L1Md2 (L2) lineage

The L2 lineage is named after a member, L1Md2. It is not intended to be of the same rank as the abbreviation L1 for the whole of the LINE-1 family. The L2 lineage splits off below ftenode and at about the same time as the M lineage.

The L2 lineage is well represented in GenBank, and so presumably accounts for a significant fraction of total mouse LINE-1s, although a copy number has not been determined.

The L2 lineage has yet to reveal any bursts of output, but rather seems to be continuously populated along its length. There are splits to at least 3 sub lineages apparent so far. All of the sequences indicated have substantial numbers of private substitutions, and so all of the structure indicated occurred well before the domesticus/spretus split. It is not known if there was any activity within this lineage in more recent times.

The closest thing to a full length element currently known in the L2 lineage is PG14LH. This sequence has a large internal deletion, but is still surrounded by a target site duplication, indicating that the two ends are part of the same original insert. PG14LH has a composite AF promoter, and hence the AF composite promoter clade defined by Adey et al., 1991 tentatively may encompass part or all of the L2 lineage.

Another member of the AF composite clade is AF37352b. AF37352b is full length and has an AF composite promoter with 4 of the 118 bp F-type repeats typical of this group. Unfortunately, AF37352b is a recombinant with a nonL2 sequence in the 3' end, and so can not be placed on the tree developed here from 3' end sequence.