Table 1

miRNAs cloned from C. elegans. 300 RNA clones represented 54 different miRNAs. Also included are miR-39, miR-65, and miR-69, three miRNAs predicted based on homology and/or proximity to cloned miRNAs. miR-39 and miR-69 have been validated by Northern analysis (Fig. 3), whereas miR-65 is not sufficiently divergent to be readily distinguished by Northern analysis. AllC. elegans sequence analyses relied on WormBase, release WS45 (33). Some miRNAs were represented by clones of different lengths, due to heterogeneity at the miRNA 3′ terminus. The observed lengths are indicated, as is the sequence of the most abundant length. Comparison to C. briggsaeshotgun sequencing traces revealed miRNA orthologs with 100% sequence identity (+++) and potential orthologs with >90% (++) and >75% (+) sequence identity (24, 34). Five miRNA genomic clusters are indicated with square brackets. Naming of miRNAs was coordinated with the Tuschl and Ambros groups (25,26).

miRNA gene Number of clonesmiRNA sequenceLengthC. briggsaehomologyFold-back armChromosome and distance to nearest gene
mir-1 9UGGAAUGUAA AGAAGUAUGU A21+++3′I 3.7 kb from start of T09B4.3, antisense
mir-2 24UAUCACAGCC AGCUUUGAUG UGC22–23+++3′I 0.6 kb from start of M04C9.6b
mir-34 3AGGCAGUGUG GUUAGCUGGU UG22+++5′X 2.1 kb from end of Y41G9A.4, antisense
mir-35 9UCACCGGGUG GAAACUAGCA GU22+3′II 1.3 kb from end of F54D5.12, antisense
mir-36 1UCACCGGGUG AAAAUUCGCA UG22+3′II 1.2 kb from end of F54D5.12, antisense
mir-37 2UCACCGGGUG AACACUUGCA GU22++3′II 1.1 kb from end of F54D5.12, antisense
mir-38 1UCACCGGGAG AAAAACUGGA GU22+3′II 1.0 kb from end of F54D5.12, antisense
mir-39 0UCACCGGGUG UAAAUCAGCU UGPredicted++3′II 0.8 kb from end of F54D5.12, antisense
mir-40 2UCACCGGGUG UACAUCAGCU AA22+3′II 0.7 kb from end of F54D5.12, antisense
mir-41 2UCACCGGGUG AAAAAUCACC UA22+3′II 0.6 kb from end of F54D5.12, antisense
mir-42 1CACCGGGUUA ACAUCUACAG20+++3′II 1.2 kb from end of ZK930.2, antisense
mir-43 1UAUCACAGUU UACUUGCUGU CGC23+++3′II 1.1 kb from end of ZK930.2, antisense
mir-44 3* UGACUAGAGA CACAUUCAGC U21+++3′II 1.0 kb from end of ZK930.2, antisense
mir-45 +++3′II 0.7 kb from end of K12D12.1, antisense
mir-46 2UGUCAUGGAG UCGCUCUCUU CA22+++3′III 3.0 kb from end of ZK525.1, antisense
mir-47 6UGUCAUGGAG GCGCUCUCUU CA22+++3′X 1.8 kb from end of K02B9.2, antisense
mir-48 11UGAGGUAGGC UCAGUAGAUG CGA22–24+++5′V 6.1 kb from start of Y49A3A.4
mir-49 1AAGCACCACG AGAAGCUGCA GA22+++3′X 2.7kb from end of F19C6.1, antisense
mir-50 2UGAUAUGUCU GGUAUUCUUG GGUU24++5′I in intron of Y71G12B.11a
mir-51 6UACCCGUAGC UCCUAUCCAU GUU23++5′IV 0.4 kb from end of F36H1.6, antisense
mir-52 47CACCCGUACA UAUGUUUCCG UGCU22–25+++5′IV 4.6 kb from end of Y37A1B.6, antisense
mir-53 2CACCCGUACA UUUGUUUCCG UGCU245′IV 1.9 kb from end of F36H1.6, antisense
mir-54 2UACCCGUAAU CUUCAUAAUC CGAG24+3′X 5.5 kb from end of F09A5.2, antisense
mir-55 5UACCCGUAUA AGUUUCUGCU GAG23+3′X 5.3 kb from end of F09A5.2, antisense
mir-56 5UACCCGUAAU GUUUCCGCUG AG22+3′X 5.2 kb from end of F09A5.2, antisense
mir-56 2UGGCGGAUCC AUUUUGGGUU GUA23+5′X 5.2 kb from end of F09A5.2, antisense
mir-57 9UACCCUGUAG AUCGAGCUGU GUGU24+++5′II 0.9 kb from start of AF187012-1.T09A5
mir-58 31UGAGAUCGUU CAGUACGGCA AU21–22+++3′I Vin intron of Y67D8A.1
mir-59 1UCGAAUCGUU UAUCAGGAUG AUG23+3′IV 1.8 kb from start of B0035.1a, antisense
mir-60 1UAUUAUGCAC AUUUUCUAGU UCA23++3′II 1.5 kb from end of C32D5.5
mir-61 1UGACUAGAAC CGUUACUCAU C21+3′V 0.4 kb from end of F55A11.3, antisense
mir-62 1UGAUAUGUAA UCUAGCUUAC AG22+++3′X in intron of T07C5.1
mir-63 1UAUGACACUG AAGCGAGUUG GAAA243′X 1.7 kb from start of C16H3.2, antisense
mir-64 2UAUGACACUG AAGCGUUACC GAA235′III 0.25 kb from start of Y48G9A.1
mir-65 0UAUGACACUG AAGCGUAACC GAAPredicted+5′III 0.10 kb from start of Y48G9A.1
mir-66 10CAUGACACUG AUUAGGGAUG UGA23–245′III in coding sequence of Y48G9A.1
mir-67 2UCACAACCUC CUAGAAAGAG UAGA24+++3′III 4.4 kb from end of EGAP1.1
mir-68 1UCGAAGACUC AAAAGUGUAG A213′IV 3.3 kb from start of Y51H4A.22
mir-69 0UCGAAAAUUA AAAAGUGUAG APredicted3′IV 0.6 kb from start of Y41D4B.21, antisense
mir-70 1UAAUACGUCG UUGGUGUUUC CAU23+3′V in intron of T10H9.5
mir-71 5UGAAAGACAU GGGUAGUGA19, 20, 22+++5′I 7.8 kb from start of M04C9.6b
mir-72 9AGGCAAGAUG UUGGCAUAGC20, 21, 233′II 0.21 kb from end of F53G2.4, antisense
mir-73 2UGGCAAGAUG UAGGCAGUUC AGU23++3′X 2.9 kb from start of T24D8.6, antisense
mir-74 7UGGCAAGAAA UGGCAGUCUA CA22++3′X 3.2 kb from start of T24D8.6, antisense
mir-75 2UUAAAGCUAC CAACCGGCUU CA22++3′X 3.5 kb from start of F47G3.3
mir-76 1UUCGUUGUUG AUGAAGCCUU GA22++3′III 3.0 kb from start of C44B11.3, antisense
mir-77 1UUCAUCAgGC CAUAGCUGUC CA22+++3′II 1.5 kb from start of T21B4.9, antisense
mir-78 2UGGAGGCCUG GUUGUUUGUG C213′IV 2.0 kb from start of Y40H7A.3, antisense
mir-79 1AUAAAGCUAG GUUACCAAAG CU22+++3′I 2.3 kb from end of C12C8.2
mir-80 25UGAGAUCAUU AGUUGAAAGC CGA23+++3′III 4.7 kb from end of F44E2.2, antisense
mir-81 7UGAGAUCAUC GUGAAAGCUA GU22+++3′X in intron of T07D1.2, antisense
mir-82 6UGAGAUCAUC GUGAAAGCCA GU22+++3′X 0.11 kb from start of T07D1.2
mir-83 1UAGCACCAUA UAAAUUCAGu AA22++3′IV 5.0 kb from start of C06A6.2
mir-84 3UGAGGUAGUA UGUAAUAUUG UA22, 24+5′X 0.8 kb from end of B0395.1, antisense
mir-85 1UACAAAGUAU UUGAAAAGUC GUGC24++3′II in intron of F49E12.8, antisense
mir-86 6UAAGUGAAUG CUUUGCCACA GUC23+++5′III in intron of Y56A3A.7
  • * Because mir-44 and mir-45 encode identical miRNAs, the three clones represent either or both genes.