Investigation of noncoding RNAs (ncRNAs) in the physiological mechanisms have been accumulating, whereas the cellular function of small noncoding RNA including small nucleolar RNAs (snoRNAs) and their relative form of small Cajal body-specific RNAs (scaRNAs) in neuropathologies remain unclear. Therefore, scaRNA has shown notable regulatory patterns in the cortical region of brain from Alzheimer’s disease condition of 5xFAD mouse model, in turn we hypothesize that the scaRNA may participate in the pathophysiological process of Alzheimer’s disease. To identify the scaRNA-participated mechanism, high-throughput total RNA sequencing and analysis has been performed with the scaRNA overexpressed neuroblastoma cell line. Compare to the 5xFAD mice and scaRNA overexpressed cell-derived gene dataset, the intersection of genes has been sorted in differential expression analysis. The proteomics analysis has shown several interactive proteins. These findings suggest that the scaRNA might have ability to be involved in Alzheimer’s disease progression and be a potential pharmaceutical candidate.