Modomics - A Database of RNA Modifications

General Data

RNA Type tRNA
SOTerm SO:0000260
Original Source None
Secondary Structure .(((((((..((((...........))))((((((.......)))))).......................(((((.......))))))))))))....
Sequence (UNICHARACTER ENCODING) GCCCCCGUUGUGJAGCGGCCUAGCACGCUGCCCUCUCACGGCAGUAGCGCCGGUUCGѢѢUCCGGUCGGGGGUACAA
Sequence (SHORT NAMES ENCODING) GCCCCCGUUGUGpUmAGCGGCCUAGCACGCUGCCCUCUCACGGCAGUAGCGCCGGUUCGpm1Apm1AUCCGGUCGGGGGUACAA
Sequence (MODOMICS CODE ENCODING) GCCCCCGUUGUG2000090551UAGCGGCCUAGCACGCUGCCCUCUCACGGCAGUAGCGCCGGUUCG2000001551A2000001551AUCCGGUCGGGGGUACAA
Consensus Secondary Structure .(((((((..((((......[....)))).(((((.......)))))........................(((((..]....))))))))))))....
Alignment with Modification -GCCCCCGUUGUGJAGC--GGCCUAGCACGCUGCCCUCUCACGGCAGUAGC--------------------GCCGGUUCGѢѢUCCGGUCGGGGGUACAA

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 58 59
Position in the sequence 13 58 59
Modification positions Um m1A m1A
Level of Experimental Evidence 5 5 5
Level of Experimental Reliability 5 5 5
Source MODOMICS MODOMICS MODOMICS