From 7e6d5e7ccbcf7160da290fa427c3125f27142dbe Mon Sep 17 00:00:00 2001 From: ahmed tarek elsayed <77227944+ahmedtarek26@users.noreply.github.com> Date: Wed, 3 Aug 2022 11:20:19 +0200 Subject: [PATCH 1/2] Test rdf file --- RDF/sbol3-small-molecule.rdf | 610 +++++++++++++++++++++++++++++++++++ 1 file changed, 610 insertions(+) create mode 100644 RDF/sbol3-small-molecule.rdf diff --git a/RDF/sbol3-small-molecule.rdf b/RDF/sbol3-small-molecule.rdf new file mode 100644 index 0000000..23c13cd --- /dev/null +++ b/RDF/sbol3-small-molecule.rdf @@ -0,0 +1,610 @@ + + + + + 1 + + Conversion of the iGEM parts registry to SBOL2.1 + + igem2sbol + iGEM to SBOL conversion + 2017-03-06T15:00:00+00:00 + Chris J. Myers + + James Alastair McLaughlin + + + In stock + + + Inverting regulatory region controlled by LacI (<bb_part>BBa_C0010</bb_part>, <bb_part>BBa_C0011</bb_part>, etc.) <p> The pLac regulatory region is a 243 base-pair sequence with standard BioBrick prefix and suffix sections on its ends. It contains two protein binding sites: CAP, which is generally present in E.coli and is assocciated with cell health and availability of glucose., and LacI, the Lac inhibitor <bb_part>BBa_C0010</bb_part> which binds in an dimerized cooperative manner to inhibit the transcription of the protein that follows. In the presence of lactose or IPTG, an analog of lactose, LacI is unable to correctly bind and inhibit transcription. This allows <bb_part>BBa_R0010</bb_part> to be used as a inverter or as a detector of lactose or IPTG. + 1 + 2003-01-31T12:00:00Z + true + Released HQ 2013 + 24 + + 0 + The Plac insert was PCR'd from the MG1655 strain of E.coli K12. + 7 + + + + LacI + <P> <P><P> LacI binds to this regulator. This part is incompatible with species containing active LacI coding regions. Lactose and IPTG disable the operation of LacI and this regulator. This part is incompatible with environments containing lactose or lactose analogs. + false + true + 2015-05-08T01:14:14Z + promoter (lacI regulated) + + false + BBa_R0010 + _1_ + + + + + + + 1 + + LacI binding site + annotation1961226 + LacI binding site + + + + + + range1961226 + + 1 + 166 + 200 + + + + + + + + + start + 1 + annotation1961227 + start + + + + + 1 + + range1961227 + + 173 + 173 + + + + + + + + annotation1961225 + 1 + -10 + + -10 + + + + + + range1961225 + + 1 + 161 + 166 + + + + + + + + + CAP binding site + annotation1961223 + 1 + CAP binding site + + + + + + range1961223 + 1 + + 89 + 126 + + + + + + + + + 1 + end of LacI coding region (inactive) + annotation1961221 + end of LacI coding region (inactive) + + + + + + 1 + + range1961221 + 1 + 88 + + + + + + + + 1 + annotation1961224 + + -35 + -35 + + + + + 1 + + range1961224 + + 137 + 142 + + + + + + + + 1 + + BBa_R0010 + annotation1961222 + BBa_R0010 + + + + + 1 + + range1961222 + + 1 + 200 + + + + + + + + + + + + 1 + BBa_R0010_sequence + + + + caatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcagtgagcgcaacgcaattaatgtgagttagctcactcattaggcaccccaggctttacactttatgcttccggctcgtatgttgtgtggaattgtgagcggataacaatttcacaca + + + + BBa_I0500 + true + _1_ + + 2003-12-05T12:00:00Z + + + + 24 + true + pBad/araC + In stock + 1 + + -- No description -- + + Inducible pBad/araC promoter + false + 0 + 7 + Sri Kosuri + 2015-08-31T04:07:29Z + false + + + + + + + + 1 + Pbad + annotation1498841 + Pbad + + + + + + 1 + range1498841 + + 1080 + 1210 + + + + + + + + AraC + annotation1498843 + + 1 + AraC + + + + + + + 1 + range1498843 + 1 + 1079 + + + + + + + + + PC + 1 + annotation1498842 + PC + + + + + range1498842 + + + 1 + 1043 + 1114 + + + + + + + + + 1 + + + + + + BBa_I0500_sequence + + ttatgacaacttgacggctacatcattcactttttcttcacaaccggcacggaactcgctcgggctggccccggtgcattttttaaatacccgcgagaaatagagttgatcgtcaaaaccaacattgcgaccgacggtggcgataggcatccgggtggtgctcaaaagcagcttcgcctggctgatacgttggtcctcgcgccagcttaagacgctaatccctaactgctggcggaaaagatgtgacagacgcgacggcgacaagcaaacatgctgtgcgacgctggcgatatcaaaattgctgtctgccaggtgatcgctgatgtactgacaagcctcgcgtacccgattatccatcggtggatggagcgactcgttaatcgcttccatgcgccgcagtaacaattgctcaagcagatttatcgccagcagctccgaatagcgcccttccccttgcccggcgttaatgatttgcccaaacaggtcgctgaaatgcggctggtgcgcttcatccgggcgaaagaaccccgtattggcaaatattgacggccagttaagccattcatgccagtaggcgcgcggacgaaagtaaacccactggtgataccattcgcgagcctccggatgacgaccgtagtgatgaatctctcctggcgggaacagcaaaatatcacccggtcggcaaacaaattctcgtccctgatttttcaccaccccctgaccgcgaatggtgagattgagaatataacctttcattcccagcggtcggtcgataaaaaaatcgagataaccgttggcctcaatcggcgttaaacccgccaccagatgggcattaaacgagtatcccggcagcaggggatcattttgcgcttcagccatacttttcatactcccgccattcagagaagaaaccaattgtccatattgcatcagacattgccgtcactgcgtcttttactggctcttctcgctaaccaaaccggtaaccccgcttattaaaagcattctgtaacaaagcgggaccaaagccatgacaaaaacgcgtaacaaaagtgtctataatcacggcagaaaagtccacattgattatttgcacggcgtcacactttgctatgccatagcatttttatccataagattagcggatcctacctgacgctttttatcgcaactctctactgtttctccatacccgtttttttgggctagc + + + TetR repressible promoter + p(tetR) + 2015-05-08T01:14:14Z + false + true + + _1_ + + + 1 + + <P> <P>BBa_R0040 TetR-Regulated Promoter is based on a cI promoter. It has been modified to include two TetR binding sites and the BioBrick standard assembly head and tail restriction sites.<P> + 2003-01-31T12:00:00Z + true + Released HQ 2013 + Lutz, R., Bujard, H., <em>Nucleic Acids Research</em> (1997) 25, 1203-1210. + 24 + + Sequence for pTet inverting regulator driven by the TetR protein.</P> + In stock + June Rhee, Connie Tao, Ty Thomson, Louis Waldman + + BBa_R0040 + + 7 + 0 + false + + + + + + + annotation1986786 + 1 + TetR 2 + + TetR 2 + + + + + + 1 + + range1986786 + 26 + 44 + + + + + + + + annotation1986784 + 1 + + BBa_R0040 + BBa_R0040 + + + + + + + 1 + range1986784 + 1 + 54 + + + + + + + + annotation1986785 + -35 + 1 + + -35 + + + + + + range1986785 + 1 + + 20 + 25 + + + + + + + + annotation1986783 + TetR 1 + 1 + + TetR 1 + + + + + range1986783 + + 1 + + 1 + 19 + + + + + + + + 1 + + -10 + annotation1986787 + -10 + + + + + range1986787 + + 1 + + 43 + 48 + + + + + + + + + + + + 1 + + + BBa_R0040_sequence + + tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac + + + + + + true + + 24 + + lacI repressor from E. coli (+LVA) + BBa_C0012 + In stock + 1 + represillator of Elowitz and Leibler (2000) + 2003-01-31T12:00:00Z + lacI + Released HQ 2013 + Grace Kenney, Daniel Shen, Neelaksh Varshney, Samantha Sutton + + 2015-08-31T04:07:23Z + + Coding region for the LacI protein with an LVA degradation tail and without an RBS. LacI binds to the pLac regulator <bb_part>BBa_R0010</bb_part> and PLlac01 hybrid regulator <bb_part>BBa_R0011</bb_part> and inhibits transcription. IPTG (Isopropylthiogalactoside) binds to LacI and inhibits its operation, therefore promoting transcription.</P> <P>A rapid degredation tail (LVA) has been added to improve the High to Low performance of this part.</P> + 0 + false + 7 + false + References (unparsed) here: <p>Elowitz, M.B., Leibler, S. A synthetic oscillatory network of transcriptional regulators. <em>Nature</em> 403, 335-338 (2000). <a href="http://biobricks.ai.mit.edu/BB_References.htm#ELOW00">[ELOW00]</a><br> <br> </P> <P> References (unparsed) here: <p>Elowitz, M.B., Leibler, S. A synthetic oscillatory network of transcriptional regulators. <em>Nature</em> 403, 335-338 (2000). <a href="http://biobricks.ai.mit.edu/BB_References.htm#ELOW00">[ELOW00]</a><br> <br> </P> <P>Sequence taken from the repressilator of Elowitz and Leibler (2000). The obtained sequence was compared to the wild-type sequence for LacI obtained through a database search. The sequence had been modified from the wild-type in that wild-type GTG start was changed to an ATG start (note, actual ORF in E.coli has several GTG starts it would seem). The LVA tag has been added for quicker degradation.<P> Incompatible with systems containing LacI, lactose, or IPTG. + false + _1_ + + + + + + + + annotation1723 + lacI-LVA + 1 + lacI-LVA + + + + + range1723 + + + 1 + 1 + 1128 + + + + + + + + BBa_C0012 + + 1 + annotation7031 + BBa_C0012 + + + + + 1 + range7031 + + + 1 + 1128 + + + + + + + + annotation1722 + 1 + + LVA + LVA + + + + + 1 + range1722 + + + 1090 + 1128 + + + + + + + + Help:Barcodes + 1 + + annotation2213988 + Help:Barcodes + + + + + range2213988 + + + 1 + 1129 + 1153 + + + + + + + + + + + + 1 + + + BBa_C0012_sequence + + atggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagacagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcaggctgcaaacgacgaaaactacgctttagtagcttaataactctgatagtgctagtgtagatctc + + From 191a11a8a2399f75fee904503e1a80da563e8e50 Mon Sep 17 00:00:00 2001 From: ahmed tarek elsayed <77227944+ahmedtarek26@users.noreply.github.com> Date: Wed, 3 Aug 2022 11:25:56 +0200 Subject: [PATCH 2/2] Test gb file --- GenBank/BBa_J23101.gb | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 GenBank/BBa_J23101.gb diff --git a/GenBank/BBa_J23101.gb b/GenBank/BBa_J23101.gb new file mode 100644 index 0000000..99d07a8 --- /dev/null +++ b/GenBank/BBa_J23101.gb @@ -0,0 +1,12 @@ +LOCUS BBa_J23101 35 bp DNA linear UNK 01-JAN-1980 +DEFINITION constitutive promoter family member. +ACCESSION BBa_J23101 +VERSION BBa_J23101.1 +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers +ORIGIN + 1 tttacagcta gctcagtcct aggtattatg ctagc +//