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Retrieve PseudoKnots by class

PseudoBase is a collection of RNA pseudoknots that we make available for retrieval to the scientific community. If you used our database for your research, kindly mention this, referring to its publication (see Batenburg et al. (2000)).

On this page you can pick a pseudoknot by first selecting the appropriate class...

Viral ribosomal frameshifting signals
Viral ribosomal readthrough signals
Viral tRNA like structures
Other viral 5'-UTR
Other viral 3'-UTR
Viral others
rRNA
mRNA
tmRNA
Ribozymes
Aptamers
Artifical molecules
Others

Viral ribosomal frameshifting signals

ALFV (Alfuy virus)
BChV (beet chlorosis virus)
BEV (Berne virus)
BLV (Bovine leukemia virus)
BWYV (Beet western yellows virus)
BYDV-NY-RPV (barley yellow dwarf virus)
CABYV (cucurbit aphid-borne yellows virus)
EAV (equine arteritis virus)
EIAV (Equine infectious anemia virus)
FIV (Feline immunodeficiency virus)
HCV_229E (human coronavirus 229E)
Hs_Ma3 (Homo sapiens)
IBV (infectious bronchitis virus)
JEV (Japanese encephalitis virus)
KUNV (West Nile virus, Kunijn subtype)
LDV-C (lactate dehydrogenase-elevating virus, strain C)
MIDV (Middelburg virus)
MMTV_gag/pro (mouse mammary tumor virus)
MVEV (Murray Valley encephalitis virus)
Mm_Edr (Mus musculus (mouse))
PEMV (pea enation mosaic virus)
PLRV-S (potato leafroll virus)
PLRV-W (potato leafroll virus)
PRRSV-16244B (Porcine reproductive and respiratory syndrome virus, North American isolate (16244B))
PRRSV-LV (Porcine reproductive and respiratory syndrome virus, European Lelystad strain (LV))
RSV (Rous sarcoma virus)
SARS-CoV (SARS coronavirus)
SESV (Seal louse virus)
SRV1_gag/pro (simian retrovirus-1)
ScYLV (sugarcane yellow leaf virus)
USUV (Usutu virus)
VMV (Visna-Maedi virus)
WBV (White Bream Virus)
WNV (West Nile virus)

Viral ribosomal readthrough signals

AKV-MuLV (AKV murine leukemia virus)
BaEV (baboon endogenous virus)
Cas-Br-E-MuLV (Cas-Br-E murine leukemia virus)
FeLV (Feline leukemia virus)
GaLV (gibbon ape leukemia virus)
Mo-MuLV (Moloney murine leukemia virus)
SNV (spleen necrosis virus)

Viral tRNA like structures

AMV3 (alfalfa mosaic virus)
APLPV3 (American plum line pattern virus)
APLV (andean potato latent virus)
AV-2_3 (Asparagus virus 2)
ApMV3 (Apple mosaic virus)
BBMV3 (broad bean mottle virus)
BCRV1 (Blackberry chlorotic ringspot virus)
BMV3 (brome mosaic virus)
BSBV1 (beet soil-borne virus)
BSBV2 (beet soil-borne virus)
BSBV3 (beet soil-borne virus)
BSMVbeta (barley stripe mosaic virus)
BVQ1 (beet virus Q)
BVQ2 (beet virus Q)
BVQ3 (beet virus Q)
CCMV3 (cowpea chlorotic mottle virus)
CGMMV (cucumber green mottle mosaic virus)
CGMMV_PKbulge (cucumber green mottle mosaic virus)
CMV3 (cucumber mosaic virus)
CVV3 (Citrus variegation virus)
CYVV (clitoria yellow vein virus)
CaYMV (cacao yellow mosaic virus)
CaYVV (calopogonium yellow vein virus)
CcTMV (tobacco mosaic virus)
CiLRV3 (Citrus leaf rugose virus)
DYMV (desmodium yellow mottle virus)
EMV (eggplant mosaic virus)
EMoV3 (Elm mottle virus)
FCiLV3 (Fragaria chiloensis latent virus)
HJLV3 (Humulus japonicus latent virus)
IPCV1 (Indian peanut clump virus)
KYMV-BP (kennedya yellow mosaic virus )
LRSVbeta (lychnis ringspot virus)
LiRMV3 (Lilac ring mottle virus)
NeRNV_PKa (Nemesia ring necrosis virus)
NeRNV_PKb (Nemesia ring necrosis virus)
OMV (okra mosaic virus)
ORMV (oilseed rape mosaic virus)
ORSV-S1 (odontoglossum ringspot virus)
ORSV-S1_PKbulge1 (odontoglossum ringspot virus)
ORSV-S1_PKbulge2 (odontoglossum ringspot virus)
ORSV-S1_PKbulge3 (odontoglossum ringspot virus)
OYMV (ononis yellow mosaic virus)
PCV1 (peanut clump virus)
PCV2 (peanut clump virus)
PDV3 (Prune dwarf virus)
PMMV-I (pepper mild mottle virus)
PMMV-S (pepper mild mottle virus)
PMMV-S_PKbulge (pepper mild mottle virus)
PMTV2 (potato mop-top virus)
PMoV3 (Parietaria mottle virus)
PNRSV3 (Prunus necrotic ringspot virus)
PSLVbeta (poa semilatent virus)
PaMMV (paprika mild mottle virus)
PhyMV (physalis mottle virus)
SBRMV1-PKa (soil-borne rye mosaic virus)
SBWMV1 (soil-borne wheat mosaic virus)
SBWMV2 (soil-borne wheat mosaic virus)
SNSV1 (Strawberry necrotic shock virus)
STMV (satellite tobacco mosaic virus)
STMV_PKbulge (satellite tobacco mosaic virus)
SpLV3 (Spinach latent virus)
TAMV1 (Tulare apple mosaic virus)
TCV1 (Tobacco streak virus)
TMGMV (tobacco mild green mosaic virus)
TMGMV_PKbulge (tobacco mild green mosaic virus)
TMV (tobacco mosaic virus)
TMV_PKbulge (tobacco mosaic virus)
TMV-L (tobacco mosaic virus)
TMV-L_PKbulge (tobacco mosaic virus)
TMVcg (tobacco mosaic virus)
TRV-PSG (tobacco rattle virus)
TVCV (turnip vein-clearing virus)
TYMV (turnip yellow mosaic virus)
WCMV (wild cucumber mosaic virus)

Other viral 5'-UTR

AV_ori (Aichi virus)
BKV_ori (Bovine Kobuvirus)
BVDV_IRES (Bovine viral diarrhea virus)
CKoV_ori (Canine Kobuvirus)
CSFV_IRES (Classical swine fever virus (hog cholera virus))
EMCV-R_PKB (encephalomyocarditis virus)
EMCV-R_PKC (encephalomyocarditis virus)
FMDV-A_PKI (foot-and-mouth disease virus)
FMDV-A_PKII (foot-and-mouth disease virus)
FMDV-A_PKIII (foot-and-mouth disease virus)
FMDV-C_PKI (foot-and-mouth disease virus, serotype C)
FMDV-C_PKII (foot-and-mouth disease virus, serotype C)
FMDV-C_PKIII (foot-and-mouth disease virus, serotype C)
FMDV-C_PKIV (foot-and-mouth disease virus, serotype C)
FMDV-O1K_PKI (foot-and-mouth disease virus)
FMDV-O1K_PKII (foot-and-mouth disease virus)
FMDV-O1K_PKIII (foot-and-mouth disease virus)
FMDV-O1K_PKIV (foot-and-mouth disease virus)
HAV_PK1 (hepatitis A virus)
HAV_PK2 (hepatitis A virus)
HCV (Hepatitis C Virus)
HCV_IRES (hepatitis C virus)
HPeV1 (Human Parechovirus 1)
Mengo_PKB (Mengovirus)
Mengo_PKC (Mengovirus)
PKV_ori (Porcine Kobuvirus)
SKV_ori (Sheep Kobuvirus)
TEV_PK1 (tobacco etch virus)
TEV_PK2 (tobacco etch virus)
TEV_PK3 (tobacco etch virus)
TMEV (Theiler\'s murine encephalomyelitis virus)
TV3_ori (Turdivirus 3)

