Multiple sequence alignments of conceptual translations of HML-2 type 1 and type 2 Np9 and Rec ORFs. HML-2 loci potentially encoding Np9 (A) or Rec (B) protein and loci encoding only shorter proteins are shown. Chromosomal positions are given for each locus with respect to the human hg18 reference genome sequence. ‘Tr’ indicates that the locus was identified as transcribed in the present study. Protein sequences of a previously identified Np9-encoding mRNA  and a Rec-encoding mRNA (GenBank acc. no. X72790; ref. ) are given on the top of each alignment. Previously reported Np9 and Rec functional domains are indicated in each alignment. Full-length protein-encoding HML-2 loci are given in chromosomal order followed by shorter Np9-like and Rec-like ORFs. Proteins encoded by type 1 loci HERV-K111 and the Venter locus (see text) are included in the Np9 alignment. Amino acid positions different among each other are highlighted. NES, nuclear export signal; NLS, nuclear localization sequence; PLZF, promyelocytic zinc finger protein; TZFP, testicular zinc finger protein.