Modomics - A Database of RNA Modifications

General Data

RNA Type tRNA
SOTerm SO:0000261
Original Source tdbR00000105
Secondary Structure (((((((..(((.....[...)))((((((.......))))))...(((((..]....))))))))))))....
Sequence (UNICHARACTER ENCODING) GCGCUGGUALUGPAGUGGUAUCACGUGACCUUGCCAUGGUCACAA??UGGG]PBOAAUCCCAGCCAGCGCACCA
Sequence (SHORT NAMES ENCODING) GCGCUGGUApm2GUGpYAGUGGUAUCACGUGACCUUGCCAUGGUCACAApm5Cpm5CUGGGpm1YpYpCmpm1IAAUCCCAGCCAGCGCACCA
Sequence (MODOMICS CODE ENCODING) GCGCUGGUA2000002551GUG2000009551UAGUGGUAUCACGUGACCUUGCCAUGGUCACAA2000005551C2000005551CUGGG2000019551U2000009551U2000090551C2000019551AAAUCCCAGCCAGCGCACCA
Consensus Secondary Structure .(((((((..((((......[....)))).(((((.......)))))........................(((((..]....))))))))))))....
Alignment with Modification -GCGCUGGUALUGPAGU--GGU--AUCACGUGACCUUGCCAUGGUCACAA?--------------------?UGGG]PBOAAUCCCAGCCAGCGCACCA

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 13 45B 49 54 55 56 57
Position in the sequence 10 13 46 47 52 53 54 55
Modification positions m2G Y m5C m5C m1Y Y Cm m1I
Level of Experimental Evidence 5 5 5 5 5 5 5 5
Level of Experimental Reliability 5 5 5 5 5 5 5 5
Source MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS