Browse Rfam/CisReg families with 3D structures

Rfam includes 20 CisReg families with three-dimensional structures, 8 of these are in the A set either mRNA or Genomic.

 

CisReg ID Accession Type Seed Full Average length Sequence
identity (%)
Number of structures Description
A-Genomic Alfamo_CPB RF00252 Cis-reg; 18 36 182.10 89.00 1 (Does not include structured RNA) Alfalfa mosaic virus coat protein binding (CPB) RNA
A-Genomic Entero_5_CRE RF00386 Cis-reg; 160 732 89.20 86.00 1 (structure is 32 bases of 89 base model) Enterovirus 5' cloverleaf cis-acting replication element
B FMN RF00050 Cis-reg;riboswitch; 146 1,789 136.50 72.00 12 (structure is 51 bases of 137 base model) FMN riboswitch (RFN element)
A-Genomic Gammaretro_CES RF00374 Cis-reg; 23 1,308 100.70 91.00 4 (structures are 87 bases of 101 base model) Gammaretrovirus core encapsidation signal
B GEMM_RNA_motif RF01051 Cis-reg; 162 1,049 86.70 64.00 13 GEMM cis-regulatory element
B glmS RF00234 Cis-reg;riboswitch; 17 411 182.60 59.00 37 glmS glucosamine-6-phosphate activated ribozyme
B Glycine RF00504 Cis-reg;riboswitch; 44 4,223 100.90 55.00 21 Glycine riboswitch
A-Genomic HIV-1_DIS RF00175 Cis-reg; 70 2,394 40.10 88.00 44 (structures are 30 bases of 40 base model) Human immunodeficiency virus type 1 dimerisation initiation site
B HIV_FE RF00480 Cis-reg;frameshift_element; 145 11,088 51.90 82.00 2 HIV Ribosomal frameshift signal
A-mRNA IRE RF00037 Cis-reg; 53 2,151 28.90 66.00 2 (structure corresponds to model) Iron response element
B IRES_Cripavirus RF00458 Cis-reg;IRES; 7 16 198.70 53.00 7 Cripavirus internal ribosome entry site (IRES)
B IRES_HCV RF00061 Cis-reg;IRES; 79 6,496 246.90 85.00 3 Hepatitis C virus internal ribosome entry site
B IRES_L-myc RF00261 Cis-reg;IRES; 11 86 220.70 90.00 2 L-myc internal ribosome entry site (IRES)
A-mRNA K10_TLS RF00207 Cis-reg; 5 12 44.00 100.00 3 (structures are 31 bases of 44 base model) K10 transport/localisation element (TLS)
B Lysine RF00168 Cis-reg;riboswitch; 47 1,126 183.50 51.00 14 Lysine riboswitch
B PreQ1 RF00522 Cis-reg;riboswitch; 42 415 45.70 67.00 5 PreQ1 riboswitch
B Purine RF00167 Cis-reg;riboswitch; 133 1,244 100.80 56.00 26 Purine riboswitch
A-mRNA R2_retro_el RF00524 Cis-reg; 15 732 215.90 66.00 12 (structures do not include the 215 base model R2 RNA element
A-genomic Rhino_CRE RF00220 Cis-reg; 12 95 86.00 85.00 1 (structure is 32 bases of 86 base model) Human rhinovirus internal cis-acting regulatory element (CRE)
B S15 RF00114 Cis-reg;leader; 79 406 116.70 62.00 2 Ribosomal S15 leader
B s2m RF00164 Cis-reg; 38 438 42.90 82.00 1 Coronavirus 3' stem-loop II-like motif (s2m)
B SAM RF00162 Cis-reg;riboswitch; 228 2,828 109.10 69.00 16 SAM riboswitch (S box leader)
B TCV_H5 RF00500 Cis-reg; 5 6 45.20 100.00 1 Turnip crinkle virus (TCV) repressor of minus strand synthesis H5
B TPP RF00059 Cis-reg;riboswitch; 115 5,398 111.60 57.00 18 TPP riboswitch (THI element)
B UnaL2 RF00436 Cis-reg; 30 16,952 54.10 78.00 1 UnaL2 LINE 3' element
B ykoK RF00380 Cis-reg; 96 600 168.80 62.00 3 ykoK leader