Other viral 3'-UTR

BCV (bovine coronavirus)
BMV3_UPD-PK1 (brome mosaic virus)
BMV3_UPD-PK2 (brome mosaic virus)
BMV3_UPD-PK3 (brome mosaic virus)
BMV3_UPD-PK4 (brome mosaic virus)
BSBV1_UPD-PKb (beet soil-borne virus)
BSBV1_UPD-PKc (beet soil-borne virus)
BSBV2_UPD-PKb (beet soil-borne virus)
BSBV2_UPD-PKc (beet soil-borne virus)
BSBV3_UPD-PKb (beet soil-borne virus)
BSBV3_UPD-PKc (beet soil-borne virus)
BSMVbeta_UPD-PK1 (barley stripe mosaic virus)
BSMVbeta_UPD-PK2 (barley stripe mosaic virus)
BSMVbeta_UPD-PK3 (barley stripe mosaic virus)
BVQ1_UPD-PKb (beet virus Q)
BVQ1_UPD-PKc (beet virus Q)
BVQ2_UPD-PKb (beet virus Q)
BVQ2_UPD-PKc (beet virus Q)
BVQ3_UPD-PKb (beet virus Q)
BVQ3_UPD-PKc (beet virus Q)
BYV (beet yellows virus)
BaMV (bamboo mosaic virus)
CGMMV_UPD-PK1 (cucumber green mottle mosaic virus)
CGMMV_UPD-PK2 (cucumber green mottle mosaic virus)
CGMMV_UPD-PK3 (cucumber green mottle mosaic virus)
CMMV_psiA (Cocksfoot mild mosaic virus)
CMMV_psiB (Cocksfoot mild mosaic virus)
CTV (citrus tristeza virus)
CYSDV1 (cucurbit yellow stunting disorder virus)
CYSDV2 (cucurbit yellow stunting disorder virus)
CcTMV_UPD-PK1 (tobacco mosaic virus)
CcTMV_UPD-PK2 (tobacco mosaic virus)
CcTMV_UPD-PK3 (tobacco mosaic virus)
CoxB3 (Coxsackie B virus)
CuYV1 (cucumber yellows virus)
DEN2_PK1 (Dengue virus type 2)
GLRaV-3 (Grapevine leafroll-associated virus - 2)
HAV (hepatitis A virus)
LChV-1 (little cherry virus 1)
LIYV1 (lettuce infectious yellows virus)
MHV (mouse hepatitis virus)
MMLV_PKb (Montana Myotis leukoencephalitis virus)
NeRNV_UPD-PK1 (Nemesia ring necrosis virus)
NeRNV_UPD-PK2 (Nemesia ring necrosis virus)
NeRNV_UPD-PK3 (Nemesia ring necrosis virus)
ORSV-S1_UPD1-PK2 (odontoglossum ringspot virus)
ORSV-S1_UPD1-PK3 (odontoglossum ringspot virus)
ORSV-S1_UPD2-PK2 (odontoglossum ringspot virus)
ORSV-S1_UPD2-PK3 (odontoglossum ringspot virus)
ORSV-S1_UPD3-PK1 (odontoglossum ringspot virus)
ORSV-S1_UPD3-PK2 (odontoglossum ringspot virus)
ORSV-S1_UPD3-PK3 (odontoglossum ringspot virus)
PMMV-S_UPD-PK1 (pepper mild mottle virus)
PMMV-S_UPD-PK2 (pepper mild mottle virus)
PMMV-S_UPD-PK3 (pepper mild mottle virus)
PMV_psiA (Panicum mosaic virus)
PMV_psiB (Panicum mosaic virus)
PMWaV-2 (Pineapple mealybug wilt associated virus - 2)
