Team:Hong Kong HKUST/riboregulator/regulatory RNAs catalog
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Revision as of 12:10, 22 September 2014
RNA devices catalogue
With better understanding of the regulatory ability of RNA devices, more RNA devices are discovered and make available to user, and the number of RNA devices in part registry is increasing over time. Among those RNA devices, not all of them share the same nature and mechanism, some of them may inhibit translation while other devices may activate transcription. Based on different mode of action and natures of RNA devices, they can be grouped into different categories. However without accurate categorizing methods or guidelines in part registry, a part of the RNA devices are grouped under type "RNA", while some of them are grouped under other types. These type or grouping methods are not very helpful for yielding and utilizing those RNA devices. Realizing this problem, our team want to regroup RNA devices according to the natures and function of those devices by using "part categories" features available in part registry. We hope that by adding categories, other user can find and use those parts efficiently.
Riboregulator
Riboregulators regulate translation by having two elements, a cis-repressive sequence upstream of RBS in mRNA, and a non-coding RNA device, called trans-activating RNA. The cis-repressive sequence will binds to the 5'UTR, including the RBS by Watson-Crick base pairing, the sequestration of RBS represses translation. While trans-activating RNA will form complementary bases to cis-repressive sequence and exposing RBS for ribosomal binding and allow translation.
Proposed Categories: /RNA/non_coding/post_transcriptional/Riboregulator
Part number | Description | Designer |
---|---|---|
Delft 2009 | BBa_K175029 | Weak lock |
Delft 2009 | BBa_K175030 | Key for lcok of weak RBS |
Delft 2009 | BBa_K175030 | Medium lock |
Delft 2009 | BBa_K175030 | Key for Medium lock |
Delft 2009 | BBa_K175034 | (Constitutive expression of GFP with weak RBS lock and inducible production of key for the lock Composite of K175029 + K175030 |
Delft 2009 | BBa_K175034 | Constitutive expression of GFP with medium RBS lock and inducible production of key for the lock Composite of K175031 + K175032 |
Caltech 2007 | BBa_I759015 | cis3-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759016 | cis4-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759020 | cis8-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759027 | cis3-repressed, tet-regulated Q |
Caltech 2007 | BBa_I759028 | cis4-repressed, tet-regulated Q |
Caltech 2007 | BBa_I759014 | (cis2-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759017 | cis5-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759018 | cis6-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759019 | cis7-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759013 | cis1-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759032 | Ptet_cis1_YFP |
Caltech 2007 | BBa_I759034 | Ptet_cis2_YFP |
Caltech 2007 | BBa_I759036 | Ptet_cis3_YFP |
Caltech 2007 | BBa_I759038 | Ptet_cis4_YFP |
Caltech 2007 | BBa_I759040 | Ptet_cis5_YFP |
Caltech 2007 | BBa_I759042 | Ptet_cis6_YFP |
Caltech 2007 | BBa_I759044 | Ptet_cis7_YFP |
Caltech 2007 | BBa_I759046 | Ptet_cis8_YFP |
Caltech 2007 | BBa_I759023 | pBAD-trans2 |
Caltech 2007 | BBa_I759022 | pBAD-trans1 |
Caltech 2007 | BBa_I759024 | pBAD-trans3 |
Caltech 2007 | BBa_I759025 | pBAD-trans4 |
Caltech 2007 | BBa_I759026 | pBAD-trans5 |
Peking 2007 | BBa_I714070 | R0040-J23078-pTet-Lock3 |
Peking 2007 | BBa_I714080 | [R0040][J23078][E0040][B0015] |
Peking 2007 | BBa_I714081 | R0040-J01010-E0040-B0015 |
Peking 2007 | BBa_I714037 | R751+ C600 E.coli cells with traI-R751 knockout |
Peking 2007 | BBa_I714074 | R0010-J23066-pLac-Key3-DblTerm Uses Lock and Key 3 from berkeley |
K.U. Leuven 2008 | BBa_K145215 | FILTER Key (TetR promoter + key) |
K.U. Leuven 2008 | BBa_K145216 | FILTER T7 RNA pol Lock from berkeley |
K.U. Leuven 2008 | BBa_K145217 | FILTER Complete The two previous together |
K.U. Leuven 2008 | BBa_K145220 | INVERTED TIMER |
K.U. Leuven 2008 | BBa_K145225 | RESET lactonase |
K.U. Leuven 2008 | BBa_K145300 | Lactonase controlled by key/lock |
K.U. Leuven 2008 | BBa_K145301 | lacI controlled by key/lock |
K.U. Leuven 2008 | BBa_K145302 | luxI generator controlled by key/lock |
K.U. Leuven 2008 | BBa_K145303 | GFP generator controlled by key/lock |
K.U. Leuven 2008 | BBa_K145003 | T7 PoPS -> RiboKey 3d |
K.U. Leuven 2008 | BBa_K145004 | T7 PoPS + RiboLock |> LuxI |
K.U. Leuven 2008 | BBa_K145005 | T7 PoPS + PR -> cI |
K.U. Leuven 2008 | BBa_K145216 | FILTER T7 RNA pol |
K.U. Leuven 2008 | BBa_K145251 | OLD RESET lactonase |
K.U. Leuven 2008 | BBa_K145253 | OLD INVERTIMER Part 1 |
K.U. Leuven 2008 | BBa_K145255 | NEW INVERTIMER part 1 |
K.U. Leuven 2008 | BBa_K145264 | test FILTER (new) |
K.U. Leuven 2008 | BBa_K145265 | test FILTER (old) |
K.U. Leuven 2008 | BBa_K145271 | GFP regulated by AND-gate |
K.U. Leuven 2008 | BBa_K145272 | GFP regulated by AND-gate |
K.U. Leuven 2008 | BBa_K145275 | T7 polymerase generator under TetR repressible promoter (filter) |
K.U. Leuven 2008 | BBa_K145276 | T7 polymerase generator under TetR repressible promoter |
K.U. Leuven 2008 | BBa_K145277 | T7 DNA polymerase regulated by lock |
K.U. Leuven 2008 | BBa_K145278 | T7 DNA polymerase regulated by [lock3d] |
K.U. Leuven 2009 | BBa_K238004 | Vanillin synthesis |
K.U. Leuven 2009 | BBa_K238006 | Short version of vanillin synthesis |
K.U. Leuven 2009 | BBa_K238012 | short version II of vanillin synthesis |
Groningen 2011 | BBa_K607005 | short version II of vanillin synthesis |
Groningen 2011 | BBa_K607000 | PhybB_taRNA |
VictoriaBC 2009 | BBa_K235010 | [K145303] (ribokey-controlled GFP generator) |
VictoriaBC 2009 | BBa_K235000 | [R0010][J23066] (pLac+ribokey+stop) |
VictoriaBC 2009 | BBa_K235001 | [J23102][J23066] (constitutive promoter+ribokey+stop) |
VictoriaBC 2009 | BBa_K235009 | [J23102][J23032] (constitutive promoter+ribolocked RBS) |
VictoriaBC 2009 | BBa_K235011 | [K235009][K235005] (ribokey-controlled mCherry generator) |
VictoriaBC 2009 | BBa_K235013 | [K145303][K235000] (ribokey-mediated pLac-controlled GFP reporter) |
VictoriaBC 2009 | BBa_K235014 | [K145303][K235001] (ribokey-mediated GFP generator) |
VictoriaBC 2009 | BBa_K235016 | [I0500][J23032] (pAra+ribolocked RBS) |
VictoriaBC 2009 | BBa_K235019 | [K235016][K235003] (ribokey-mediated pAra-controlled lambda repressor generator) |
VictoriaBC 2009 | BBa_K235021 | [K235009][K235003] (ribokey-mediated lambda repressor generator) |
VictoriaBC 2009 | BBa_K235022 | [K235018][K235019] (mCherry generator, pAra-controlled ribokey-mediated signal inversion) |
VictoriaBC 2009 | BBa_K235024 | [K235018][K235021] (mCherry generator, ribokey-mediated signal inversion) |
VictoriaBC 2009 | BBa_K235025 | [K235022][K235000] (NAND gate, pAra and pLac input signal control, mCherry output signal) |
VictoriaBC 2009 | BBa_K235026 | [K235022][K235001] (NAND gate control test, pLac positive control) |
VictoriaBC 2009 | BBa_K235027 | [K235024][K235000] (NAND gate control test, arabinose positive control) |
VictoriaBC 2009 | BBa_K235028 | [K235024][K235001] (NAND gate control test, positive control) |
Melborne2008 | BBa_K085000 | (lacI)promoter->key3c |
Melborne2008 | BBa_K085002 | pTet->lock3d->GFP |
Calgary 2007 | BBa_I737003 | OmpF controlled RNA Key |
Calgary 2007 | BBa_I737006 | Temperature induced repression/activation of an RNA key |
Calgary 2007 | BBa_I737005 | AHL and RNA lock controlled AraC |
Riboswitch
A riboswitch is a segment on mRNA that have the ability to detect small molecules or temperature, and regulate gene expression in on or off manner. Riboswitches usually contain a region for binding of small molecules, as known as sensor domain, and a region for gene regulation, as known as regulatory domain.In the presence of suitable ligand in the sensor domain, the structure of riboswitch will change. This change in conformation of riboswitch may give various action including translation inhibition or mRNA degradation.
