Table 1.
Most Frequent Motives Recovered by the Selection Process
| BLAST Result with Representative Sequence of Each Group | Abbreviation | MR | Motive Core Area (nt) | Number of Clones | Percentage of Clones | RNA Library Reads (%) × 10−3 |
|---|---|---|---|---|---|---|
| DnaJ (Hsp40) homolog, subfamily C, member 4, mRNA | DNAJC4 | 5′ UTR + CDS | 170 | 13 | 3.2 | 0.7 |
| Fc fragment of IgG, receptor, transporter, alpha, mRNA | FCGRT | 3′ UTR | 143 | 50 | 12.4 | 0.6 |
| MRS2 magnesium homeostasis factor homolog, mRNA | MRS2 | 5′ UTR + CDS | 142 | 11 | 2.7 | 0.6 |
| Lymphocyte-specific protein 1, mRNA | LSP1 | 3′ UTR | 149 | 22 | 5.5 | 4.6 |
| Chemokine (C-C motif) ligand 22, mRNA | CCL22 | 3′ UTR | 155 | 13 | 3.2 | 6.4 |
| Amino-terminal enhancer of split, mRNA | AES | 3′ UTR | 136 | 4 | 1.0 | 0.3 |
| Phospholipase D family, member 3, mRNA | PLD3 | CDS + 3′ UTR | 190 | 15 | 3.7 | 1.7 |
| Polymerase I and transcript release factor, mRNA | PTRF | 5′ UTR + CDS | 172 | 8 | 2.0 | 0.3 |
| Mitochondrially encoded 12S rRNA | mtRNR1 | ncRNA | 142 | 17 | 4.2 | 14.0 |
| Major histocompatibility complex, class II, DR beta 4, mRNA | HLA-DRB4 | 3′ UTR | 233 | 22 | 5.5 | 1.4 |
| Coiled-coil domain containing 124, mRNA | CCDC124 | CDS | 170 | 16 | 4.0 | 2.2 |
| Prothymosin, alpha, mRNA | PTMA | 5′ UTR | 142 | 8 | 2.0 | 6.4 |
| Myosin, heavy chain 9, non-muscle, mRNA | MYH9 | CDS | 167 | 5 | 1.2 | 0.0 |
| Chemokine (C-C motif) ligand 3, mRNA | CCL3 | 5′ UTR + CDS | 109 | 4 | 1.0 | 0.1 |
| Glutaminase, nuclear gene encoding mitochondrial protein, mRNA | GLS | 5′ UTR | 126 | 8 | 2.0 | 0.2 |
The mRNA origins of the most frequent motives as determined by BLAST are shown. The number of analyzed clones aligned to the respective motive and their percentage within the total 402 clones harvested in rounds 5 and 6, the region they map to in the respective genes of origin (MR), and the length of their core area defined as motive and used for further analysis in nucleotides (nt) are provided. Moreover, it is listed which fraction of reads in the NGS data of the starting mRNA library these motives represent. CDS, coding sequence; ncRNA, non-coding RNA.