Modomics - A Database of RNA Modifications

General Data

RNA Type tRNA
SOTerm SO:0000270
Original Source tdbR00000435
Secondary Structure (((((((..((((.....[..)))).(((((.......))))).....(((((..]....))))))))))))....
Sequence (UNICHARACTER ENCODING) GCUGACU4AGCUCAGCAGGCAGAGCAACUGACUUGU6APCAGUAG7UCGUAGGUPCGAUUCCUAUAGUCAGCACCA
Sequence (SHORT NAMES ENCODING) GCUGACUps4UAGCUCAGCAGGCAGAGCAACUGACUUGUpt6AApYCAGUAGpm7GUCGUAGGUpYCGAUUCCUAUAGUCAGCACCA
Sequence (MODOMICS CODE ENCODING) GCUGACU2000074551UAGCUCAGCAGGCAGAGCAACUGACUUGU2000062551AA2000009551UCAGUAG2000007551GUCGUAGGU2000009551UCGAUUCCUAUAGUCAGCACCA
Consensus Secondary Structure .(((((((..((((......[....)))).(((((.......)))))........................(((((..]....))))))))))))....
Alignment with Modification -GCUGACU4AGCUCAGCA-GGC--AGAGCAACUGACUUGU6APCAGUAG7UC-------------------GUAGGUPCGAUUCCUAUAGUCAGCACCA

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 8 37 39 45A 55
Position in the sequence 8 37 39 46 55
Modification positions s4U t6A Y m7G Y
Level of Experimental Evidence 5 5 5 5 5
Level of Experimental Reliability 5 5 5 5 5
Source MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS