Conserved junction sites within TRs. A. Conserved junction site of TRs. JP1: Conserved junction position 1 which is within the DBD encoding region. JP2: Conserved junction position 2 which is at the end of the DBD coding region. JP3: Conserved junction position 3 which is within the LBD motif I coding region and is gene group specific. JP4: Conserved junction position 4 which is within the motif II of LBD encoding region. JP4 is conserved in all vertebrate NR genes. B. Shows the splice junction of invertebrate TRs within motif I which is at the same position as that found in all vertebrate TRs (NR1A) . DBD: DNA binding domain, LBD: ligand binding domain. CiTR: Ciona NR1, DpTR: water flea Daphnia pulex TR, hTRα: Human thyroid receptor alpha, hTRβ: Human thyroid receptor beta, LgTR: owl limpet Lottia gigantean TR, SeTRα: turbellarian Schmidtea mediterranea TRα, SeTRβ: S. mediterranea TRβ, SjTRα: blood fluke Schistosoma japonium TR alpha, SjTRβ: S. japonium TR beta, SmTRα: blood fluke S. mansoni TR alpha, SmTRβ: S. mansoni TR beta, SpTR: sea urchin Strongylocentrotu purpuratus TR. H3: helix 3, H4: helix 4, H5: helix 5. The accession number of each sequence used for analysis can be found in Additional file 1.