SwiSpot Dataset

The reference dataset is made of both riboswitches and non-riboswitches.

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 -


Non-Riboswitches

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

Structures predicted via RNAbor

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.