PSLVbeta_UPD-PK1 (poa semilatent virus)
PSLVbeta_UPD-PK2 (poa semilatent virus)
PSLVbeta_UPD-PK3 (poa semilatent virus)
PYVV1 (potato yellow vein virus)
PYVV2 (potato yellow vein virus)
PYVV3 (potato yellow vein virus)
RBV_PKb (Rio Bravo virus)
SBRMV1_UPD-PKc (soil-borne rye mosaic virus)
SBRMV1_UPD-PKd (soil-borne rye mosaic virus)
SBRMV1_UPD-PKe (soil-borne rye mosaic virus)
SBRMV1_UPD-PKf (soil-borne rye mosaic virus)
SBRMV1_UPD-PKg (soil-borne rye mosaic virus)
SBRMV1_UPD-PKh (soil-borne rye mosaic virus)
SBRMV1-UPD-PKb (soil-borne rye mosaic virus)
SBWMV1_UPD-PKb (soil-borne wheat mosaic virus)
SBWMV1_UPD-PKc (soil-borne wheat mosaic virus)
SBWMV1_UPD-PKd (soil-borne wheat mosaic virus)
SBWMV1_UPD-PKe (soil-borne wheat mosaic virus)
SBWMV1_UPD-PKf (soil-borne wheat mosaic virus)
SBWMV1_UPD-PKg (soil-borne wheat mosaic virus)
SBWMV1_UPD-PKh (soil-borne wheat mosaic virus)
SBWMV2_UPD-PKb (soil-borne wheat mosaic virus)
SBWMV2_UPD-PKi (soil-borne wheat mosaic virus)
SBWMV2_UPD-PKk (soil-borne wheat mosaic virus)
SBWMV2_UPD-PKl (soil-borne wheat mosaic virus)
SCFaV (strawberry chlorotic fleck associated virus)
SPCSV1 (sweet potato chlorotic stunt virus)
STMV_UPD1-PK1 (satellite tobacco mosaic virus)
STMV_UPD1-PK2 (satellite tobacco mosaic virus)
STMV_UPD1-PK3 (satellite tobacco mosaic virus)
STMV_UPD2-PK1 (satellite tobacco mosaic virus)
STMV_UPD2-PK2 (satellite tobacco mosaic virus)
STMV_UPD2-PK3 (satellite tobacco mosaic virus)
STNV1_PK1 (satellite tobacco necrosis virus 1)
STNV1_PK2 (satellite tobacco necrosis virus 1)
STNV1_PK3 (satellite tobacco necrosis virus 1)
STNV2_PK1 (satellite tobacco necrosis virus 2)
STNV2_PK2 (satellite tobacco necrosis virus 2)
STNV2_PK3 (satellite tobacco necrosis virus 2)
TMGMV_UPD-PK1 (tobacco mild green mosaic virus)
TMGMV_UPD-PK2 (tobacco mild green mosaic virus)
TMGMV_UPD-PK3 (tobacco mild green mosaic virus)
TMV_UPD-PK1 (tobacco mosaic virus)
TMV_UPD-PK2 (tobacco mosaic virus)
TMV_UPD-PK3 (tobacco mosaic virus)
TMV-L_UPD-PK1 (tobacco mosaic virus)
TMV-L_UPD-PK2 (tobacco mosaic virus)
TMV-L_UPD-PK3 (tobacco mosaic virus)
TPAV_psiA (Thin paspalum asymptomatic virus strain 2005)
TPAV_psiB (Thin paspalum asymptomatic virus strain 2005)
WNV_PK3end (West Nile virus)

Viral others

Ad2_VA_RNAI (Adenovirus type 2)
BQCV_IRES-PKI (Black queen cell virus)
BQCV_IRES-PKII (Black queen cell virus)
BQCV_IRES-PKIII (Black queen cell virus)
CrPV_IRES-PKI (Cricket paralysis virus)
CrPV_IRES-PKII (Cricket paralysis virus)
CrPV_IRES-PKIII (Cricket paralysis virus)
DCV_IRES-PKI (Drosophila C virus)
DCV_IRES-PKII (Drosophila C virus)
DCV_IRES-PKIII (Drosophila C virus)
GLV_IRES (Giardiavirus)
HIV1_lrPK (human immunodeficiency virus type 1 (Mal isolate))
HiPV_IRES-PKI (Himetobi P virus)
HiPV_IRES-PKII (Himetobi P virus)
HiPV_IRES-PKIII (Himetobi P virus)
IAV_PK_M (influenza A virus)
IAV_PK_NP (influenza A virus, strain A/PR/8/34)
IAV_PK_NS (influenza A virus, strain A/PR/8/34)
IBV_PK_NS (influenza B virus, strain B/Victoria/02/1987)
PSIV_IRES (Plautia stali intestine virus)
PSIV_IRES-PKII (Plautia stali intestine virus)
PSIV_IRES-PKIII (Plautia stali intestine virus)
Qbeta_PKldX (bacteriophage Q-beta)
RhPV_IRES-PKI (Rhopalosiphum padi virus)
RhPV_IRES-PKII (Rhopalosiphum padi virus)
RhPV_IRES-PKIII (Rhopalosiphum padi virus)
TRV-PSG2_PK1 (tobacco rattle virus, strain PSG)
TRV-PSG2_PK2 (tobacco rattle virus, strain PSG)
TRV-PSG2_PK3 (tobacco rattle virus, strain PSG)
TRV-PSG2_PK4 (tobacco rattle virus, strain PSG)
TRV-PSG2_PK5 (tobacco rattle virus, strain PSG)
TrV_IRES-PKI (Triatoma virus)
TrV_IRES-PKII (Triatoma virus)
TrV_IRES-PKIII (Triatoma virus)

rRNA

rRNA pseudoknot entries are representatives for many similar pseudoknots in diverse species. See the database of RNA families Rfam (http://rfam.sanger.ac.uk/), accessions RF00177; RF01960; RF01118. for all others.

Ec_16S-PKcentre (E.coli)
Ec_16S-PK505/526 (E.coli)
Ec_16S-PK570/866 (E.coli)
Ec_23S-PKG12 (Escherichia coli)
Pp_18S-PKE23-9/12 (Palmaria palmata)
Sc_18S-PKE21-7/8 (Saccharomyces cerevisiae)

mRNA

Bt_PrP (Bos Taurus (cow))
CCR5_PRF (Homo sapiens)
ColIb-P9_repZ (plasmid ColIb-P9)
Ec_S15 (E.coli)
Ec_alpha (E.coli)
Ec_rpmI (Escherichia coli)
Hs_PrP (Homo sapiens)
IFNG_PK (Homo sapiens)
IFNG_PK_B_Taurus (Bos taurus(cow))
IFNG_PK_C_familiaris (Canis familiaris(dog))
IFNG_PK_C_jacchus (Callitrix jacchus(marmoset))
IFNG_PK_M_musculus (Mus musculus(mouse))
IFNG_PK_S_scrofa (Sus scrofa(pig))
T2_gene32 (T2 bacteriophage)
T4_gene32 (bacteriophage T4)
pMU407_repBA (plasmid pMU407.1 (IncL/M))
pMU720_repBA (plasmid pMU720 (IncB))

tmRNA

tmRNA pseudoknot entries are representatives for many similar pseudoknots in diverse species. See the database of RNA families Rfam (http://rfam.sanger.ac.uk/), accession RF00023.

Bp_PK2 (Bordetella pertussis)
Ec_PK1 (E.coli)
Ec_PK2 (E.coli)
Ec_PK3 (E.coli)
Ec_PK4 (E.coli)
Lp_PK1 (Legionella pneumophila)
Lp_PK2 (Legionella pneumophila)
Lp_PK3 (Legionella pneumophila)
Lp_PK4 (Legionella pneumophila)
Vp_PK2 (Variovorax paradoxus)

Ribozymes

RNaseP RNA and HDV pseudoknot entries are representatives for many similar pseudoknots in diverse species. See the database of RNA families Rfam (http://rfam.sanger.ac.uk/), accessions RF00010; RF00094.

(Drosophila pseudoobscura)
Bs_glmS_P1.1 (Bacillus subtilis)
Bs_glmS_P3.1 (Bacillus subtilis)
CPEB3_rz_Bt (Bos tauris(cow))
CPEB3_rz_Cf (Canis familiaris(dog))
CPEB3_rz_Hs (Homo sapiens)
CPEB3_rz_La (elephant)
CPEB3_rz_Md (opossum)
CPEB3_rz_Mn (Mus musculus(mouse))
CPEB3_rz_Oc (Rabbit)
CPEB3_rz_Pt (chimpanzee)
Ec_RNaseP-P4 (Escherichia coli)
Ec_RNaseP-P6 (Escherichia coli)
HDV-It_ag (hepatitis delta virus ("Italy" variant))
HDV-It_g (hepatitis delta virus ("Italy" variant))
Ni_VS (Neurospora intermedia)
R2_rz_Da (Drosophila ananassae)
R2_rz_Df (Drosophila falleni)
R2_rz_Ds (Drosophila simulans)
R2_rz_Dy (Drosophila yakuba)
SCPEB3_rz_Rn (rat)
Tt-LSU_P3/P7 (Tetrahymena thermophila)
drz_Agam_1_1 (Anopheles gambiae)
drz_Agam_1_2 (Anopheles gambiae)
drz_Agam_1_3 (Anopheles gambiae)
drz_Agam_2_1 (Anopheles gambiae)
drz_Agam_2_2 (Anopheles gambiae)
drz_Bflo_1 (Branchiostoma floridae)
drz_Bflo_2 (Branchiostoma floridae)
drz_CIV_1 (Invertebrate iridescent virus 6)
drz_Cjap_1 (Caenorhabditis japonica)
drz_Dpap_1 (Diplonema papillatum)
drz_Fpra_1 (Faecalibacterium prausnitzii)
drz_Pmar_1 (Petromyzon marinus)
drz_Ppac_1_1 (Pristionchus pacificus)
drz_Ppac_1_2 (Pristionchus pacificus)
drz_Spur_1_1 (Strongylocentrotus purpuratus)
drz_Spur_1_2 (Strongylocentrotus purpuratus)
drz_Spur_2 (Strongylocentrotus purpuratus)
drz_Spur_3 (Strongylocentrotus purpuratus)
drz_Spur_4 (Strongylocentrotus purpuratus)
drz_Tatr_1 (Trichoderma atroviride)
ribox02 ()
satRPV (Satellite cereal yellow dwarf virus-RPV RNA)

Aptamers

NGF-H1 ()
NGF-L2 ()
NGF-L6 ()
SAH_riboswitch (Ralstonia solanacearum)
SAM-I_riboswitch (Thermoanaerobacter tengcongensis)
SAM-II_riboswitch (Sargasso Sea metagenome)
SBU (B. subtilis)
TPK-70.28 ()
antiHIV1-NC_psi-50-1 ()
antiHIV1-RT_1.1 ()
antiHIV1-RT_1.3a ()
biotin-PK ()
biotin-PK-AN69.1 ()
ydaO_riboswitch_Bs (Bacillus subtilis)
ydaO_riboswitch_Tl (Thermovirga lienii)
ydaO_riboswitch_Tp (Thermoanaerobacter pseudethanolicus)
ydaO_riboswitch_Tt (Thermoanaerobacter tengcongensis)

Artifical molecules

oligo_PK5 ()

Others

The SRP and telomerase pseudoknot entries are representatives for many similar pseudoknots in diverse species. See the database of RNA families Rfam (http://rfam.sanger.ac.uk/), accessions RF00017; RF00024; RF00025.

Ec_RydC (Escherichia coli K-12)
Hs_SRP-pkn (Homo sapiens)
K.lac_telo (Kluyveromyces lactis)
R2_retroPK (Bombyx mori)
R2_retroPK_Ch (Coscinocera hercules)
R2_retroPK_Cpr (Callosamia promethea)
R2_retroPK_Sc (Samia cynthia)
R2_retroPK_Spy (Saturmia Pyri)
Rr_ODCanti (Rattus rattus (black rat))
T.the_telo (Tetrahymena thermophila)
ToxI_Pa (Pectobacterium atrosepticum)
hTER (Homo sapiens)

Contact:
Prototyping: Jacky Ng & Jan Oliehoek.
© final design and maintenance: F.H.D.(Eke) van Batenburg, 1998-12-18;...; .