Modomics - A Database of RNA Modifications

General Data

RNA Type tRNA
SOTerm SO:0000269
Original Source tdbR00000421
Secondary Structure (((((((..(((.....[....)))((((((.......))))))((((...))))..(((((..]....))))))))))))....
Sequence (UNICHARACTER ENCODING) GUAGUCGUGGCMGAGD#GDDAAGGCRAPGGAЩUIGAЧAZCCAUJGGGGUЩUCCCCG?GCAGGTPCGѢAUCCUGCCGACUACGCCA
Sequence (SHORT NAMES ENCODING) GUAGUCGUGGCpac4CGAGpDpGmGpDpDAAGGCpm2,2GApYGGApm3CUpIGApi6AApYmCCAUpUmGGGGUpm3CUCCCCGpm5CGCAGGpm5UpYCGpm1AAUCCUGCCGACUACGCCA
Sequence (MODOMICS CODE ENCODING) GUAGUCGUGGC2000042551CGAG2000008551U2000090551GG2000008551U2000008551UAAGGC2000022551GA2000009551UGGA2000003551CU2000009551AGA2000061551AA2000909551UCCAU2000090551UGGGGU2000003551CUCCCCG2000005551CGCAGG2000005551U2000009551UCG2000001551AAUCCUGCCGACUACGCCA
Consensus Secondary Structure .(((((((..((((......[....)))).(((((.......)))))........................(((((..]....))))))))))))....
Alignment with Modification -GUAGUCGUGGCMGAGD--#GDD-AAGGCRAPGGAЩUIGAЧAZCCAUJGGGGUЩUCCCCG?----------GCAGGTPCGѢAUCCUGCCGACUACGCCA

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 12 16 18 20 20A 26 28 32 34 37 39 44 45E 45L 54 55 58
Position in the sequence 12 16 17 19 20 26 28 32 34 37 39 44 50 57 63 64 67
Modification positions ac4C D Gm D D m2,2G Y m3C I i6A Ym Um m3C m5C m5U Y m1A
Level of Experimental Evidence 5 5 5 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 5 5 5
Source MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS