LOCUS       sequence-160605-        3974 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  The sgRNA at the stop codon of human Brachyury(T) locus.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 3974)
  AUTHORS   Chu LF, Leng N, Zhang J, Hou Z, Mamott D, Vereide DT, Choi J, 
            Kendziorski C, Stewart R, Thomson JA
  TITLE     Single-cell RNA-seq reveals novel regulators of human embryonic stem
            cell differentiation to definitive endoderm.
  JOURNAL   Genome Biol. 2016 Aug 17;17(1):173. doi: 10.1186/s13059-016-1033-x.
  PUBMED    27534536
REFERENCE   2  (bases 1 to 3974)
  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: "Genome 
            Biol."; date: "2016-08-17"; volume: "17(1):173. doi"; pages: " 
            10.1186/s13059-016-1033-x"
COMMENT     Sequence Label: T-STOP sgRNA-1
FEATURES             Location/Qualifiers
     source          1..3974
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     protein_bind    107..128
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(143..148,149..166,167..173)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    181..197
                     /label=lac operator
                     /bound_moiety="lac repressor encoded by lacI"
                     /note="The lac repressor binds to the lac operator to 
                     inhibit transcription in E. coli. This inhibition can be 
                     relieved by adding lactose or 
                     isopropyl-beta-D-thiogalactopyranoside (IPTG)."
     primer_bind     186..208
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     205..221
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     205..221
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     promoter        239..257
                     /label=SP6 promoter
                     /note="promoter for bacteriophage SP6 RNA polymerase"
     primer_bind     239..256
                     /label=SP6
                     /note="SP6 promoter, forward primer"
     promoter        406..654
                     /label=U6 promoter
                     /note="RNA polymerase III promoter for human U6 snRNA 
                     (Domitrovich & Kunkel, 2003)"
     primer_bind     406..426
                     /label=hU6-F
                     /note="Human U6 promoter, forward primer"
     primer_bind     577..596
                     /label=LKO.1 5'
                     /note="Human U6 promoter, forward primer"
     misc_RNA        675..750
                     /label=gRNA scaffold
                     /note="guide RNA scaffold for the Streptococcus pyogenes 
                     CRISPR/Cas9 system"
     protein_bind    complement(762..786)
                     /gene="mutant version of attB"
                     /label=attB2
                     /bound_moiety="BP Clonase(TM)"
                     /note="recombination site for the Gateway(R) BP reaction"
     primer_bind     complement(861..880)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(862..880)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(887..904)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(887..903)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(896..918)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     CDS             1041..1343
                     /codon_start=1
                     /gene="ccdB"
                     /product="CcdB, a bacterial toxin that poisons DNA gyrase"
                     /label=ccdB
                     /note="Plasmids containing the ccdB gene cannot be 
                     propagated in standard E. coli strains."
                     /translation="QFKVYTYKRESRYRLFVDVQSDIIDTPGRRMVIPLASARLLSDKV
                     SRELYPVVHIGDESWRMMTTDMASVPVSVIGEEVADLSHRENDIKNAINLMFWGI"
     primer_bind     1222..1241
                     /label=ccdB-fwd
