Modomics - A Database of RNA Modifications

General Data

RNA Type tRNA
SOTerm SO:0000264
Original Source tdbR00000229
Secondary Structure (((((((..(((......[....))).(((((.......))))).((.((....))))..(((((..]....))))))))))))....
Sequence (UNICHARACTER ENCODING) GGGGAUAUGGCGAAAUU#GDAGACGCPACGGACUJAAHAPCCGUCGACUUAAGAAAUCAUGAGGGTPCAAGUCCCUCUAUCCCCACCA
Sequence (SHORT NAMES ENCODING) GGGGAUAUGGCGAAAUUpGmGpDAGACGCpYACGGACUpUmAAxAApYCCGUCGACUUAAGAAAUCAUGAGGGpm5UpYCAAGUCCCUCUAUCCCCACCA
Sequence (MODOMICS CODE ENCODING) GGGGAUAUGGCGAAAUU2000090551GG2000008551UAGACGC2000009551UACGGACU2000090551UAA2000000999AA2000009551UCCGUCGACUUAAGAAAUCAUGAGGG2000005551U2000009551UCAAGUCCCUCUAUCCCCACCA
Consensus Secondary Structure .(((((((..((((......[....)))).(((((.......)))))........................(((((..]....))))))))))))....
Alignment with Modification -GGGGAUAUGGCGAAAUU-#GDA-GACGCPACGGACUJAAHAPCCGUCGACUUAAGAAAUCAU--------GAGGGTPCAAGUCCCUCUAUCCCCACCA

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 18 20 26 34 37 39 54 55
Position in the sequence 18 20 27 35 38 40 66 67
Modification positions Gm D Y Um xA Y m5U Y
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