Identification of a human endogenous LTR-like sequence using HIV-1 LTR specific primers

Using 'consensus' primers derived from the LTR region of 15 HIV-1 isolates, a fragment of 583 bp was amplified from human DNA. Even though specificity was confirmed by Southern blot analysis with a conserved LTR oligonucleotide probe, no significant homologies were detected to either retroviral regions or human or non-human published sequences. Nevertheless, when used as a probe, the 583-bp fragment identified a unique DNA sequence in the human genome on chromosome 1, and cross-reactive sequences in monkey, but not mouse, DNA. This novel, unique and conserved sequence of 583 bp was used to isolate a human HS-1 clone in which the structural property of a viral LTR could be identified.