Table 1. Rat miRNA sequences identified by cloning from E18 primary cortical neurons.
| Precursors
|
||||
|---|---|---|---|---|
| miRNA names | miRNA clone sequence | Northern | Rat | Mouse |
| mir-322 | AAACATGAAGCGCTGCAACA | — | + | + |
| mir-323 | GCACATTACACGGTCGACCTCT (8×) | + | + | + |
| mir-324-3p | CCACTGCCCCAGGTGCTGCTGG (6×) | + | + | + |
| mir-324-5p | CGCATCCCCTAGGGCATTGGTGT (7×) | + | + | + |
| mir-325 | CCTAGTAGGTGCTCAGTAAGTGT (4×) | — | + | + |
| mir-326 | CCTCTGGGCCCTTCCTCCAGT | + | + | + |
| mir-327 | CCTTGAGGGGCATGAGGGT | — | + | |
| mir-328 | CTGGCCCTCTCTGCCCTTCCGT (2×) | + | + | + |
| mir-329 | AACACACCCAGCTAACCTTTTT (2×) | + | + | + |
| mir-330 | GCAAAGCACAGGGCCTGCAGAGAA (2×) | — | + | + |
| mir-331 | GCCCCTGGGCCTATCCTAGAA (4×) | + | + | + |
| mir-332 | GGTCCCACCAGAGTCGCCA | — | + | |
| mir-333 | GTGGTGTGCTAGTTACTTTT | — | + | |
| mir-334 | TAAACGGTGCAGAGATGTG | — | + | |
| mir-335 | TCAAGAGCAATAACGAAAAATGT | + | + | + |
| mir-336 | TCACCCTTCCATATCTAGTCT | — | + | + |
| mir-337 | TTCAGCTCCTATATGATGCCTTT (2×) | — | + | + |
| mir-338 | TCCAGCATCAGTGATTTTGTTGA | + | + | + |
| mir-339 | TCCCTGTCCTCCAGGAGCTCATT | — | + | + |
| mir-340 | TCCGTCTCAGTTACTTTATAGCC (2×) | — | + | + |
| mir-341 | TCGATCGGTCGGTCGGTCAGT | — | + | + |
| mir-342 | TCTCACACAGAAATCGCACCCGTC | + | + | + |
| mir-343 | TCTCCCTCCGTGTGCCCAGTT | — | + | + |
| mir-344 | TGATCTAGCCAAAGCCTGACCGT | + | + | + |
| mir-345 | TGCTGACCCCTAGTCCAGTGC (2×) | + | + | + |
| mir-346 | TGTCTGCCTGAGTGCCTGCCTCTAA | — | + | + |
| mir-347 | TGTCCCTCTGGGTCGCCA | — | + | |
| mir-348 | TGCCCACCCTTTACCCCACTCCAGT | — | + | |
| mir-349 | CAGCCCTGCTGTCTTAACCTCT | + | + | |
| mir-350 | ATTCACAAAGCCCATACACTTTCAC | — | + | + |
| mir-351 | TCCCTGAGGAGCCCTTTGAGCCTGT (7×) | + | + | + |
| mir-352 | AGAGTAGTAGGTTGCATAGTA (2×) | — | + | |
| let-7a | TGAGGTAGTAGGTTGTATAGTT (5×) | NA | + | + |
| let-7b | TGAGGTAGTAGGTTGTGTGGTTT (11×) | NA | + | + |
| let-7c | TGAGGTAGTAGGTTGTATGGTTT (28×) | NA | + | + |
| let-7d | AGAGGTAGTAGGTTGCATAGTT (13×) | NA | + | |
| let-7d* | CTATACGACCTGCTGCCTTTCTA (2×) | + | + | + |
| let-7e | TGAGGTAGGAGGTTGTATAGTTA (2×) | NA | + | + |
| let-7f | TGAGGTAGTAGATTGTATAGTT (10×) | NA | + | + |
| let-7gL | TGAGGTAGTAGTTTGTACAGTT (5×) | + | + | |
| let-7i | TGAGGTAGTAGTTTGTGCTGTT (4×) | NA | + | + |
| mir-7-1* | CAACAAATCACAGTCTGCCATA (2×) | + | + | + |
| mir-9 | TCTTTGGTTATCTAGCTGTATGA (9×) | NA | + | + |
| mir-15 | TAGCAGCACATAATGGTTTGT (2×) | NA | + | |
| mir-15b | TAGCAGCACATCATGGTTTACA (2×) | NA | + | + |
| mir-16 | TAGCAGCACGTAAATATTGGCGT (20×) | + | + | + |
| mir-18 | TAAGGTGCATCTAGTGCAGATAG (3×) | NA | + | + |
| mir-19b | TGTGCAAATCCATGCAAAACTGA | NA | + | + |
| mir-20 | TAAAGTGCTTATAGTGCAGGTAG (3×) | NA | + | + |
| mir-20* | ACTGCATTACGAGCACTTACA | — | + | + |
| mir-21 | TAGCTTATCAGACTGATGTTGA (3×) | NA | + | + |
| mir-22 | AAGCTGCCAGTTGAAGAACTGT | NA | + | + |
| mir-29a | TAGCACCATCTGAAATCGGTTA | NA | + | + |
| mir-30b | TGTAAACATCCTACACTCAGCT (6×) | + | + | + |
| mir-30c | TGTAAACATCCTACACTCTCAGCT (7×) | NA | + | + |
| mir-30d | TGTAAACATCCCCGACTGGAAGCT (3×) | NA | + | + |
