Rfam cis-Reg families (209 entries)
Accession ID Description
RF00031 SECIS Selenocysteine insertion sequence
RF00032 Histone3 Histone 3' UTR stem-loop
RF00036 RRE HIV Rev response element
RF00037 IRE Iron response element
RF00038 PrfA PrfA thermoregulator UTR
RF00040 rne5 RNase E 5' UTR
RF00041 Entero_OriR Enteroviral 3' UTR element
RF00048 Entero_CRE Enterovirus cis-acting replication element
RF00050 FMN FMN riboswitch (RFN element)
RF00059 TPP TPP riboswitch (THI element)
RF00061 IRES_HCV Hepatitis C virus internal
RF00080 yybP-ykoY yybP-ykoY leader
RF00109 Vimentin3 Vimentin 3' UTR protein-binding
RF00114 S15 Ribosomal S15 leader
RF00140 Alpha_RBS Alpha operon ribosome binding
RF00161 nos_TCE Nanos 3' UTR translation
RF00162 SAM SAM riboswitch (S box
RF00164 s2m Coronavirus 3' stem-loop II-like
RF00165 Corona_pk3 Coronavirus 3' UTR pseudoknot
RF00167 Purine Purine riboswitch
RF00168 Lysine Lysine riboswitch
RF00171 Tombus_5 Tombusvirus 5' UTR
RF00172 CAESAR ctgf/hcs24 CAESAR
RF00174 Cobalamin Cobalamin riboswitch
RF00175 HIV-1_DIS Human immunodeficiency virus type
RF00176 Tombus_3_IV Tombusvirus 3' UTR region
RF00179 GAIT GAIT element
RF00180 REN-SRE Renin stability regulatory element
RF00182 Corona_package Coronavirus packaging signal
RF00183 G-CSF_SLDE G-CSF factor stem-loop destabilising
RF00184 PVX_3 Potato virus X cis-acting
RF00185 Flavi_CRE Flavivirus 3' UTR cis-acting
RF00192 BLV_package Bovine leukaemia virus RNA
RF00193 CTV_rep_sig Citrus tristeza virus replication
RF00194 Rubella_3 Rubella virus 3' cis-acting
RF00196 AMV_RNA1_SL Alfalfa mosaic virus RNA
RF00207 K10_TLS K10 transport/localisation element (TLS)
RF00209 IRES_Pesti Pestivirus internal ribosome entry
RF00210 IRES_Aptho Aphthovirus internal ribosome entry
RF00214 Retro_dr1 Retrovirus direct repeat 1
RF00215 Tombus_3_III Tombus virus defective interfering
RF00216 IRES_c-myc c-myc internal ribosome entry
RF00220 Rhino_CRE Human rhinovirus internal cis-acting
RF00222 IRES_Bag1 Bag-1 internal ribosome entry
RF00223 IRES_Bip bip internal ribosome entry
RF00224 IRES_FGF2 FGF-2 internal ribosome entry
RF00225 IRES_Tobamo Tobamovirus internal ribosome entry
RF00226 IRES_n-myc n-myc internal ribosome entry
RF00227 FIE3 FIE3 (ftz instability element
RF00228 IRES_HepA Hepatitis A virus internal
RF00229 IRES_Picorna Picornavirus internal ribosome entry
RF00230 T-box T-box leader
RF00232 Spi-1 Spi-1 (PU.1) 5' UTR
RF00233 Tymo_tRNA-like Tymovirus/Pomovirus tRNA-like 3' UTR
RF00234 glmS glmS glucosamine-6-phosphate activated ribozyme
RF00243 traJ_5 traJ 5' UTR
RF00250 TAR Trans-activation response element (TAR)
RF00252 Alfamo_CPB Alfalfa mosaic virus coat
RF00259 IFN_gamma Interferon gamma 5' UTR
RF00260 HepC_CRE Hepatitis C virus (HCV)
RF00261 IRES_L-myc L-myc internal ribosome entry
RF00290 BaMV_CRE Bamboo mosaic potexvirus (BaMV)
RF00362 Pospi_RY Pospiviroid RY motif stem
RF00374 Gammaretro_CES Gammaretrovirus core encapsidation signal
RF00375 HIV_PBS HIV primer binding site
RF00376 HIV_GSL3 HIV gag stem loop
RF00379 ydaO-yuaA ydaO/yuaA leader
RF00380 ykoK ykoK leader
RF00381 Antizyme_FSE Antizyme RNA frameshifting stimulation
RF00382 DnaX DnaX ribosomal frameshifting element
