Despite their importance in determining protein abundance, a comprehensive catalogue of sequence features controlling protein-to-mRNA ratios (PTR) and a quantification of their effects is still lacking. Here we quantified PTRs for 11,575 proteins across 29 human tissues using matched transcriptomes and proteomes. We analyzed the contribution of known sequence determinants of protein synthesis and degradation and 13 novel mRNA and protein sequence motifs that we found by association testing. While the dynamic range of PTR spans more than 2 orders of magnitude, our integrative model predicts PTR at a median precision of 3.2-fold. A reporter assay provided significant functional support for two novel UTR motifs and a proteome-wide competition-binding assay identified motif-specific bound proteins for one of them. Moreover, our direct comparison of protein to RNA level leads to a new metrics of codon optimality. Altogether, this study shows that a large fraction of PTR variance across genes can be predicted from sequence and identify many new candidate post-transcriptional regulatory elements in the human genome.