Part number | Description | Designer |
---|---|---|
Delft 2009 | BBa_K175029 | Weak lock |
Delft 2009 | BBa_K175030 | Key for lcok of weak RBS |
Delft 2009 | BBa_K175030 | Medium lock |
Delft 2009 | BBa_K175030 | Key for Medium lock |
Delft 2009 | BBa_K175034 | (Constitutive expression of GFP with weak RBS lock and inducible production of key for the lock Composite of K175029 + K175030 |
Delft 2009 | BBa_K175034 | Constitutive expression of GFP with medium RBS lock and inducible production of key for the lock Composite of K175031 + K175032 |
Caltech 2007 | BBa_I759015 | cis3-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759016 | cis4-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759020 | cis8-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759027 | cis3-repressed, tet-regulated Q |
RNA-IN-RNA-OUT
RNA-OUT is a small non-coding RNA that works at RNA level . RNA-OUT will bind to 5'UTR, which include RBS, of mRNA and prevents ribosome from binding to mRNA to inhibit translation of downstream gene. RNA-IN is also a non-coding RNA that is antisense to RNA-OUT and the binding of RNA-IN and RNA-OUT will prevent RNA-OUT from binding to mRNA, thus allowing ribosome to bind to mRNA and initiate translation.
Part number | Description | Designer |
---|---|---|
Delft 2009 | BBa_K175029 | Weak lock |
Delft 2009 | BBa_K175030 | Key for lcok of weak RBS |
Delft 2009 | BBa_K175030 | Medium lock |
Delft 2009 | BBa_K175030 | Key for Medium lock |
Delft 2009 | BBa_K175034 | (Constitutive expression of GFP with weak RBS lock and inducible production of key for the lock Composite of K175029 + K175030 |
Delft 2009 | BBa_K175034 | Constitutive expression of GFP with medium RBS lock and inducible production of key for the lock Composite of K175031 + K175032 |
Caltech 2007 | BBa_I759015 | cis3-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759016 | cis4-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759020 | cis8-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759027 | cis3-repressed, tet-regulated Q |
Small interfering RNAs (siRNAs)
siRNAs usually involved in RNA interference pathway. siRNA s are produced by "dicing" long double stranded RNA into 21-nucleotides small fragments. The siRNAs will then bind to a protein and one strand of siRNA is removed. Then siRNA, which have complementary base pairs with its target mRNA, will binds to target mRNA. The binding of siRNA usually causes the degradation of target mRNA, result in inhibition of gene expression.
Part number | Description | Designer |
---|---|---|
Delft 2009 | BBa_K175029 | Weak lock |
Delft 2009 | BBa_K175030 | Key for lcok of weak RBS |
Delft 2009 | BBa_K175030 | Medium lock |
Delft 2009 | BBa_K175030 | Key for Medium lock |
Delft 2009 | BBa_K175034 | (Constitutive expression of GFP with weak RBS lock and inducible production of key for the lock Composite of K175029 + K175030 |
Delft 2009 | BBa_K175034 | Constitutive expression of GFP with medium RBS lock and inducible production of key for the lock Composite of K175031 + K175032 |
Caltech 2007 | BBa_I759015 | cis3-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759016 | cis4-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759020 | cis8-repressed, tet-regulated YFP |
Caltech 2007 | BBa_I759027 | cis3-repressed, tet-regulated Q |
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