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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

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)
LDV-C (lactate dehydrogenase-elevating virus, strain C)
MMTV_gag/pro (mouse mammary tumor 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)
SRV1_gag/pro (simian retrovirus-1)
ScYLV (sugarcane yellow leaf virus)
VMV (Visna-Maedi virus)
WBV (White Bream 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)
APLV (andean potato latent virus)
BBMV3 (broad bean mottle 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)
CaYMV (cacao yellow mosaic virus)
CaYVV (calopogonium yellow vein virus)
CcTMV (tobacco mosaic virus)
CCMV3 (cowpea chlorotic mottle virus)
CGMMV (cucumber green mottle mosaic virus)
CGMMV_PKbulge (cucumber green mottle mosaic virus)
CMV3 (cucumber mosaic virus)
CYVV (clitoria yellow vein virus)
DYMV (desmodium yellow mottle virus)
EMV (eggplant mosaic virus)
IPCV1 (Indian peanut clump virus)
KYMV-BP (kennedya yellow mosaic virus )
LRSVbeta (lychnis ringspot 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)
PaMMV (paprika mild mottle virus)
PCV1 (peanut clump virus)
PCV2 (peanut clump virus)
PhyMV (physalis mottle 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)
PSLVbeta (poa semilatent virus)
SBRMV1-PKa (soil-borne rye mosaic virus)
SBWMV1 (soil-borne wheat mosaic virus)
SBWMV2 (soil-borne wheat mosaic virus)
STMV (satellite tobacco mosaic virus)
STMV_PKbulge (satellite tobacco mosaic virus)
TMGMV (tobacco mild green mosaic virus)
TMGMV_PKbulge (tobacco mild green mosaic virus)
TMV (tobacco mosaic virus)
TMVcg (tobacco mosaic virus)
TMV-L (tobacco mosaic virus)
TMV-L_PKbulge (tobacco mosaic virus)
TMV_PKbulge (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

BVDV_IRES (Bovine viral diarrhea virus)
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)
TEV_PK1 (tobacco etch virus)
TEV_PK2 (tobacco etch virus)
TEV_PK3 (tobacco etch virus)
TMEV (Theiler\'s murine encephalomyelitis virus)

Other viral 3'-UTR

BaMV (bamboo mosaic virus)
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-PKc (beet soil-borne virus)
BSBV1_UPD-PKb (beet soil-borne virus)
BSBV2_UPD-PKc (beet soil-borne virus)
BSBV2_UPD-PKb (beet soil-borne virus)
BSBV3_UPD-PKc (beet soil-borne virus)
BSBV3_UPD-PKb (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-PKc (beet virus Q)
BVQ1_UPD-PKb (beet virus Q)
BVQ2_UPD-PKc (beet virus Q)
BVQ2_UPD-PKb (beet virus Q)
BVQ3_UPD-PKc (beet virus Q)
BVQ3_UPD-PKb (beet virus Q)
BYV (beet yellows virus)
CcTMV_UPD-PK1 (tobacco mosaic virus)
CcTMV_UPD-PK2 (tobacco mosaic virus)
CcTMV_UPD-PK3 (tobacco 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)
CoxB3 (Coxsackie B virus)
CTV (citrus tristeza virus)
CuYV1 (cucumber yellows virus)
CYSDV1 (cucurbit yellow stunting disorder virus)
CYSDV2 (cucurbit yellow stunting disorder 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_UPD3-PK1 (odontoglossum ringspot virus)
ORSV-S1_UPD1-PK3 (odontoglossum ringspot virus)
ORSV-S1_UPD1-PK2 (odontoglossum ringspot virus)
ORSV-S1_UPD2-PK3 (odontoglossum ringspot virus)
ORSV-S1_UPD2-PK2 (odontoglossum ringspot virus)
ORSV-S1_UPD3-PK3 (odontoglossum ringspot virus)
ORSV-S1_UPD3-PK2 (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)
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-PKb (soil-borne rye mosaic 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)
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-L_UPD-PK1 (tobacco mosaic virus)
TMV-L_UPD-PK2 (tobacco mosaic virus)
TMV-L_UPD-PK3 (tobacco mosaic virus)
TMV_UPD-PK1 (tobacco mosaic virus)
TMV_UPD-PK2 (tobacco mosaic virus)
TMV_UPD-PK3 (tobacco mosaic virus)
WNV_PK3end (West Nile virus)

Viral others

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)
HiPV_IRES-PKI (Himetobi P virus)
HiPV_IRES-PKII (Himetobi P virus)
HiPV_IRES-PKIII (Himetobi P virus)
HIV1_lrPK (human immunodeficiency virus type 1 (Mal isolate))
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_IRES-PKI (Triatoma virus)
TrV_IRES-PKII (Triatoma virus)
TrV_IRES-PKIII (Triatoma 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)

rRNA

The following pseudoknots are representatives for many similar pseudoknots residing in different species. See the rRNA website (http://rrna.uia.ac.be/) 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))
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

Ec_PK# and Lp_PK# are representatives for many similar pseudoknots residing in different species. See the tmRNA website (http://www.indiana.edu/~tmrna/) for all others.

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

Ec_RNaseP are representatives for many similar pseudoknots. See the RNase P website (http://www.mbio.ncsu.edu/RNaseP/) for all others.

HDV-it are representatives for many similar pseudoknots. See the hepatitis delta website (http://www.callisto.si.usherb.ca/~jpperra/) for all others.

Bs_glmS_P1.1 (Bacillus subtilis)
Bs_glmS_P3.1 (Bacillus subtilis)
CPEB3_rz_Bt (cow)
CPEB3_rz_Cf (dog)
CPEB3_rz_Hs (Homo sapiens)
CPEB3_rz_La (elephant)
CPEB3_rz_Md (opossum)
CPEB3_rz_Mm (mouse)
CPEB3_rz_Oc (rabbit)
CPEB3_rz_Pt (chimpanzee)
CPEB3_rz_Rn (rat)
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)
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

Artifical molecules

oligo_PK5 ()

Others

Hs_SRP-pk and T.the_telo are representatives for many similar pseudoknots. See the SRP website (//psyche.uthct.edu/dbs/SRPDB/SRPDB.HTML) for all others.

Hs_SRP-pkn (Homo sapiens)
R2_retroPK (Bombyx mori)
R2_retroPK_Ch (Coscinocera hercules)
R2_retroPK_Cpr (Callosamia promethea)
R2_retroPK_Sc (Samia cynthia)
R2_retroPK_Spy (Saturnia pyri)
Rr_ODCanti (Rattus rattus (black rat))
T.the_telo (Tetrahymena thermophila)
hTER (Homo sapiens)

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

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