Modomics - A Database of RNA Modifications

General Data

RNA Type tRNA
SOTerm SO:0000265
Original Source tdbR00000175
Secondary Structure (((((((..((((......[..)))).(((((.......))))).....(((((..]....))))))))))))....
Sequence (UNICHARACTER ENCODING) GGGCUGGUAGCUCA(UUAGGCAGAGCRUCUGGBUNUU6ACCAGACGGU?GGGGG]PBOAGUCCCUCCCAGCCCGCCA
Sequence (SHORT NAMES ENCODING) GGGCUGGUAGCUCApG+UUAGGCAGAGCpm2,2GUCUGGpCmUxUUUpt6AACCAGACGGUpm5CGGGGGpm1YpYpCmpm1IAGUCCCUCCCAGCCCGCCA
Sequence (MODOMICS CODE ENCODING) GGGCUGGUAGCUCA2000103551GUUAGGCAGAGC2000022551GUCUGG2000090551CU2000000999UUU2000062551AACCAGACGGU2000005551CGGGGG2000019551U2000009551U2000090551C2000019551AAGUCCCUCCCAGCCCGCCA
Consensus Secondary Structure .(((((((..((((......[....)))).(((((.......)))))........................(((((..]....))))))))))))....
Alignment with Modification -GGGCUGGUAGCUCA(UUAGGC--AGAGCRUCUGGBUNUU6ACCAGACGGU?-------------------GGGGG]PBOAGUCCCUCCCAGCCCGCCA

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 15 26 32 34 37 45C 54 55 56 57
Position in the sequence 15 27 33 35 38 49 55 56 57 58
Modification positions G+ m2,2G Cm xU t6A m5C m1Y Y Cm m1I
Source MODOMICS 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 15 26 32 34 37 45C 54 55 56 57
Position in the sequence 15 27 33 35 38 49 55 56 57 58
Source: 6746655 G+ m2,2G Cm xU t6A m5C m1Y Y Cm m1I
Level of Experimental Reliability 3 3 3 3 3 3 3 3 3 3
Level of Experimental Evidence 3 3 3 3 3 3 3 3 3 3