The Transcript Explorer (TREX) tool is now available. The tool will allow you to fetch genome coordinates of Lotus transcripts based on their IDs, which you will have to provide. The tool only works for L. japonicus genome ≥v3.0.

Update: As of March 5th, 2016, the TREX tool now supports queries in v2.5 of the L. japonicus genome. Read more about it in this announcement.