left target site duplication. In some cases of differences between the target site duplications, it has been possible to identify the ancestral state (shown in boldface) by comparison with other mys-9 alleles.
—Location of inserts >50 bp found in mys-9 alleles. A mys-9 allele with no major inserts is shown, including single-copy flanking sequence (dotted lines) through the regions complementary to the M9-17 and M9-16 primers used for amplification of the locus. The arrows associated with each SINE or LINE-1 indicate the orientation of that insert. The LINE-1 insert contains the 5′ end of a LINE-1, including most of its open reading frame-1 (ORF-1), followed by a region containing nonrepetitive DNA that includes a portion showing homology with a human X2 box repressor cDNA.
Corrected pairwise differences between LTRs and between mys-9 alleles
The numbers in italics on the diagonal are the corrected pairwise sequence differences (changes per 100 bp) between the common parts of the left and right LTRs (209-bp alignment). All other numbers are the corrected pairwise differences between alleles, using assembled sequences that contain the flanks of each allele out to the PCR primer binding sites plus each of the LTRs (903-bp alignment). The allele names shown in the top row give the species from which the allele was obtained (first three letters), a designation in capital letters of either the allele (Y or Z) or the location from which the mouse was obtained (MX, Mexico; CA, California; IA, Iowa; ME, Maine; GA, Georgia; MA, Massachusetts; TX, Texas; CT, Connecticut), and the size of the amplified allele in kilobases (e.g., 3.78). The criY3.78 and criZ3.78 alleles came from the same individual, as did the manIA4.10 and manIA3.75 alleles. GenBank accession nos. for the sequences in the order shown in this table are AY017268–AY017293. There are two accession numbers assigned to each allele, the first for the left flank and left LTR, the second for the right LTR and right flank.