RF00383 IS1222_FSE Insertion sequence IS1222 ribosomal
RF00384 Pox_AX_element Poxvirus AX element late
RF00385 IBV_D-RNA Infectious bronchitis virus D-RNA
RF00386 Entero_5_CRE Enterovirus 5' cloverleaf cis-acting
RF00387 IRES_FGF1 FGF-1 internal ribosome entry
RF00389 satBaMV_CRE Bamboo mosaic virus satellite
RF00390 UPSK UPSK RNA
RF00391 RtT RtT RNA
RF00433 Hsp90_CRE Hsp90 cis-regulatory element
RF00434 BTE Luteovirus cap-independent translation element
RF00435 ROSE Repression of heat shock
RF00436 UnaL2 UnaL2 LINE 3' element
RF00437 HLE Hairy RNA localisation element
RF00442 ykkC-yxkD ykkC-yxkD leader
RF00447 IRES_Kv1_4 Voltage-gated potassium-channel Kv1.4 IRES
RF00448 IRES_EBNA Epstein-Barr virus nuclear antigen
RF00449 IRES_HIF1 HIF-1 alpha IRES
RF00453 Cardiovirus_CRE Cardiovirus cis-acting replication element
RF00454 p27_CRE p27 cis-regulatory element
RF00457 IRES_mnt Mnt IRES
RF00458 IRES_Cripavirus Cripavirus internal ribosome entry
RF00459 MPMV_package Mason-Pfizer monkey virus packaging
RF00460 U1A_PIE U1A polyadenylation inhibition element
RF00461 IRES_VEGF_A Vascular endothelial growth factor
RF00462 IRES_APC APC internal ribosome entry
RF00463 ApoB_5_CRE Apolipoprotein B (apoB) 5'
RF00465 JEV_hairpin Japanese encephalitis virus (JEV)
RF00467 RSV_PBS Rous sarcoma virus (RSV)
RF00468 HCV_SLVII Hepatitis C virus stem-loop
RF00469 HCV_SLIV Hepatitis C stem-loop IV
RF00470 Toga_5_CRE Togavirus 5' plus strand
RF00480 HIV_FE HIV Ribosomal frameshift signal
RF00481 HCV_X3 Hepatitis C virus 3'X
RF00483 IRES_IGF2 Insulin-like growth factor II
RF00484 IRES_Cx32 Connexin-32 internal ribosome entry
RF00485 K_chan_RES Potassium channel RNA editing
RF00487 IRES_Cx43 Connexin-43 internal ribosome entry
RF00490 S-element S-element
RF00491 SVLPA Simian virus 40 late
RF00495 IRES_Hsp70 Heat shock protein 70
RF00496 Corona_SL-III Coronavirus SL-III cis-acting replication
RF00498 EAV_LTH Equine arteritis virus leader
RF00499 Parecho_CRE Human parechovirus 1 (HPeV1)
RF00500 TCV_H5 Turnip crinkle virus (TCV)
RF00501 Rota_CRE Rotavirus cis-acting replication element
RF00502 TCV_Pr Turnip crinkle virus (TCV)
RF00504 Glycine Glycine riboswitch
RF00506 Thr_leader Threonine operon leader
RF00507 Corona_FSE Coronavirus frameshifting stimulation element
RF00510 Tombus_IRE Tombusvirus internal replication element
RF00511 IRES_KSHV Kaposi's sarcoma-associated herpesvirus internal
RF00512 Leu_leader Leucine operon leader
RF00513 Trp_leader Tryptophan operon leader
RF00514 His_leader Histidine operon leader
RF00515 PyrR PyrR binding site
RF00516 ylbH ylbH leader
RF00517 serC serC leader
RF00518 speF speF leader
RF00520 ybhL ybhL leader
RF00521 SAM_alpha SAM riboswitch (alpha-proteobacteria)
RF00522 PreQ1 PreQ1 riboswitch
RF00523 Prion_pknot Prion pseudoknot
RF00524 R2_retro_el R2 RNA element
RF00525 Flavivirus_DB Flavivirus DB element
RF00547 IRES_TrkB TrkB IRES
RF00549 IRES_c-sis c-sis internal ribosome entry
RF00550 HepE_CRE Hepatitis E virus cis-reactive
RF00551 bicoid_3 Bicoid 3'-UTR regulatory element
RF00552 rncO rncO
RF00555 L13_leader Ribosomal protein L13 leader
RF00556 L19_leader Ribosomal protein L19 leader
RF00557 L10_leader Ribosomal protein L10 leader
RF00558 L20_leader Ribosomal protein L20 leader
RF00559 L21_leader Ribosomal protein L21 leader
RF00617 cHP flavivirus capsid hairpin cHP
RF00620 HCV_ARF_SL Hepatitis C alternative reading
RF00626 Gurken Gurken localisation signal
RF00632 sxy sxy 5' UTR element
RF00634 SAM-IV S-adenosyl methionine (SAM) riboswitch,
RF01046 WLE3 Wingless localisation element 3
RF01047 HBV HBV RNA encapsidation signal
RF01051 GEMM_RNA_motif GEMM cis-regulatory element
RF01054 preQ1-II preQ1-II (pre queuosine) riboswitch
RF01055 MOCO_RNA_motif Moco (molybdenum cofactor) riboswitch
RF01056 Mg_sensor Magnesium Sensor
RF01057 SAH_riboswitch S-adenosyl-L-homocysteine riboswitch
RF01065 23S-methyl 23S methyl RNA motif
RF01066 6C 6C RNA
RF01068 mini-ykkC mini-ykkC RNA motif
RF01069 purD purD RNA motif
RF01070 sucA SucA RNA motif
RF01072 UPD-PK13b Pseudoknot of upstream pseudoknot
RF01073 GP_knot1 Gag/pol translational readthrough site
RF01074 RF_site1 Putative RNA-dependent RNA polymerase
RF01075 TLS-PK1 Pseudoknot of tRNA-like structure
RF01076 RF_site2 Polymerase ribosomal frameshift site
RF01077 TLS-PK2 Pseudoknot of tRNA-like structure
RF01078 PK-PYVV 3'-terminal pseudoknot in PYVV
RF01079 RF_site3 Putative RNA-dependent RNA polymerase
RF01080 UPD-PKib Pseudoknot of upstream pseudoknot
RF01081 UPD-PKe Pseudoknot of upstream pseudoknot
RF01082 UPD-PKh Pseudoknot of upstream pseudoknot
RF01083 UPD-PK2 Pseudoknot of upstream pseudoknot
RF01084 TLS-PK3 Pseudoknot of tRNA-like structure
RF01085 TLS-PK4 Pseudoknot of tRNA-like structure
RF01086 LR-PK1 Long range pseudoknot
RF01087 PK-repZ Pseudoknot of the regulatory
RF01088 TLS-PK5 Pseudoknot of tRNA-like structure
RF01089 PK-repBA Pseudoknot of the regulatory
RF01090 RF_site4 Edr gene ribosomal frameshift
RF01091 PK-SPCSV 3'-terminal pseudoknot in sweet
RF01092 GP_knot2 Gag/pol translational readthrough site
RF01093 RF_site5 Ma3 gene ribosomal frameshift
RF01094 RF_site6 Polymerase ribosomal frameshift site
RF01095 PK-CuYV_BPYV 3'-terminal pseudoknot of CuYV/BPYV
RF01096 PK-HAV 3'end pseudoknot of HepA
RF01097 RF_site8 Gag/pro ribosomal frameshift site
RF01098 RF_site9 Gag/pro ribosomal frameshift site
RF01099 PK-IAV Pseudoknot of influenza A
RF01100 PK-BYV 3'-terminal pseudoknot in BYV
RF01101 TLS-PK6 Pseudoknot of tRNA-like structure
RF01102 PK1-TEV_CVMV 5'-leader pseudoknot of TEV/CVMV
RF01103 UPD-PKc Pseudoknot of upstream pseudoknot
RF01104 UPD-PKb Pseudoknot of upstream pseudoknot
RF01105 UPD-PKl Pseudoknot of upstream pseudoknot
RF01106 UPD-PKb1 Pseudoknot of upstream pseudoknot
RF01107 UPD-PKf Pseudoknot of upstream pseudoknot
RF01108 UPD-PK1 Pseudoknot of upstream pseudoknot
RF01109 UPD-PKd Pseudoknot of upstream pseudoknot
RF01110 UPD-PK2b Pseudoknot of upstream pseudoknot
RF01111 UPD-PKk Pseudoknot of upstream pseudoknot
RF01112 UPD-PKg Pseudoknot of upstream pseudoknot
RF01113 UPD-PK3 Pseudoknot of upstream pseudoknot
RF01114 UPD-PK1TMV Pseudoknot of upstream pseudoknot
RF01115 UPD-PK2a Pseudoknot of upstream pseudoknot
RF01313 HHBV_epsilon Heron HBV RNA encapsidation
RF01380 HIV-1_SD Human immunodeficiency virus type
RF01381 HIV-1_SL3 HIV-1 stem-loop 3 Psi
RF01382 HIV-1_SL4 HIV-1 stem-loop 4 packaging