Modomics - A Database of RNA Modifications

General Data

RNA Type tRNA
SOTerm SO:0000261
Original Source tdbD00005348
Secondary Structure (((((((..(((.....[....)))((((((.......))))))...(((((..]....))))))))))))....
Sequence (UNICHARACTER ENCODING) GGGCGGUUAGUGPAGDGGDDAUCAUCCCACCCUNCCAAGGUGGGGACACGGGTPCGAUUCUCGUACCGCUCACCA
Sequence (SHORT NAMES ENCODING) GGGCGGUUAGUGpYAGpDGGpDpDAUCAUCCCACCCUxUCCAAGGUGGGGACACGGGpm5UpYCGAUUCUCGUACCGCUCACCA
Sequence (MODOMICS CODE ENCODING) GGGCGGUUAGUG2000009551UAG2000008551UGG2000008551U2000008551UAUCAUCCCACCCU2000000999UCCAAGGUGGGGACACGGG2000005551U2000009551UCGAUUCUCGUACCGCUCACCA
Consensus Secondary Structure .(((((((..((((......[....)))).(((((.......)))))........................(((((..]....))))))))))))....
Alignment with Modification -GGGCGGUUAGUGPAGD--GGDD-AUCAUCCCACCCUNCCAAGGUGGGGAC--------------------ACGGGTPCGAUUCUCGUACCGCUCACCA

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 13 16 20 20A 34 54 55
Position in the sequence 13 16 19 20 34 53 54
Modification positions Y D D D xU m5U Y
Level of Experimental Evidence 5 5 5 5 5 5 5
Level of Experimental Reliability 5 5 5 5 5 5 5
Source MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS