Table 5.
Conserved nucleotides of O. sativa tRNAs.
| tRNA | AC arm | D-arm | D-loop | ANC- arm | ANC loop | Variable region | Ψ-arm | Ψ-loop |
|---|---|---|---|---|---|---|---|---|
| Glycine (Gly) | G | G | A-G-x-G-G-U-x-A | G | U-x-U-G | **** | C-x3−4-G | U-U-C-x-A-A-U |
| Alanine (Ala) | G | G-C | A-x3-G | C-x2-G | G-C-A | G-G | G-G-x-G | U-C-G-A |
| Proline (Pro) | G-G-G-x3-U | C | U-G-G-U-A | G-x-U | U-x-G-G-G-U | A-x-G-U-C | **** | U-U-C-x-A-x-U |
| Valine (Val) | G | G | U-x-G-x2-U-x-U | U | U-x-A-C | G-U-C | C-x-G | U-U-C-G-A |
| Leucine (Leu) | G | **** | A-x-U-x-G-G-U | C | U-x-A | U-x-C-x4−8-G | G | U-U-C-x-A-x-U |
| Isoleucine (Ile) | G-G-x-C | G-C-U-C | A-G-x-U-G-G-U-U-A | G | U-x-A-U-x-A | A-G-G-U-C | G-C-x-G-G | U-U-C-G-A-G |
| Methionine (Met) | **** | **** | **** | **** | C-A-U-A | U | G | U-C-x-A |
| Phenylalanine (Phe) | G-x4-G-A | G | A-x-U-x-G | G-A | C-U-G-A-A-x-A | **** | C-x2-G | U-U-C-x-A |
| Tyrosine (Tyr) | G | C | A-G-x2-G-x2-A | G-A | C-U-x-U-A-x-A | G-x2−12-C | G-C-x-G-G | U-U-C-x-A-A-U |
| Tryptophan (Trp) | G-x4-C | G-x2-C | A-x-U-x0−2-G-G-U-A | G-x-C | U-C-C-A-x-A | A-x-G-U | G | U-U-C-x-A-x-U |
| Serine (Ser) | U | G | ***** | U | **** | C | G | U-U-x-G-A-x-U-C |
| Threonine (Thr) | G-C | **** | G-x2-G-x3-A | **** | U-x-G-U-A-A | G-U-C | G | U-U-C-x-A |
| Cysteine (Cys) | G | G-C | A-G-x2-G-x1−2-U-A | G | C-U-x-C-A-x-A | U-C | G | U-U-C-x-A |
| Asparagine (Asn) | C | G-C-U | A-G-U-x-G-U | G | U-G-U-U | G-G-U | G-x2-G-G | U-U-C-x-A |
| Glutamine (Gln) | G | G | A-G-x-G-G-U-x-A | G | U-x-U-G | **** | C-x3−4-G | U-U-C-x-A-A-U |
| Lysine (Lys) | G | G-C-x-C | A-G-x2-G-G-x-A | G-G | C-U-x-U-U-A | U-C | G-x2-G-G | U-U-x2-A |
| Histidine (His) | G-G | G | A-G-U-x-G | G | U-U-G-U-G | A-x2-C | G-G-G | U-C-x-A-x-U |
| Arginine (Arg) | G | G | A-x2-G-G-A-U-x-A | G | U-x-C-x2−3-A | U | x-x-G-G | U-U-C-x-A |
| Aspartate (Asp) | G | G | A-x-U-x-G-G-U-x-A | C | U-x-U-C-A | **** | C-G-G-G | U-U-C-G-A-x-C |
| Glutamate (Glu) | C-C-x2-U | U-C-U | A-x3−8-G-x-U | **** | C-U-x-U-C-A | C | G-G | U-U-C-x-A-x-U |
Multiple sequence alignment of individual tRNA family shows highly conserved region in different parts of the tRNA. The majority of tRNAs contain consensus nucleotide sequence in D-loop and Ψ-loop. The nucleotide sequences of tRNAMet and tRNASer are highly diverse and only conserved in few positions. Analyses shows, the variable region of tRNA also conserved in individual group of tRNA. However, there are lots of isodecoders in the O. sativa tRNA. Multiple sequence alignment was conducted using Multalin server. AC, Acceptor, ANC, anti-codon.