                     /note="ccdB gene, forward primer"
     CDS             1692..2486
                     /codon_start=1
                     /product="aminoglycoside phosphotransferase"
                     /label=NeoR/KanR
                     /note="confers resistance to neomycin, kanamycin, and G418 
                     (Geneticin(R))"
                     /translation="MIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRP
                     VLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLS
                     SHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQ
                     GLAPAELFARLKASMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIA
                     LATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF"
     CDS             1692..2486
                     /codon_start=1
                     /gene="aph(3')-II (or nptII)"
                     /product="aminoglycoside phosphotransferase from Tn5"
                     /label=NeoR/KanR
                     /note="confers resistance to neomycin, kanamycin, and G418 
                     (Geneticin(R))"
                     /translation="MIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRP
                     VLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLS
                     SHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQ
                     GLAPAELFARLKASMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIA
                     LATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF"
     primer_bind     complement(1746..1765)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     2356..2375
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     regulatory      2687..2696
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             2693..3067
                     /codon_start=1
                     /gene="Sh ble from Streptoalloteichus hindustanus"
                     /product="antibiotic-binding protein"
                     /label=BleoR
                     /note="confers resistance to bleomycin, phleomycin, and 
                     Zeocin(TM)"
                     /translation="MAKLTSAVPVLTARDVAGAVEFWTDRLGFSRDFVEDDFAGVVRDD
                     VTLFISAVQDQVVPDNTLAWVWVRGLDELYAEWSEVVSTNFRDASGPAMTEIGEQPWGR
                     EFALRDPAGNCVHFVAEEQD"
     rep_origin      3205..3793
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     3694..3713
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     3947..3964
                     /label=L4440
                     /note="L4440 vector, forward primer"
ORIGIN
        1 agcgcccaat acgcaaaccg cctctccccg cgcgttggcc gattcattaa tgcagctggc
       61 acgacaggtt tcccgactgg aaagcgggca gtgagcgcaa cgcaattaat gtgagttagc
      121 tcactcatta ggcaccccag gctttacact ttatgcttcc ggctcgtatg ttgtgtggaa
      181 ttgtgagcgg ataacaattt cacacaggaa acagctatga ccatgattac gccaagctat
      241 ttaggtgaca ctatagaata ctcaagctat gcatcaagct tggtaccgag ctcggatcca
      301 ctagtaacgg ccgccagtgt gctggaattc gccctttgta caaaaaagca ggctttaaag
      361 gaaccaattc agtcgactgg atccggtacc aaggtcgggc aggaagaggg cctatttccc
      421 atgattcctt catatttgca tatacgatac aaggctgtta gagagataat tagaattaat
      481 ttgactgtaa acacaaagat attagtacaa aatacgtgac gtagaaagta ataatttctt
      541 gggtagtttg cagttttaaa attatgtttt aaaatggact atcatatgct taccgtaact
      601 tgaaagtatt tcgatttctt ggctttatat atcttgtgga aaggacgaaa caccgccttc
      661 catgtgaagc agcagtttta gagctagaaa tagcaagtta aaataaggct agtccgttat
      721 caacttgaaa aagtggcacc gagtcggtgc tttttttcta gacccagctt tcttgtacaa
      781 agttggcatt aaagggcgaa ttctgcagat atccatcaca ctggcggccg ctcgagcatg
      841 catctagagg gcccaattcg ccctatagtg agtcgtatta caattcactg gccgtcgttt
      901 tacaacgtcg tgactgggaa aaccctggcg ttacccaact taatcgcctt gcagcacatc
