Fig. 5

Env(−like) proteins potentially encoded by HERV-K(HML-2) loci identified as transcribed by this study. A full-length, canonical Env protein of 699 aa, as encoded by the HERV-K(HML-2.HOM) type 2 locus, is represented by sequence chr7p22.1_K-6 (=HERV-K(HML-2.HOM); Genbank acc. no.  AF074086; ref. [89]). Grey boxes indicate locations of ORFs within the env gene region relative to full-length Env. Amino acid sequence differences among the various sequences are highlighted. Protein sequences as encoded by type 2 and type 1 loci are separated accordingly. The 292-bp indel region distinguishing type 1 and type 2 proviruses on the DNA level is depicted for the topmost sequence. Signal peptide peptidase (SPPase) and furin cleavage sites are annotated and define signal peptide (SP), surface/outer membrane (SU/OM) and transmembrane (TM) regions, if proteins are so processed. Note that the size of the full-length TM domain is around 26 kDa. Predicted protein masses of selected potential TM variants are indicated. Three HML-2 loci, labelled “*” left of sequence names, were identified as transcribed based on a PCR amplicon within the env 5′ region. Two different Env partial proteins may be encoded by HML-2 locus 3q13.2_K-3 and are named ORFa and ORFb. HML-2 loci chr1p31.1_K-1, chr5q33.3_K-10, HERV-K111 and the Venter locus harbor longer Pol-Env fusion ORFs extending into upstream proviral regions (see the text). Most of those proteins’ N-terminal portions are omitted from the figure. Relative cloning frequencies of locus-specific cDNAs, as determined by the gag amplicon (see Table 1), are given right of the sequence names. Note that locus chr3q12.3_K-5 was found transcribed at the highest relative level (~ 53%)