Provided is an isolated nucleic acid molecule having a right border flanking region, a left border flanking region and a transgene sequence between the right border flanking region and the left border flanking region, wherein the right border flanking region having at least 90% homology with the sequence set forth in SEQ ID NO: 29; the left border flanking region having at least 90% homology with the sequence set forth in SEQ ID NO: 31; and the transgene sequence having a papaya ringspot virus coat protein gene and a promoter operably linked to the papaya ringspot virus coat protein gene. Primers, probes and kit derived from the isolated nucleic acid molecule are proved to be useful for identifying the transgenic papaya line 16-0-1 in a specific, reproducible, sensitive and reliable way.