LOCUS       sequence-404931-        5953 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Transcribes rapZ from the arabinose-inducible PBAD promoter; RapZ 
            directs RNase E to cleave fusion RNAs transcribed from pYG215 or 
            derivatives.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 5953)
  AUTHORS   Schilder A, Gorke B
  TITLE     Role of the 5' end phosphorylation state for small RNA stability and
            target RNA regulation in bacteria.
  JOURNAL   Nucleic Acids Res. 2023 Mar 29:gkad226. doi: 10.1093/nar/gkad226.
  PUBMED    36987877
REFERENCE   2  (bases 1 to 5953)
  AUTHORS   .
  TITLE     Direct Submission
  JOURNAL   Exported Dec 15, 2025 from SnapGene Server 8.0.1
            https://www.snapgene.com
COMMENT     SGRef: number: 1; type: "Journal Article"; journalName: "Nucleic 
            Acids Res. 2023 Mar 29:gkad226. doi: 10.1093/nar/gkad226."
COMMENT     Sequence Label: pYG205
FEATURES             Location/Qualifiers
     source          1..5953
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     CDS             complement(120..998)
                     /codon_start=1
                     /gene="araC"
                     /product="L-arabinose regulatory protein"
                     /label=araC
                     /translation="MAEAQNDPLLPGYSFNAHLVAGLTPIEANGYLDFFIDRPLGMKGY
                     ILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEAREWYHQWVYFRPRAYW
                     HEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLLLRR
                     MEAINESLHPPMDNRVREACQYISDHLADSNFDIASVAQHVCLSPSRLSHLFRQQLGIS
                     VLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFRAGCE
                     EKVNDVAVKLS"
     promoter        1025..1309
                     /gene="araBAD"
                     /label=araBAD promoter
                     /note="promoter of the L-arabinose operon of E. coli; the 
                     araC regulatory gene is transcribed in the opposite 
                     direction (Guzman et al., 1995)"
     primer_bind     1232..1251
                     /label=pBAD Forward
                     /note="For vectors with E. coli araBAD promoter, forward 
                     primer"
     protein_bind    2352..2583
                     /gene="attP"
                     /label=lambda attP
                     /bound_moiety="lambda integrase"
                     /note="integrase from phage lambda"
     primer_bind     complement(2831..2848)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(3006..3594)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(3086..3105)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(3828..4487)
                     /codon_start=1
                     /gene="cat"
                     /product="chloramphenicol acetyltransferase"
                     /label=CmR
                     /note="confers resistance to chloramphenicol"
                     /translation="MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFL
                     KTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSS
                     LWSEYHDDFRQFLHIYSQDVACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANM
                     DNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"
     primer_bind     4402..4421
                     /label=CAT-R
                     /note="Chloramphenicol resistance gene, reverse primer"
     promoter        complement(4488..4590)
                     /label=cat promoter
                     /note="promoter of the E. coli cat gene encoding 
                     chloramphenicol acetyltransferase"
     primer_bind     complement(4857..4875)
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     promoter        4947..5051
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(5052..5120,5121..5912)
                     /codon_start=1
                     /gene="bla"
                     /product="beta-lactamase"
                     /label=AmpR
                     /note="confers resistance to ampicillin, carbenicillin, and
                     related antibiotics"
                     /translation="MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYI
                     ELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYS
                     PVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRW
                     EPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSA
                     LPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGAS
                     LIKHW"
     primer_bind     complement(5270..5289)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
ORIGIN
        1 aattctcatg tttgacagct tatcatcgat gcataatgtg cctgtcaaat ggacgaagca
       61 gggattctgc aaaccctatg ctactccgtc aagccgtcaa ttgtctgatt cgttaccaat
      121 tatgacaact tgacggctac atcattcact ttttcttcac aaccggcacg gaactcgctc
      181 gggctggccc cggtgcattt tttaaatacc cgcgagaaat agagttgatc gtcaaaacca
      241 acattgcgac cgacggtggc gataggcatc cgggtggtgc tcaaaagcag cttcgcctgg
      301 ctgatacgtt ggtcctcgcg ccagcttaag acgctaatcc ctaactgctg gcggaaaaga
      361 tgtgacagac gcgacggcga caagcaaaca tgctgtgcga cgctggcgat atcaaaattg
      421 ctgtctgcca ggtgatcgct gatgtactga caagcctcgc gtacccgatt atccatcggt
      481 ggatggagcg actcgttaat cgcttccatg cgccgcagta acaattgctc aagcagattt
      541 atcgccagca gctccgaata gcgcccttcc ccttgcccgg cgttaatgat ttgcccaaac
      601 aggtcgctga aatgcggctg gtgcgcttca tccgggcgaa agaaccccgt attggcaaat
      661 attgacggcc agttaagcca ttcatgccag taggcgcgcg gacgaaagta aacccactgg
      721 tgataccatt cgcgagcctc cggatgacga ccgtagtgat gaatctctcc tggcgggaac
      781 agcaaaatat cacccggtcg gcaaacaaat tctcgtccct gatttttcac caccccctga
      841 ccgcgaatgg tgagattgag aatataacct ttcattccca gcggtcggtc gataaaaaaa
      901 tcgagataac cgttggcctc aatcggcgtt aaacccgcca ccagatgggc attaaacgag
      961 tatcccggca gcaggggatc attttgcgct tcagccatac ttttcatact cccgccattc
     1021 agagaagaaa ccaattgtcc atattgcatc agacattgcc gtcactgcgt cttttactgg
     1081 ctcttctcgc taaccaaacc ggtaaccccg cttattaaaa gcattctgta acaaagcggg
     1141 accaaagcca tgacaaaaac gcgtaacaaa agtgtctata atcacggcag aaaagtccac
     1201 attgattatt tgcacggcgt cacactttgc tatgccatag catttttatc cataagatta
     1261 gcggatccta cctgacgctt tttatcgcaa ctctctactg tttctccata cccgtttttt
     1321 tgggctagcg aattcgagct cgtcgacaaa aggagacatg acatatggta ctgatgatcg
     1381 tcagcggacg ttcaggttca ggtaaatctg tcgccctgcg tgcgctggaa gatatgggtt
     1441 tttactgcgt ggataacctt cccgtagtgt tgttacccga tctggctcga accctggccg
     1501 atcgcgagat ttctgccgcc gtcagcattg atgttcgtaa tatgccggag tcaccagaaa
     1561 tattcgaaca ggcgatgagt aacctgcctg acgctttctc accgcaactc ctgttcctgg
     1621 atgccgaccg taatacctta attcgtcgtt acagtgacac gcgccgactg catccgcttt
     1681 ccagcaaaaa cctgtcgctg gaaagtgcta tcgacaaaga aagcgatttg ctggagcctc
     1741 tgcgttcgcg agcggatctg attgtcgata cctcagaaat gtccgttcac gagctggctg
     1801 aaatgctgcg tacccgtctg ctgggtaaac gtgaacgcga actgaccatg gtctttgagt
     1861 ctttcggctt caaacacggt atccctatcg atgcagatta cgtctttgac gtgcgcttct
     1921 tgccgaaccc gcactgggat ccgaaactgc gtccaatgac aggtcttgat aaacctgtcg
     1981 ccgcgttcct cgaccgccac acagaagtac acaattttat ctaccagacg cgaagctatc
     2041 ttgagctatg gttacctatg ctggaaacca acaaccgtag ctacttgacg gtcgccattg
     2101 gttgtaccgg cgggaagcac cgttcggtgt atattgcaga gcaactggca gactacttcc
     2161 gctcgcgcgg taaaaacgtc cagtcacgcc atcgtacgct ggaaaaacgt aaaccatgat
     2221 aatctagaga gctcgaattc gaagcagctt tgcactggat tgcgaggctt tgtgcttctc
     2281 tggagtgcga caggtttgat gacaaaaaat tagcgcaaga agacaaaaat caccttgcgc
     2341 taatgctctg ttacaggtca ctaataccat ctaagtagtt gattcatagt gactgcatat
     2401 gttgtgtttt acagtattat gtagtctgtt ttttatgcaa aatctaattt aatatattga
     2461 tatttatatc attttacgtt tctcgttcag cttttttata ctaagttggc attataaaaa
     2521 agcattgctt atcaatttgt tgcaacgaac aggtcactat cagtcaaaat aaaatcatta
     2581 tttgatttca attttgtccc actccctgcc tctgtcatca cgatactgtg atgccatggt
     2641 gtccgactta tgcccgagaa gatgttgagc aaacttatcg cttatctgct tctcatagag
     2701 tcttgcagac aaactgcgca actcgtgaaa ggtaggcgga tctattctta ctcctagatc
