Modomics - A Database of RNA Modifications

General Data

RNA Type tRNA
SOTerm SO:0000259
Original Source tdbR00000342
Secondary Structure (((((((..((((....[...)))).(((((.......)))))....(((((..]....))))))))))))....
Sequence (UNICHARACTER ENCODING) GGUUCCAUKGUGPAAD#GDDAGCACUCPGGABUCUGAAPCCAGCGAU?CGAGPPCAѢAUCUCGGUGGAACCUCCA
Sequence (SHORT NAMES ENCODING) GGUUCCAUpm1GGUGpYAApDpGmGpDpDAGCACUCpYGGApCmUCUGAApYCCAGCGAUpm5CCGAGpYpYCApm1AAUCUCGGUGGAACCUCCA
Sequence (MODOMICS CODE ENCODING) GGUUCCAU2000001551GGUG2000009551UAA2000008551U2000090551GG2000008551U2000008551UAGCACUC2000009551UGGA2000090551CUCUGAA2000009551UCCAGCGAU2000005551CCGAG2000009551U2000009551UCA2000001551AAUCUCGGUGGAACCUCCA
Consensus Secondary Structure .(((((((..((((......[....)))).(((((.......)))))........................(((((..]....))))))))))))....
Alignment with Modification -GGUUCCAUKGUGPAAD--#GDD-AGCACUCPGGABUCUGAAPCCAGCGAU--------------------?CGAGPPCAѢAUCUCGGUGGAACCUCCA

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 9 13 16 18 20 20A 28 32 39 49 54 55 58
Position in the sequence 9 13 16 17 19 20 28 32 39 48 53 54 57
Modification positions m1G Y D Gm D D Y Cm Y m5C Y Y m1A
Level of Experimental Evidence 5 5 5 5 5 5 5 5 5 5 5 5 5
Level of Experimental Reliability 5 5 5 5 5 5 5 5 5 5 5 5 5
Source MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS