Table 1.
An example of putative miRNAs predicted by miRDeep2.
| A. Unknown 3p or 5p counterparts of known bovine miRNAs. | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| miRNA | Pre-miRNA | Type | Blast results | Mismatch | Chr. | Strand | Start | End | miRNA sequence (5ʹ-3ʹ) | Pre-miRNA sequence (5ʹ-3ʹ) |
| bta-let-7d-3p | bta-let-7d | known | hsa-let-7d-3p | 0 | 8 | + | 86,887,437 | 86,887,513 | CUAUACGACCUGCUGCCUUUCU | CCUAGGAAGAGGUAGUAGGUUGCAUAGUUUUCGGGCAGGGAUUUUGCCCACAAGGAGGUAACUAUACGACCUGCUGCCUUUCUUAGG |
| bta-miR-101–1-5p | bta-mir-101–1 | known | hsa-miR-101-5p | 1 | 3 | + | 80,666,430 | 80,666,486 | CAGUUAUCACAGUGCUGAUGC | AGGCUGCCCUGGCUCAGUUAUCACAGUGCUGAUGCUGUCCAUUCUAAAGGUACAGUACUGUGAUAACUGAAGGAUGGCAGCCA |
| bta-miR-24–2-5p | bta-mir-24–2 | known | dno-miR-24b-5p | 0 | 7 | - | 12,981,641 | 12,981,702 | GUGCCUACUGAGCUGAAACACAGU | CUCUGCCUCCCGUGCCUACUGAGCUGAAACACAGUUGAUUUGUGCACACUGGCUCAGUUCAGCAGGAACAGG |
| bta-miR-339b-3-3p | bta-mir-339b-3 | putative | ssc-miR-339-3p | 1 | 25 | + | 42,294,010 | 42,294,067 | CGCUCCUCGAGGCCAGAGCCC | UCCCUGUCCUCCAGGAGCUCACUUGGUCCGGCCGUGCGCUCCUCGAGGCCAGAGCCC |
| bta-miR-432-3p | bta-mir-432 | known | hsa-miR-432-3p | 0 | 21 | + | 67,431,249 | 67,431,318 | CUGGAUGGCUCCUCCAUGUCU | GCAUGACUCCUCCAAGUCUUGGAGUAGGUCAUUGGGUGGAUCCUUUAUUUCCCUAUGUGGGCCACUGGAUGGCUCCUCCAUGUCUUGGCG |
| bta-miR-500-3p | bta-mir-500 | known | pha-miR-502b | 0 | X | + | 92,899,709 | 92,899,771 | AUGCACCUGGGCAAGGAUUCUGA | GCUCCCCCUCUCUAAUCCUUGCUACCUGGGUGAGAGUGCUUUCUGAAUGCAAUGCACCUGGGCAAGGAUUCUGAGAGAGGGAGC |
| B. Putative bovine miRNAs with conservation in vertebrate species represented by miRBase. | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| miRNA | Blast results | Mismatch | Align to tRNA | Chr. | Strand | Start | End | miRNA sequence (5ʹ-3ʹ) | Pre-miRNA sequence (5ʹ-3ʹ) |
| bta-miR-temp11-5p | hsa-miR-4531 | 2 | yes | 5 | - | 39,604,147 | 39,604,189 | AUGGAUAAGGCGUCUGA | AUGGAUAAGGCGUCUGAUUCUGGAUCAGAAGAUUGAAGGUUC |
| bta-miR-temp14-3p | mdo-miR-1388-3p | 3 | - | 13 | - | 54,375,941 | 54,376,002 | UUCUCAGGUUGGACAGUCCUGA | CGGGCUGACAAACCUGAGAUUGUCCCUGGAUGCUCACCAUUCUCAGGUUGGACAGUCCUGA |
| bta-miR-temp15-5p | mmu-miR-802-5p | 1 | - | 1 | + | 149,720,314 | 149,720,371 | UCAGUAACAAAGAUUCAUCCUUG | UCAGUAACAAAGAUUCAUCCUUGUGUCCAUCAAGCAACAAGGAGAAUCUUUGUCACU |
