The present invention relates to gene and peptide sequences of a diabetes-specific endogenous retrovirus which is derived from type 1 diabetes patients. In particular, the present invention relates to a whole genome of the diabetes-specific variant of endogenous retrovirus (ERV-9) purified from pancreatic tissues of type 1 diabetes (insulin-dependent diabetes mellitus [IDDM]) patients and its genes and peptide and their sequences, which can be used as a diagnosing reagent for type 1 diabetes and as an immunogen. The diabetes-specific retrovirus expressed exclusively in pancreatic beta cells was purified from deceased type 1 diabetes patients. Subsequently, the retroviral gene sequences were determined, and by analyzing the amino acid sequence of the peptide deduced from the gene, 21 domains of the peptide having hydrophilicity and immuno-dominancy were identified. Therefore, the variant gene of the endogenous retrovirus and the peptide deduced from the gene can be effectively used as a diagnosing reagent of autoimmune-antibody for type 1 diabetes and as a vaccine for the variant ERV-9 related diseases.