The reference dataset is made of both
riboswitches and non-riboswitches.
Click on the name to download the fasta file for the full riboswitch.
For the first group of riboswitches, the SwSeq is known,
while it is not for the others.
Pseudoknots are indicated by an asterisk *.
ID
Riboswitch Class
Gene - Organism
Switching
Mechanism SwSeq
thiM_TPP
Thiamine Pyrophosphate
thiM - Escherichia coli
Translation
100 - 104
add_Adenine
Adenine
add - Vibrio vulnificus
Translation
75 - 64
folT_THF*
Tetrahydrofolate
folT - Alkaliphilus metalliredigens
Translation
93 - 101
xpt_Guanine
Guanine
xpt - Bacillus subtilis
Transcription
123 - 135
pbuE_Adenine
Adenine
pbuE (ydhL) - Bacillus subtilis
Transcription
56 - 68
mtgE_Mg
Magnesium
mgtE - Bacillus subtilis
Transcription
152 - 157
yitJ_SAM*
S-adenosylmethionine
yitJ - Bacillus subtilis
Transcription
120 - 131
lysC_Lysine
Lysine
lysC - Bacillus subtilis
Transcription
173 - 183
tenA_TPP
Thiamine Pyrophosphate
tenA - Bacillus subtilis
Transcription
112 - 121
metH_SAH
S-adenosylhomocisteine
metH - Dechloromonas aromatica
Transcription
58 - 64
VEGFA
Het. nuclear ribonucleoprotein L
VEGFA - Homo sapiens
Alt. Splicing
73 - 82
thiC_TPP
Thiamine Pyrophosphate
thiC - Arabidopsis thaliana
Alt. Splicing
107 - 117
moaA_Moco
Molybdenum Cofactor
moaA - Escherichia coli
Translation
-
btuB_Cobalamin
Cobalamin
btuB -Escherichia coli
Translation
-
alx_PH
PH
alx - Escherichia coli
Translation
-
GEMM_CDA
Cyclic-di-Guanosine Monoph.
Daud_1768 - Desulforudis audaxviator
Transcription
-
crcB_Flouride
Flouride
crcB - Bacillus cereus
Transcription
-
PreQ1*
Pre-Queosine
glyS - Fusobacterium nucleatum
Transcription
-
ydaO_ATP
ATP
ydaO - Bacillus subtilis
Transcription
-
metA_SAMII
S-adenosylmethionine
metA - Agrobacterium tumefaciens
Transcription
-
ID
ncRNA Class
Organism
Function
NC_01
MS2_RNA
Bacteriophage virus
5' uRNA of MS2 Virus Genome
NC_02
MDV_1_RNA
Escherichia coli
uRNA from MDV-1
NC_03
5S_rRNA
Aegilopsis crassa
5S ribosomal RNA
NC_04
tRNA
Escherichia coli
Transfert RNA
NC_05
IRES_Pesti
Hog cholera virus
Internal ribosome entry site (IRES)
NC_06
Hammerhead Ribozyme
Peach latent mosaic viroid
Hammerhead Ribozyme
NC_07
Group I Intron
Porana volubilis
Self splicing group I intron
NC_08
Ribosomial S15
Salmonella enterica
Ribosomal S15 leader
NC_09
U1 RNA
Homo sapiens
U1 spliceosomal RNA
NC_10
Hammerhead Ribozyme Type II
Marine metagenome
Hammerhead Ribozyme Type II
NC_11
IMES-2
Marine metagenome
IMES-2 RNA motif
NC_12
23S-methyl
Streptococcus agalactiae
23S methyl RNA motif
NC_13
mir-1937
Mus musculus
microRNA 1937
NC_14
RNaseP_nuc
Felis catus breed Abyssinian
nuclear ribonuclease P
NC_15
t44
Yersinia enterocolitica
t44 RNA
NC_16
Phe_leader
Enterobacter cancerogenus
Phenylalanine leader peptide
NC_17
U6atac
Ochotona princeps
U6atac minor spliceosomal RNA
NC_18
RsaD
Staphylococcus hominis subsp. hominis
RNA Staph. aureus D
NC_19
S_pombe_snR93
Schizosaccharomyces pombe
small nucleolar RNA snR93
NC_20
RivX
Streptococcus pyogenes
RivX sRNA
As recalled in the SwiSpot paper, some RNAbor profiles for our reference dataset are suitable to be used to predict alternative conformations, indeed yielding less accurate results than Swispot ones. Such predicted conformations from RNAbor are available here in a compressed file.