Modomics - A Database of RNA Modifications

General Data

RNA Type tRNA
SOTerm SO:0000262
Original Source tdbR00000146
Secondary Structure ((((((((..((((....[...)))).(((((.......)))))....(((((..]....)))))))))))))...
Sequence (UNICHARACTER ENCODING) GGUGGCUGUAGUUPAGDGGDDAGAACACAACGPUGUGKCCGUUGAAAC?UGGGUPCGѢAUCCCAGCAGCCACACCA
Sequence (SHORT NAMES ENCODING) GGUGGCUGUAGUUpYAGpDGGpDpDAGAACACAACGpYUGUGpm1GCCGUUGAAACpm5CUGGGUpYCGpm1AAUCCCAGCAGCCACACCA
Sequence (MODOMICS CODE ENCODING) GGUGGCUGUAGUU2000009551UAG2000008551UGG2000008551U2000008551UAGAACACAACG2000009551UUGUG2000001551GCCGUUGAAAC2000005551CUGGGU2000009551UCG2000001551AAUCCCAGCAGCCACACCA
Consensus Secondary Structure .(((((((..((((......[....)))).(((((.......)))))........................(((((..]....))))))))))))....
Alignment with Modification GGUGGCUGUAGUUPAGD--GGDD-AGAACACAACGPUGUGKCCGUUGAAAC--------------------?UGGGUPCGѢAUCCCAGCAGCCACACCA

Score Table

Table containing the score explanation. Score identify the level of experimental reliability and evidence so as exaplained in the 2023 release manuscript. Class 1 should be considered as highlyrelevant. Class 2 evidences are considered as Solid, namely large errors are unlikely and minor errors should not undermine the meaning of data. Class 3 is considered as speculative and errors are expected. Class 4 is considered as questionable. Class 5 evidence means that verification and data are still to be collected. Class 6 data cannot be estimated.
Method Classification Score
Multiple direct experimental evidence 1
Direct experimental evidence 2
Inferred based on indirect experimental evidence 3
Predicted computationally 4
Evidence not yet annotated (Unknown) 5
Irrelevant 6

RNA-2D Representation

RNA Secondary Structure

RNA Consensus Secondary Structure

Modification Positions

Table containing the original modifications present in the MODOMICS sequences. Edit locations not originally present in the RNA sequences are marked by their source. Their scores are in third row.

Position in the alignment 13 16 20 20A 32 37 49 55 58
Position in the sequence 14 17 20 21 33 38 49 55 58
Modification positions Y D D D Y m1G m5C Y m1A
Source MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS

Modification Annotation

Table containing the data present in the literature relating to the modification positions present in the RNA sequences. Some of the modified residuals may differ from the modifications originally present in MODOMICS. It follows the same format as the previous table. The table reports the scores that have been associated to the modified nucleotides so to have an estimation of the reliability of their presence.
Position in the alignment 13 16 20 20A 32 37 49 55 58
Position in the sequence 14 17 20 21 33 38 49 55 58
Source: https://doi.org/10.1016/0168-9452(86)90056-7 Y D D D Y m1G m5C Y m1A
Level of Experimental Reliability 3 3 3 3 3 3 3 3 3
Level of Experimental Evidence 3 3 3 3 3 3 3 3 3