      961 cccctttcgc cagctggcgt aatagcgaag aggcccgcac cgatcgccct tcccaacagt
     1021 tgcgcagcct atacgtacgg cagtttaagg tttacaccta taaaagagag agccgttatc
     1081 gtctgtttgt ggatgtacag agtgatatta ttgacacgcc ggggcgacgg atggtgatcc
     1141 ccctggccag tgcacgtctg ctgtcagata aagtctcccg tgaactttac ccggtggtgc
     1201 atatcgggga tgaaagctgg cgcatgatga ccaccgatat ggccagtgtg ccggtctccg
     1261 ttatcgggga agaagtggct gatctcagcc accgcgaaaa tgacatcaaa aacgccatta
     1321 acctgatgtt ctggggaata taaatgtcag gcatgagatt atcaaaaagg atcttcacct
     1381 agatcctttt cacgtagaaa gccagtccgc agaaacggtg ctgaccccgg atgaatgtca
     1441 gctactgggc tatctggaca agggaaaacg caagcgcaaa gagaaagcag gtagcttgca
     1501 gtgggcttac atggcgatag ctagactggg cggttttatg gacagcaagc gaaccggaat
     1561 tgccagctgg ggcgccctct ggtaaggttg ggaagccctg caaagtaaac tggatggctt
     1621 tcttgccgcc aaggatctga tggcgcaggg gatcaagctc tgatcaagag acaggatgag
     1681 gatcgtttcg catgattgaa caagatggat tgcacgcagg ttctccggcc gcttgggtgg
     1741 agaggctatt cggctatgac tgggcacaac agacaatcgg ctgctctgat gccgccgtgt
     1801 tccggctgtc agcgcagggg cgcccggttc tttttgtcaa gaccgacctg tccggtgccc
     1861 tgaatgaact gcaagacgag gcagcgcggc tatcgtggct ggccacgacg ggcgttcctt
     1921 gcgcagctgt gctcgacgtt gtcactgaag cgggaaggga ctggctgcta ttgggcgaag
     1981 tgccggggca ggatctcctg tcatctcacc ttgctcctgc cgagaaagta tccatcatgg
     2041 ctgatgcaat gcggcggctg catacgcttg atccggctac ctgcccattc gaccaccaag
     2101 cgaaacatcg catcgagcga gcacgtactc ggatggaagc cggtcttgtc gatcaggatg
     2161 atctggacga agagcatcag gggctcgcgc cagccgaact gttcgccagg ctcaaggcga
     2221 gcatgcccga cggcgaggat ctcgtcgtga cccatggcga tgcctgcttg ccgaatatca
     2281 tggtggaaaa tggccgcttt tctggattca tcgactgtgg ccggctgggt gtggcggacc
     2341 gctatcagga catagcgttg gctacccgtg atattgctga agagcttggc ggcgaatggg
     2401 ctgaccgctt cctcgtgctt tacggtatcg ccgctcccga ttcgcagcgc atcgccttct
     2461 atcgccttct tgacgagttc ttctgaatta ttaacgctta caatttcctg atgcggtatt
     2521 ttctccttac gcatctgtgc ggtatttcac accgcataca ggtggcactt ttcggggaaa
     2581 tgtgcgcgga acccctattt gtttattttt ctaaatacat tcaaatatgt atccgctcat
     2641 gagacaataa ccctgataaa tgcttcaata atagcacgtg aggagggcca ccatggccaa
     2701 gttgaccagt gccgttccgg tgctcaccgc gcgcgacgtc gccggagcgg tcgagttctg
     2761 gaccgaccgg ctcgggttct cccgggactt cgtggaggac gacttcgccg gtgtggtccg
     2821 ggacgacgtg accctgttca tcagcgcggt ccaggaccag gtggtgccgg acaacaccct
     2881 ggcctgggtg tgggtgcgcg gcctggacga gctgtacgcc gagtggtcgg aggtcgtgtc
     2941 cacgaacttc cgggacgcct ccgggccggc catgaccgag atcggcgagc agccgtgggg
     3001 gcgggagttc gccctgcgcg acccggccgg caactgcgtg cacttcgtgg ccgaggagca
     3061 ggactgacac gtgctaaaac ttcattttta atttaaaagg atctaggtga agatcctttt
     3121 tgataatctc atgaccaaaa tcccttaacg tgagttttcg ttccactgag cgtcagaccc
     3181 cgtagaaaag atcaaaggat cttcttgaga tccttttttt ctgcgcgtaa tctgctgctt
     3241 gcaaacaaaa aaaccaccgc taccagcggt ggtttgtttg ccggatcaag agctaccaac
     3301 tctttttccg aaggtaactg gcttcagcag agcgcagata ccaaatactg tccttctagt
     3361 gtagccgtag ttaggccacc acttcaagaa ctctgtagca ccgcctacat acctcgctct
     3421 gctaatcctg ttaccagtgg ctgctgccag tggcgataag tcgtgtctta ccgggttgga
     3481 ctcaagacga tagttaccgg ataaggcgca gcggtcgggc tgaacggggg gttcgtgcac
     3541 acagcccagc ttggagcgaa cgacctacac cgaactgaga tacctacagc gtgagctatg
     3601 agaaagcgcc acgcttcccg aagggagaaa ggcggacagg tatccggtaa gcggcagggt
     3661 cggaacagga gagcgcacga gggagcttcc agggggaaac gcctggtatc tttatagtcc
     3721 tgtcgggttt cgccacctct gacttgagcg tcgatttttg tgatgctcgt caggggggcg
     3781 gagcctatgg aaaaacgcca gcaacgcggc ctttttacgg ttcctggcct tttgctggcc
     3841 ttttgctcac atgttctttc ctgcgttatc ccctgattct gtggataacc gtattaccgc
     3901 ctttgagtga gctgataccg ctcgccgcag ccgaacgacc gagcgcagcg agtcagtgag
     3961 cgaggaagcg gaag
//