| bta-miR-temp5-3p | bta-miR-2285f | 3 | - | 14 | + | 62,420,781 | 62,420,842 | AAAGCUGAAUGAACUUUUUGGC | CAAAAAGUUUGUUCAGGUUGUUAGUAAAACCGUACAGCUAAAGCUGAAUGAACUUUUUGGC |
| bta-miR-temp5-3p | bta-miR-2285f | 3 | - | X | - | 118,460,421 | 118,460,481 | AAAGCUGAAUGAACUUUUUGGC | ACAAGUUCAUUUGGGGUUUUCUGUACCAGCUUCUGGUUAAAGCUGAAUGAACUUUUUGGC |
| bta-miR-temp91-5p | mml-miR-7193-5p | 5 | - | 7 | + | 41,231,662 | 41,231,740 | GAAUACUGGGUGCUGUAGGCUU | GAAUACUGGGUGCUGUAGGCUUAAAAAUAAAGAAAGAAAAGAAAAUAUUAACACUUACAGUGGUUCAGUUGGCUUCUC |
| C. Putative bovine miRNAs without conservation in other species. | |||||||
|---|---|---|---|---|---|---|---|
| miRNA | Align to tRNA | Chr. | Strand | Start | End | miRNA sequence (5ʹ-3ʹ) | Pre-miRNA sequence (5ʹ-3ʹ) |
| bta-miR-temp103-5p | yes | 3 | + | 116,209,371 | 116,209,419 | GGGGGUGUAGCUCAGUGGUAGAGU | GGGGGUGUAGCUCAGUGGUAGAGUGCAUACUUAGCAUCCAUGAGGCCC |
| bta-miR-temp12-3p | - | 11 | - | 72,573,707 | 72,573,763 | AACCGCGAGUGGCUGAACCUUG | UCGGUUUUUGCCCCAUGCGUUGGAAGACUUCCCCAACCGCGAGUGGCUGAACCUUG |
| bta-miR-temp1-5p | - | 4 | + | 95,112,096 | 95,112,156 | AACUUUUGCCCCUAGUAACGGACU | AACUUUUGCCCCUAGUAACGGACUGAAGGCAUGAGGAAGUCCGUGCAGGAGGCAAAGCAA |
| bta-miR-temp26-5p | yes | 25 | - | 36,566,883 | 36,566,976 | GUGGACUUCCCUGGUAGCUC | GUGGACUUCCCUGGUAGCUCAGUGGUAAAGAAUCCACCUGCCAAUACAGGAGACAUGGGUUUGAUCCCUGGGUCGGGACGAUCCACUGGAGAA |
| bta-miR-temp45-3p | yes | 22 | + | 52,110,608 | 52,110,675 | GUGGUUAUCACAUUCGCCUC | GGGAAAAAAAGUAUAUUCACAGCAGUGUAUCAAGUUUCCAUACUGUUGUGGUUAUCACAUUCGCCUC |
| bta-miR-temp58-5p | - | 24 | + | 32,811,237 | 32,811,285 | CCCACCCAGGGACGCCC | CCCACCCAGGGACGCCCUUCCCUGCUAUUUGGGCUUCCCUGGUGGGUC |
miRNA = unofficial names of putative miRNAs used in this paper. Pre-miRNA = official/unofficial precursor names of the known bovine miRNAs depending on pre-miRNA type (known = official; putative = unofficial). Type = pre-miRNA types. Blast results = known miRNAs of vertebrates with sequence similarity to the predicted miRNAs. Mismatch = number of not matched bases between the putative miRNA and the blast results. Chr. = chromosome. Start/end = starting/ending positions of the pre-miRNA on the chromosome. miRNA sequence = RNA sequences of putative miRNAs in 5' to 3' direction. Pre-miRNA sequence = RNA sequences of known/putative precursors of known bovine miRNAs in 5ʹ to 3ʹ direction. Align to tRNA = whether the putative miRNAs can be aligned to bovine tRNA sequences. Complete table refers to Supplementary Table S3A-C.