A database that identify CDS-located and 5'UTR-located miRNA binding sites and systematically evaluate miRNA regulatory effects on mRNA stability and translation by integrating multiple high-throughput experimental datasets such as Ago CLIP-seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH), mRNA profiles, ribosome-protected fragment sequencing (RPF) and pulsed stable isotope labeling with amino acids in culture (pSILAC). MtiBase used 61 Ago CLIP-seq datasets to reduce the rates of false positive target prediction. To assess miRNA regulatory effects on mRNA stability, 222 mRNA profiles in response to miRNA overexpression, knockdown, or knockout were integrated. Moreover, 28 RPF and six pSILAC were applied to assess the effects of miRNAs on translational efficiency and protein synthesis, respectively. The SNP influence to the regulatory effects of CDS-located and 5'UTR-located miRNA binding sites was also systematically investigated.