Detected as a riboswitch by 16 out of 20 classifiers
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5HSAA093270-3 Similarity: 0.982 Similarity: 0.980 Similarity: 0.975
UTR: 5HSAA093270-3
Gene: RPUSD3
MFE: -2.515
ENS: 0.920
Length: 29.
Predicted Ligands:
SAM - 8/20
preQ_1 - 7/20
unknown - 2/20
 RS: URS0000ABD446_1313296
MFE: -4.722
Ligand: preQ_1
Species: Paenibacillus uliginis N3/975 PreQ1 riboswitch
 RS: URS0001A24B50_1907202
MFE: -10.
Ligand: unknown
Species: Chains: A,C,F,I,M,O from Roseobacter sp. (PDB 6YLB, chain F)
 RS: URS000080E32E_119072
MFE: -6.098
Ligand: preQ_1
Species: PREQ1 RIBOSWITCH from Caldanaerobacter subterraneus subsp. tengcongensis (PDB 6VUH, chain A)
image of 5prime UTR secondary structure image of the secondary structure of the first Riboswitch match image of the secondary structure of the second Riboswitch match image of the secondary structure of the third Riboswitch match
circular plot of the 5prime UTR base pairs circular plot of the 5prime UTR base pairs compared with the first Riboswitch base pairs circular plot of the 5prime UTR base pairs compared with the second Riboswitch base pairs circular plot of the 5prime UTR base pairs compared with the third Riboswitch base pairs
line plot comparing the structural features of the 5prime UTR with its first riboswitch match line plot comparing the structural features of the 5prime UTR with its second riboswitch match line plot comparing the structural features of the 5prime UTR with its third riboswitch match
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heatmap comparing sequence features of the 5prime UTR and top three riboswitch matches
Heatmap of base pair probabilities for 1000 computational NUPACK foldings of the 5prime UTR
Heatmap of base pair probabilities for computational NUPACK foldings of the 5prime UTR that leave the start codon unbound
Heatmap of base pair probabilities for computational NUPACK foldings of the 5prime UTR that leave the start codon bound
Heatmap of base pair probabilities for computational NUPACK foldings of the 5prime UTR with the bound and unbound conformers overlaid
ML ensemble output for the 5prime UTR

Information

  5’UTR RS match 1 RS match 2 RS match 3
Link - RNAcentral RNAcentral RNAcentral
ID 5HSAA093270-3 URS0000ABD446_1313296 URS0001A24B50_1907202 URS000080E32E_119072
Length 29. 32. 26. 33.
Similarity - 0.982 0.980 0.975
Ensemble Norm 0.920 - - -
MFE -2.515 -4.722 -10. -6.098
Ligands - preQ_1 unknown preQ_1
Gene RPUSD3 - - -
Downstream protein Genecard - - -

Similarity metrics

  5’UTR RS match 1 RS match 2 RS match 3
Struct SE - 2.011 3.201 2.003
Length SE - 9. 9. 16.
Lev Distance - 15. 17. 17.
UBS 2. 1. 2. 1.
BS 0. 0. 0. 0.
ILL 0. 0. 1. 0.
ILR 0. 0. 1. 0.
H 1. 1. 1. 1.
BL 0. 0. 0. 0.
BR 1. 0. 0. 0.
UN 0.448 0.344 0. 0.394

Sequences

Field Description
UTR seq + 25 gcacATGGGACCGGTCGTACCTGAATTTT
UTR dot + 25 ……(((((…..)).)))…….
RS 1 seq AGAGGUUCGUGAACUCCCUCUAUAAAAAACUA
RS 1 dot (((((………..)))))………..
RS 2 seq GGUCACAACGGCUUCCUGGCGUGACC
RS 2 dot ((((((..(((….)))..))))))
RS 3 seq CUGGGUCGCAGUAACCCCAGUUAACAAAACAAG
RS 3 dot (((((……….)))))………….

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