     2761 ttcctatgcg gtgtgaaata ccgcacagat gcgtaaggag aaaataccgc atcaggcgct
     2821 cttccgcttc ctcgctcact gactcgctgc gctcggtcgt tcggctgcgg cgagcggtat
     2881 cagctcactc aaaggcggta atacggttat ccacagaatc aggggataac gcaggaaaga
     2941 agcggccgct gagcaaaagg ccagcaaaag gccaggaacc gtaaaaaggc cgcgttgctg
     3001 gcgtttttcc ataggctccg cccccctgac gagcatcaca aaaatcgacg ctcaagtcag
     3061 aggtggcgaa acccgacagg actataaaga taccaggcgt ttccccctgg aagctccctc
     3121 gtgcgctctc ctgttccgac cctgccgctt accggatacc tgtccgcctt tctcccttcg
     3181 ggaagcgtgg cgctttctca tagctcacgc tgtaggtatc tcagttcggt gtaggtcgtt
     3241 cgctccaagc tgggctgtgt gcacgaaccc cccgttcagc ccgaccgctg cgccttatcc
     3301 ggtaactatc gtcttgagtc caacccggta agacacgact tatcgccact ggcagcagcc
     3361 actggtaaca ggattagcag agcgaggtat gtaggcggtg ctacagagtt cttgaagtgg
     3421 tggcctaact acggctacac tagaaggaca gtatttggta tctgcgctct gctgaagcca
     3481 gttaccttcg gaaaaagagt tggtagctct tgatccggca aacaaaccac cgctggtagc
     3541 ggtggttttt ttgtttgcaa gcagcagatt acgcgcagaa aaaaaggatc tcaagaagat
     3601 cctttgatct tttctacggg gtctgacgct cagtggaacg aaaactcacg ttaagggatt
     3661 ttggtcatga gattatcaaa aaggatcttc acctagatcc ttttattctt gaagacgaaa
     3721 gggcgggtcg aatttgcttt cgaatttctg ccattcatcc gcttattatc acttattcag
     3781 gcgtagcaac caggcgttta agggcaccaa taactgcctt aaaaaaatta cgccccgccc
     3841 tgccactcat cgcagtactg ttgtaattca ttaagcattc tgccgacatg gaagccatca
     3901 caaacggcat gatgaacctg aatcgccagc ggcatcagca ccttgtcgcc ttgcgtataa
     3961 tatttgccca tggtgaaaac gggggcgaag aagttgtcca tattggccac gtttaaatca
     4021 aaactggtga aactcaccca gggattggct gagacgaaaa acatattctc aataaaccct
     4081 ttagggaaat aggccaggtt ttcaccgtaa cacgccacat cttgcgaata tatgtgtaga
     4141 aactgccgga aatcgtcgtg gtattcactc cagagcgatg aaaacgtttc agtttgctca
     4201 tggaaaacgg tgtaacaagg gtgaacacta tcccatatca ccagctcacc gtctttcatt
     4261 gccatacgga attccggatg agcattcatc aggcgggcaa gaatgtgaat aaaggccgga
     4321 taaaacttgt gcttattttt ctttacggtc tttaaaaagg ccgtaatatc cagctgaacg
     4381 gtctggttat aggtacattg agcaactgac tgaaatgcct caaaatgttc tttacgatgc
     4441 cattgggata tatcaacggt ggtatatcca gtgatttttt tctccatttt agcttcctta
     4501 gctcctgaaa atctcgataa ctcaaaaaat acgcccggta gtgatcttat ttcattatgg
     4561 tgaaagttgg aacctcttac gtgccgatca acgtctcatt ttcgccaaaa gttggcccag
     4621 ggcttcccgg tatcaacagg gacaccagga tttatttatt ctgcgaagtg atcttccgtc
     4681 acaggtattt attcggcgca aagtgcgtcg ggtgatgctg ccaacttact gatttagtgt
     4741 atgatggtgt ttttgaggtg ctccagtggc ttctgtttct atcagctgtc cctcctgttc
     4801 agctactgac ggggtggtgc gtaacggcaa aagcaccgcc ggacatcagc gctagggcct
     4861 cgtgatacgc ctatttttat aggttaatgt catgataata atggtttctt aggcggccgc
     4921 caggtggcac ttttcgggga aatgtgcgcg gaacccctat ttgtttattt ttctaaatac
     4981 attcaaatat gtatccgctc atgagacaat aaccctgata aatgcttcaa taatattgaa
     5041 aaaggaagag tatgagtatt caacatttcc gtgtcgccct tattcccttt tttgcggcat
     5101 tttgccttcc tgtttttgct cacccagaaa cgctggtgaa agtaaaagat gctgaagatc
     5161 agttgggtgc acgagtgggt tacatcgaac tggatctcaa cagcggtaag atccttgaga
     5221 gttttcgccc cgaagaacgt tttccaatga tgagcacttt taaagttctg ctatgtggcg
     5281 cggtattatc ccgtgttgac gccgggcaag agcaactcgg tcgccgcata cactattctc
     5341 agaatgactt ggttgagtac tcaccagtca cagaaaagca tcttacggat ggcatgacag
     5401 taagagaatt atgcagtgct gccataacca tgagtgataa cactgcggcc aacttacttc
     5461 tgacaacgat cggaggaccg aaggagctaa ccgctttttt gcacaacatg ggggatcatg
     5521 taactcgcct tgatcgttgg gaaccggagc tgaatgaagc cataccaaac gacgagcgtg
     5581 acaccacgat gcctgtagca atggcaacaa cgttgcgcaa actattaact ggcgaactac
     5641 ttactctagc ttcccggcaa caattaatag actggatgga ggcggataaa gttgcaggac
     5701 cacttctgcg ctcggccctt ccggctggct ggtttattgc tgataaatct ggagccggtg
     5761 agcgtgggtc tcgcggtatc attgcagcac tggggccaga tggtaagccc tcccgtatcg
     5821 tagttatcta cacgacgggg agtcaggcaa ctatggatga acgaaataga cagatcgctg
     5881 agataggtgc ctcactgatt aagcattggt aactgtcaga ccaagtttac tcatatatac
     5941 tttagattga ttt
//
