Modomics - A Database of RNA Modifications

General Data

RNA Type tRNA
SOTerm SO:0000258
Original Source tdbR00000157
Secondary Structure (((((((..((((.....[...)))).(((((.......))))).....(((((..]....))))))))))))....
Sequence (UNICHARACTER ENCODING) GGGCGAUUAGCUCAGCU#GUDAGAGCGCACGCCUGAU6AGCGUGAG7UCGGUGGFPCAѢGUCCACCAUCGCCCACCA
Sequence (SHORT NAMES ENCODING) GGGCGAUUAGCUCAGCUpGmGUpDAGAGCGCACGCCUGAUpt6AAGCGUGAGpm7GUCGGUGGpm5s2UpYCApm1AGUCCACCAUCGCCCACCA
Sequence (MODOMICS CODE ENCODING) GGGCGAUUAGCUCAGCU2000090551GGU2000008551UAGAGCGCACGCCUGAU2000062551AAGCGUGAG2000007551GUCGGUGG2000025551U2000009551UCA2000001551AGUCCACCAUCGCCCACCA
Consensus Secondary Structure .(((((((..((((......[....)))).(((((.......)))))........................(((((..]....))))))))))))....
Alignment with Modification -GGGCGAUUAGCUCAGCU-#GUD-AGAGCGCACGCCUGAU6AGCGUGAG7UC-------------------GGUGGFPCAѢGUCCACCAUCGCCCACCA

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 18 20A 37 45A 54 55 58
Position in the sequence 18 21 38 47 55 56 59
Modification positions Gm D t6A m7G m5s2U Y m1A
Level of Experimental Evidence 5 5 5 5 5 5 5
Level of Experimental Reliability 5 5 5 5 5 5 5
Source MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS