Modomics - A Database of RNA Modifications

General Data

RNA Type tRNA
SOTerm SO:0000269
Original Source tdbR00000409
Secondary Structure (((((((..(((.....[....))).(((((.......)))))(((((..))))).(((((..]....))))))))))))....
Sequence (UNICHARACTER ENCODING) GACACCGUGLCMCAGD#GDDACGGCRPUGGACGCAGAAPCCAUUGAGCUUGCUCG?GCGGGTPCGѢAUCCCGUCGGUGUCUCCA
Sequence (SHORT NAMES ENCODING) GACACCGUGpm2GCpac4CCAGpDpGmGpDpDACGGCpm2,2GpYUGGACGCAGAApYCCAUUGAGCUUGCUCGpm5CGCGGGpm5UpYCGpm1AAUCCCGUCGGUGUCUCCA
Sequence (MODOMICS CODE ENCODING) GACACCGUG2000002551GC2000042551CCAG2000008551U2000090551GG2000008551U2000008551UACGGC2000022551G2000009551UUGGACGCAGAA2000009551UCCAUUGAGCUUGCUCG2000005551CGCGGG2000005551U2000009551UCG2000001551AAUCCCGUCGGUGUCUCCA
Consensus Secondary Structure .(((((((..((((......[....)))).(((((.......)))))........................(((((..]....))))))))))))....
Alignment with Modification -GACACCGUGLCMCAGD--#GDD-ACGGCRPUGGACGCAGAAPCCAUUGAGCUUGCUCG?-----------GCGGGTPCGѢAUCCCGUCGGUGUCUCCA

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 12 16 18 20 20A 26 27 39 45K 54 55 58
Position in the sequence 10 12 16 17 19 20 26 27 39 56 62 63 66
Modification positions m2G ac4C D Gm D D m2,2G Y Y m5C m5U Y m1A
Source MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS MODOMICS

Modification Annotation

Table containing the data present in the literature relating to the modification positions present in the RNA sequences. Some of the modified residuals may differ from the modifications originally present in MODOMICS. It follows the same format as the previous table. The table reports the scores that have been associated to the modified nucleotides so to have an estimation of the reliability of their presence.
Position in the alignment 10 12 16 18 20 20A 26 27 39 45K 54 55 58
Position in the sequence 10 12 16 17 19 20 26 27 39 56 62 63 66
Source: 8121794 m2G ac4C D Gm D D m2,2G Y Y m5C m5U Y m1A
Level of Experimental Reliability 3 3 3 3 3 3 3 3 3 3 3 3 3
Level of Experimental Evidence 3 3 3 3 3 3 3 3 3 3 3 3 3