Modomics - A Database of RNA Modifications

General Data

RNA Type tRNA
SOTerm SO:0000265
Original Source tdbR00000205
Secondary Structure (((((((..((((.....[..)))).(((((.......))))).....(((((..]....))))))))))))....
Sequence (UNICHARACTER ENCODING) GCCUUCAUALCUCAGDCGGUAGAGCAPCAGACUNUUHAѮCUGAGG7D?UGGGG\PCGѢGUCCCCAULCGGG?UCCA
Sequence (SHORT NAMES ENCODING) GCCUUCAUApm2GCUCAGpDCGGUAGAGCApYCAGACUxUUUxAAxXCUGAGGpm7GpDpm5CUGGGGpm5UmpYCGpm1AGUCCCCAUpm2GCGGGpm5CUCCA
Sequence (MODOMICS CODE ENCODING) GCCUUCAUA2000002551GCUCAG2000008551UCGGUAGAGCA2000009551UCAGACU2000000999UUU2000000999AA2000000000XCUGAGG2000007551G2000008551U2000005551CUGGGG2000905551U2000009551UCG2000001551AGUCCCCAU2000002551GCGGG2000005551CUCCA
Consensus Secondary Structure .(((((((..((((......[....)))).(((((.......)))))........................(((((..]....))))))))))))....
Alignment with Modification -GCCUUCAUALCUCAGDC-GGU--AGAGCAPCAGACUNUUHAѮCUGAGG7D?-------------------UGGGG\PCGѢGUCCCCAULCGGG?UCCA

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 16 27 34 37 39 45A 45B 45C 54 55 58 67 72
Position in the sequence 10 16 27 34 37 39 46 47 48 54 55 58 67 72
Modification positions m2G D Y xU xA xX m7G D m5C m5Um Y m1A m2G m5C
Source MODOMICS 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 16 27 34 37 39 45A 45B 45C 54 55 58 67 72
Position in the sequence 10 16 27 34 37 39 46 47 48 54 55 58 67 72
Source: 7730314 m2G D Y xU xA xX m7G D m5C m5Um Y m1A m2G m5C
Level of Experimental Reliability 3 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 3