| mir-34 | TGGCAGTGTCTTAGCTGGTTGT (3×) | — | + | + |
| mir-91 | CAAAGTGCTTACAGTGCAGGTAG (21×) | NA | + | + |
| mir-93 | CAAAGTGCTGTTCGTGCAGGTAG (9×) | NA | + | + |
| mir-98 | TGAGGTAGTAAGTTGTATTGTT | NA | + | |
| mir-99a/miR-99 | AACCCGTAGATCCGATCTTGTG (18×) | NA | + | + |
| mir-99b | CACCCGTAGAACCGACCTTGCG (3×) | + | + | + |
| mir-100 | AACCCGTAGATCCGAACTTGTG (6×) | + | + | + |
| mir-101b | TACAGTACTGTGATAGCTGAAG | — | + | + |
| mir-103 | AGCAGCATTGTACAGGGCTATGA (10×) | + | +(2) | +(2) |
| mir-118-b, -c | ACCATCGACCGTTGATTGTACC (3×) | + | + | + |
| mir-124a | TTAAGGCACGCGGTGAATGCCAA (59×) | + | +(2) | +(2) |
| mir-125b | ATCCCTGAGACCCTAACTTGTGA (71×) | + | + | + |
| mir-127 | TCGGATCCGTCTGAGCTTGG (2×) | NA | + | + |
| mir-128 | TCACAGTGAACCGGTCTCTTTC (17×) | + | + | + |
| mir-129-2* | AAGCCCTTACCCCAAAAAGCAT (3×) | + | + | + |
| mir-130 | CAGTGCAATGTTAAAAGGGCAT (23×) | + | + | + |
| mir-130b | CAGTGCAATGATGAAAGGGCAT (2×) | + | + | + |
| mir-131 | TAAAGCTAGATAACCGAAAGTA (6×) | NA | +(2) | +(2) |
| mir-132 | TAACAGTCTACAGCCATGGTCG (16×) | NA | + | + |
| mir-135b | TATGGCTTTTCATTCCTATGTG (2×) | — | + | + |
| mir-138 | AGCTGGTGTTGTGAATCAGGCCG | + | +(2) | + |
| mir-140* | TACCACAGGGTAGAACCACGGACA | + | + | + |
| mir-148b | TCAGTGCATCACAGAACTTTGT | — | + | + |
| mir-149 | TCTGGCTCCGTGTCTTCACTCCCT | NA | + | + |
| mir-151* | TCGAGGAGCTCACAGTCTAGTA (2×) | — | + | + |
| mir-181 | AACATTCAACGCTGTCGGTGAG | + | +(2) | +(2) |
| mir-191 | CAACGGAATCCCAAAAGCAGCTGT (6×) | + | + | + |
| mir-218-1, -2 | TTGTGCTTGATCTAACCATGTG | + | +(3) | +(2) |
| mir-221 | AGCTACATTGTCTGCTGGGTTTC | + | + | + |
| mir-301 | CAGTGCAATAGTATTGTCAAAGCAT (2×) | — | + | + |
The new miRNAs identified from this study have been assigned mir annotations from mir-322 to -352. In addition, new miRNAs cloned from the opposite strand of a known precursor had an asterisk appended to the known mir annotation. Finally, new miRNAs deemed close enough to existing miRNAs, but derived from distinct loci, received the same mir annotation as the known miRNA but with a ”b” suffix. Sequences represent the longest of each miRNA sequence identified by cloning and that matches to the greatest extent with available rat or mouse genome sequence. Frequency of cloning is indicated in parentheses after the miRNA sequences, and variations between clones and genomic sequences are denoted in bold. All of the previously uncharacterized miRNAs were examined by Northern blotting with total RNA isolated from adult rat cortex, those detected by Northern blot are indicated (+). The presence of predicted precursor hairpin structures in mouse and rat genome sequences is noted for each miRNA. The number of times a particular miRNA appears in the genome is noted in parentheses in the mouse and rat ”precursor” columns when there is more than one observed occurrence. miRNAs found only in the rat genome may be rat-specific, although those found only in the mouse genome may not yet be represented in available rat genome sequence traces. Clone sequence information and precursor hairpin sequences and structures are presented in Table 2; NA, not assayed.