Modomics - A Database of RNA Modifications

General Data

RNA Type tRNA
SOTerm SO:0000265
Original Source tdbR00000200
Secondary Structure (((((((..((((.....[..)))).(((((.......))))).....(((((..]....))))))))))))....
Sequence (UNICHARACTER ENCODING) GCCCGGAUALCUCAGDCGGDAGAGCAPCAGACU3UU[APCUGAGG7D??AGGG\PCAѢGUCCCUGUUCGGGCGCCA
Sequence (SHORT NAMES ENCODING) GCCCGGAUApm2GCUCAGpDCGGpDAGAGCApYCAGACUpmcm5s2UUUpms2t6AApYCUGAGGpm7GpDpm5Cpm5CAGGGpm5UmpYCApm1AGUCCCUGUUCGGGCGCCA
Sequence (MODOMICS CODE ENCODING) GCCCGGAUA2000002551GCUCAG2000008551UCGG2000008551UAGAGCA2000009551UCAGACU2002521551UUU2002162551AA2000009551UCUGAGG2000007551G2000008551U2000005551C2000005551CAGGG2000905551U2000009551UCA2000001551AGUCCCUGUUCGGGCGCCA
Consensus Secondary Structure .(((((((..((((......[....)))).(((((.......)))))........................(((((..]....))))))))))))....
Alignment with Modification -GCCCGGAUALCUCAGDC-GGD--AGAGCAPCAGACU3UU[APCUGAGG7D?-------------------?AGGG\PCAѢGUCCCUGUUCGGGCGCCA

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 10 16 20 27 34 37 39 45A 45B 45C 49 54 55 58
Position in the sequence 10 16 20 27 34 37 39 46 47 48 49 54 55 58
Modification positions m2G D D Y mcm5s2U ms2t6A Y m7G D m5C m5C m5Um Y m1A
Level of Experimental Evidence 5 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 5
Source MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS