LOCUS       Exported                8408 bp ds-DNA     circular SYN 01-OCT-2025
DEFINITION  synthetic circular DNA
ACCESSION   .
VERSION     .
KEYWORDS    pHAGE2_EF1aL-tdTomato-W
SOURCE      synthetic DNA construct
  ORGANISM  recombinant plasmid
REFERENCE   1  (bases 1 to 8408)
  AUTHORS   Kotton Lab
  TITLE     Direct Submission
  JOURNAL   Exported Oct 30, 2025 from SnapGene 2.7.3
            http://www.snapgene.com
FEATURES             Location/Qualifiers
     source          1..8408
                     /organism="recombinant plasmid"
                     /mol_type="other DNA"
     LTR             1..636
                     /gene="LTR"
                     /note="5' LTR"
                     /note="Long Terminal Repeat"
     misc_feature    1..454
                     /note="HIV U3"
                     /note="Full Length HIV U3"
     primer_bind     complement(158..179)
                     /note="pHAGE-A0050-8050"
     primer_bind     401..421
                     /note="pHAGE-S501-1000"
     misc_feature    455..551
                     /note="HIV R"
                     /note="HIV Repeat Region"
     polyA_site      550
                     /note="pA Site"
                     /note="Exact base to which Poly-A is added"
     5'UTR           551..635
                     /note="HIV 5' UTR"
     misc_feature    552..636
                     /note="HIV U5"
     polyA_signal    570..577
                     /note="G-T cluster"
                     /note="GT Cluster shown to be necessary for Poly-A site 
                     activity by Cullen in J Virol. 1989 January; 63(1):421-424"
     misc_feature    636..658
                     /note="PBS-K"
                     /note="tRNA binding site for Lysine tRNA"
     misc_feature    637..1155
                     /gene="psi"
                     /note="PSI"
                     /note="PSI Packaging Sequence"
     primer_bind     complement(667..690)
                     /note="pHAGE-A0550-0050"
     misc_feature    697..806
                     /note="HIV-PSI"
     stem_loop       697..731
                     /note="SL-1"
                     /note="PSI Stem loop 1"
     stem_loop       736..754
                     /note="SL-2"
                     /note="PSI Stem loop 2"
     misc_feature    744..745
                     /note="5' SD 289"
                     /note="Major 5' Splice Donor 289"
     stem_loop       766..779
                     /note="SL-3"
                     /note="PSI Stem Loop 3"
     CDS             790..1144
                     /note="HIV gag"
                     /note="HIV gag sequence from 336bp to 688bp (Clone to PvuII
                     site in HIV and filled in ClaI digest to take gag CDS out 
                     of frame)"
     stem_loop       793..806
                     /note="SL-4"
                     /note="PSI Stem Loop 4"
     misc_feature    807..1144
                     /note="HR-ePSI"
                     /note="HIV gag sequence 351bp to 688bp"
     misc_feature    833..834
                     /note="Fill-in"
                     /note="Filled in Cla Site from original HIV genome to 
                     disrupt gag polyprotein ORF"
     misc_feature    853..855
                     /note="Stop Codon"
                     /note="Stop codon in gag put in frame by ClaI fill in"
     primer_bind     898..919
                     /note="pHAGE-S1001-1500"
     CDS             1156..2013
                     /note="env"
                     /note="HIV env sequence from bp7168 to 8025 (contains RRE) 
                     Cloned from BglII to BamHI out of HIV"
     primer_bind     complement(1166..1189)
                     /note="pHAGE-A1050-0550"
     misc_feature    1245..1593
                     /note="RRE"
                     /note="Rev Responsive Element according to Belasco in 
                     Molecular Cell, Vol. 7, 603-614, March, 2001"
     misc_feature    1303..1536
                     /gene="rre"
                     /note="RRE"
                     /note="Rev Responsive Element"
     misc_feature    1357
                     /note="RRE Mutation"
                     /note="This G is a C in the WT HIV-1 genome"
     primer_bind     1391..1417
                     /note="pHAGE-S1501-2000"
     primer_bind     complement(1650..1678)
                     /note="pHAGE-A1550-1050"
     primer_bind     1898..1922
                     /note="pHAGE-S2001-2500"
     misc_feature    1911..1912
                     /note="SA 7925"
     misc_feature    2014..2027
                     /note="Junk"
                     /note="Linker Junk Sequence probably left over from 
                     cloning"
     misc_feature    2034..2211
                     /gene="cppt"
                     /note="HIV cpPu (Trip)"
                     /note="Central Poly Purine Track"
     primer_bind     complement(2084..2112)
                     /note="pHAGE-A2050-1550"
     misc_feature    2188..2189
                     /note="SA 4459"
     misc_feature    2218..3402
                     /note="Human EF1a Promoter"
                     /note="Human Elongation Factor 1 alpha promoter"
     intron          2454..3045
                     /note="Human EF1a Intron"
     misc_feature    2531
                     /note="EF1a Mutation"
                     /note="Missing GCCC according to Genbank and Celera 
                     sequences"
     CDS             3412..4842
                     /codon_start=1
                     /product="tandem dimeric (pseudo-monomeric) derivative of 
                     DsRed (Shaner et al., 2004)"
                     /note="tdTomato"
                     /note="mammalian codon-optimized"
                     /translation="MVSKGEEVIKEFMRFKVRMEGSMNGHEFEIEGEGEGRPYEGTQTA
                     KLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYKKLSFPEGFKWERVMNFEDGG
                     LVTVTQDSSLQDGTLIYKVKMRGTNFPPDGPVMQKKTMGWEASTERLYPRDGVLKGEIH
                     QALKLKDGGHYLVEFKTIYMAKKPVQLPGYYYVDTKLDITSHNEDYTIVEQYERSEGRH
                     HLFLGHGTGSTGSGSSGTASSEDNNMAVIKEFMRFKVRMEGSMNGHEFEIEGEGEGRPY
                     EGTQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYKKLSFPEGFKWERVM
                     NFEDGGLVTVTQDSSLQDGTLIYKVKMRGTNFPPDGPVMQKKTMGWEASTERLYPRDGV
                     LKGEIHQALKLKDGGHYLVEFKTIYMAKKPVQLPGYYYVDTKLDITSHNEDYTIVEQYE
                     RSEGRHHLFLYGMDELYK"
     misc_feature    4849..5440
                     /gene="WPRE"
                     /note="WPRE"
                     /note="Woodchuck Hepatitis Virus Posttranscriptional 
                     Regulatory Element"
     primer_bind     complement(4877..4911)
                     /note="pHAGE 3' CDS"
     primer_bind     complement(4955..4978)
                     /note="pHAGE-A3550-3050"
     primer_bind     5108..5128
                     /note="pHAGE-S4001-4500"
     LTR             5445..5766
                     /note="3' LTR"
     misc_feature    5445..5546
                     /note="HIV nef"
     misc_feature    5495..5509
                     /note="HIV PPT"
                     /note="PolyPurine Tract"
     misc_feature    5512..5548
                     /note="dU3"
                     /note="1st Half of deleted U3"
     misc_feature    5568..5586
                     /note="dU3"
                     /note="2nd Half of deleted U3"
     misc_feature    5587..5683
                     /note="HIV R"
     misc_feature    5684..5766
                     /note="HIV U5"
     primer_bind     5798..5820
                     /note="pHAGE-S6001-6500"
     promoter        5969..6003
                     /note="P-Bla"
                     /note="Beta Lactamase Promoter"
     CDS             6022..6861
                     /gene="AMPr"
                     /note="AMPr"
                     /note="Ampicillin Resistance Gene"
     primer_bind     complement(6071..6094)
                     /note="pHAGE-A6050-5550"
     primer_bind     6271..6295
                     /note="pHAGE-S6501-7000"
     primer_bind     complement(6540..6563)
                     /note="pHAGE-A6550-6050"
     primer_bind     6791..6815
                     /note="pHAGE-S7001-7500"
     primer_bind     complement(7051..7072)
                     /note="pHAGE-A7050-6550"
     rep_origin      7090..7623
                     /gene="ORI"
                     /note="ORI"
                     /note="Bacterial Origin of Replication"
     primer_bind     7295..7319
                     /note="pHAGE-S7501-8000"
     primer_bind     complement(7562..7583)
                     /note="pHAGE-A7550-7050"
     primer_bind     7798..7817
                     /note="pHAGE-S8001-8500"
     misc_feature    7860..7983
                     /gene="SV40 ori"
                     /note="SV40 ori"
     primer_bind     complement(8038..8064)
                     /note="pHAGE-A8050-7550"
     primer_bind     8303..8331
                     /note="pHAGE-S1-500"
ORIGIN
        1 tggaagggct aattcactcc caaagaagac aagatatcct tgatctgtgg atctaccaca
       61 cacaaggcta cttccctgat tagcagaact acacaccagg gccaggggtc agatatccac
      121 tgacctttgg atggtgctac aagctagtac cagttgagcc agataaggta gaagaggcca
      181 ataaaggaga gaacaccagc ttgttacacc ctgtgagcct gcatgggatg gatgacccgg
      241 agagagaagt gttagagtgg aggtttgaca gccgcctagc atttcatcac gtggcccgag
      301 agctgcatcc ggagtacttc aagaactgct gatatcgagc ttgctacaag ggactttccg
      361 ctggggactt tccagggagg cgtggcctgg gcgggactgg ggagtggcga gccctcagat
      421 cctgcatata agcagctgct ttttgcctgt actgggtctc tctggttaga ccagatctga
      481 gcctgggagc tctctggcta actagggaac ccactgctta agcctcaata aagcttgcct
      541 tgagtgcttc aagtagtgtg tgcccgtctg ttgtgtgact ctggtaacta gagatccctc
      601 agaccctttt agtcagtgtg gaaaatctct agcagtggcg cccgaacagg gacttgaaag
      661 cgaaagggaa accagaggag ctctctcgac gcaggactcg gcttgctgaa gcgcgcacgg
      721 caagaggcga ggggcggcga ctggtgagta cgccaaaaat tttgactagc ggaggctaga
      781 aggagagaga tgggtgcgag agcgtcagta ttaagcgggg gagaattaga tcgcgatggg
      841 aaaaaattcg gttaaggcca gggggaaaga aaaaatataa attaaaacat atagtatggg
      901 caagcaggga gctagaacga ttcgcagtta atcctggcct gttagaaaca tcagaaggct
      961 gtagacaaat actgggacag ctacaaccat cccttcagac aggatcagaa gaacttagat
     1021 cattatataa tacagtagca accctctatt gtgtgcatca aaggatagag ataaaagaca
     1081 ccaaggaagc tttagacaag atagaggaag agcaaaacaa aagtaagacc accgcacagc
     1141 aagcggccgg ccgctgatct tcagacctgg aggaggagat atgagggaca attggagaag
     1201 tgaattatat aaatataaag tagtaaaaat tgaaccatta ggagtagcac ccaccaaggc
     1261 aaagagaaga gtggtgcaga gagaaaaaag agcagtggga ataggagctt tgttccttgg
     1321 gttcttggga gcagcaggaa gcactatggg cgcagcgtca atgacgctga cggtacaggc
     1381 cagacaatta ttgtctggta tagtgcagca gcagaacaat ttgctgaggg ctattgaggc
     1441 gcaacagcat ctgttgcaac tcacagtctg gggcatcaag cagctccagg caagaatcct
     1501 ggctgtggaa agatacctaa aggatcaaca gctcctgggg atttggggtt gctctggaaa
     1561 actcatttgc accactgctg tgccttggaa tgctagttgg agtaataaat ctctggaaca
     1621 gatttggaat cacacgacct ggatggagtg ggacagagaa attaacaatt acacaagctt
     1681 aatacactcc ttaattgaag aatcgcaaaa ccagcaagaa aagaatgaac aagaattatt
     1741 ggaattagat aaatgggcaa gtttgtggaa ttggtttaac ataacaaatt ggctgtggta
     1801 tataaaatta ttcataatga tagtaggagg cttggtaggt ttaagaatag tttttgctgt
     1861 actttctata gtgaatagag ttaggcaggg atattcacca ttatcgtttc agacccacct
     1921 cccaaccccg aggggacccg acaggcccga aggaatagaa gaagaaggtg gagagagaga
     1981 cagagacaga tccattcgat tagtgaacgg atctcgacgg tatcgccgaa ttcacaaatg
     2041 gcagtattca tccacaattt taaaagaaaa ggggggattg gggggtacag tgcaggggaa
     2101 agaatagtag acataatagc aacagacata caaactaaag aattacaaaa acaaattaca
     2161 aaaattcaaa attttcgggt ttattacagg gacagcagag atccagtttg gactagtcgt
     2221 gaggctccgg tgcccgtcag tgggcagagc gcacatcgcc cacagtcccc gagaagttgg
     2281 ggggaggggt cggcaattga accggtgcct agagaaggtg gcgcggggta aactgggaaa
     2341 gtgatgtcgt gtactggctc cgcctttttc ccgagggtgg gggagaaccg tatataagtg
     2401 cagtagtcgc cgtgaacgtt ctttttcgca acgggtttgc cgccagaaca caggtaagtg
     2461 ccgtgtgtgg ttcccgcggg cctggcctct ttacgggtta tggcccttgc gtgccttgaa
     2521 ttacttccac ctggctgcag tacgtgattc ttgatcccga gcttcgggtt ggaagtgggt
     2581 gggagagttc gaggccttgc gcttaaggag ccccttcgcc tcgtgcttga gttgaggcct
     2641 ggcctgggcg ctggggccgc cgcgtgcgaa tctggtggca ccttcgcgcc tgtctcgctg
     2701 ctttcgataa gtctctagcc atttaaaatt tttgatgacc tgctgcgacg ctttttttct
     2761 ggcaagatag tcttgtaaat gcgggccaag atctgcacac tggtatttcg gtttttgggg
     2821 ccgcgggcgg cgacggggcc cgtgcgtccc agcgcacatg ttcggcgagg cggggcctgc
     2881 gagcgcggcc accgagaatc ggacgggggt agtctcaagc tggccggcct gctctggtgc
     2941 ctggcctcgc gccgccgtgt atcgccccgc cctgggcggc aaggctggcc cggtcggcac
     3001 cagttgcgtg agcggaaaga tggccgcttc ccggccctgc tgcagggagc tcaaaatgga
     3061 ggacgcggcg ctcgggagag cgggcgggtg agtcacccac acaaaggaaa agggcctttc
     3121 cgtcctcagc cgtcgcttca tgtgactcca cggagtaccg ggcgccgtcc aggcacctcg
     3181 attagttctc gagcttttgg agtacgtcgt ctttaggttg gggggagggg ttttatgcga
     3241 tggagtttcc ccacactgag tgggtggaga ctgaagttag gccagcttgg cacttgatgt
     3301 aattctcctt ggaatttgcc ctttttgagt ttggatcttg gttcattctc aagcctcaga
     3361 cagtggttca aagttttttt cttccatttc aggtgtcgtg aagcggccgc catggtgagc
     3421 aagggcgagg aggtcatcaa agagttcatg cgcttcaagg tgcgcatgga gggctccatg
     3481 aacggccacg agttcgagat cgagggcgag ggcgagggcc gcccctacga gggcacccag
     3541 accgccaagc tgaaggtgac caagggcggc cccctgccct tcgcctggga catcctgtcc
     3601 ccccagttca tgtacggctc caaggcgtac gtgaagcacc ccgccgacat ccccgattac
     3661 aagaagctgt ccttccccga gggcttcaag tgggagcgcg tgatgaactt cgaggacggc
     3721 ggtctggtga ccgtgaccca ggactcctcc ctgcaggacg gcacgctgat ctacaaggtg
     3781 aagatgcgcg gcaccaactt cccccccgac ggccccgtaa tgcagaagaa gaccatgggc
     3841 tgggaggcct ccaccgagcg cctgtacccc cgcgacggcg tgctgaaggg cgagatccac
     3901 caggccctga agctgaagga cggcggccac tacctggtgg agttcaagac catctacatg
     3961 gccaagaagc ccgtgcaact gcccggctac tactacgtgg acaccaagct ggacatcacc
     4021 tcccacaacg aggactacac catcgtggaa cagtacgagc gctccgaggg ccgccaccac
     4081 ctgttcctgg ggcatggcac cggcagcacc ggcagcggca gctccggcac cgcctcctcc
     4141 gaggacaaca acatggccgt catcaaagag ttcatgcgct tcaaggtgcg catggagggc
     4201 tccatgaacg gccacgagtt cgagatcgag ggcgagggcg agggccgccc ctacgagggc
     4261 acccagaccg ccaagctgaa ggtgaccaag ggcggccccc tgcccttcgc ctgggacatc
     4321 ctgtcccccc agttcatgta cggctccaag gcgtacgtga agcaccccgc cgacatcccc
     4381 gattacaaga agctgtcctt ccccgagggc ttcaagtggg agcgcgtgat gaacttcgag
     4441 gacggcggtc tggtgaccgt gacccaggac tcctccctgc aggacggcac gctgatctac
     4501 aaggtgaaga tgcgcggcac caacttcccc cccgacggcc ccgtaatgca gaagaagacc
     4561 atgggctggg aggcctccac cgagcgcctg tacccccgcg acggcgtgct gaagggcgag
     4621 atccaccagg ccctgaagct gaaggacggc ggccactacc tggtggagtt caagaccatc
     4681 tacatggcca agaagcccgt gcaactgccc ggctactact acgtggacac caagctggac
     4741 atcacctccc acaacgagga ctacaccatc gtggaacagt acgagcgctc cgagggccgc
     4801 caccacctgt tcctgtacgg catggacgag ctgtacaagt aaggatccta atcaacctct
     4861 ggattacaaa atttgtgaaa gattgactgg tattcttaac tatgttgctc cttttacgct
     4921 atgtggatac gctgctttaa tgcctttgta tcatgctatt gcttcccgta tggctttcat
     4981 tttctcctcc ttgtataaat cctggttgct gtctctttat gaggagttgt ggcccgttgt
     5041 caggcaacgt ggcgtggtgt gcactgtgtt tgctgacgca acccccactg gttggggcat
     5101 tgccaccacc tgtcagctcc tttccgggac tttcgctttc cccctcccta ttgccacggc
     5161 ggaactcatc gccgcctgcc ttgcccgctg ctggacaggg gctcggctgt tgggcactga
     5221 caattccgtg gtgttgtcgg ggaaatcatc gtcctttcct tggctgctcg cctgtgttgc
     5281 cacctggatt ctgcgcggga cgtccttctg ctacgtccct tcggccctca atccagcgga
     5341 ccttccttcc cgcggcctgc tgccggctct gcggcctctt ccgcgtcttc gccttcgccc
     5401 tcagacgagt cggatctccc tttgggccgc ctccccgcct ggtaccttta agaccaatga
     5461 cttacaaggc agctgtagat cttagccact ttttaaaaga aaagggggga ctggaagggc
     5521 taattcactc ccaacgaaga caagatcacc tgcaggacag gcgcgccctg ctttttgctt
     5581 gtactgggtc tctctggtta gaccagatct gagcctggga gctctctggc taactaggga
     5641 acccactgct taagcctcaa taaagcttgc cttgagtgct tcaagtagtg tgtgcccgtc
     5701 tgttgtgtga ctctggtaac tagagatccc tcagaccctt ttagtcagtg tggaaaatct
     5761 ctagcacccg ggcgattaag gaaagggcta gatcattctt gaagacgaaa gggcctcgtg
     5821 atacgcctat ttttataggt taatgtcatg ataataatgg tttcttagac gtcaggtggc
     5881 acttttcggg gaaatgtgcg cggaacccct atttgtttat ttttctaaat acattcaaat
     5941 atgtatccgc tcatgagaca ataaccctga taaatgcttc aataatattg aaaaaggaag
     6001 agtatgagta ttcaacattt ccgtgtcgcc cttattccct tttttgcggc attttgcctt
     6061 cctgtttttg ctcacccaga aacgctggtg aaagtaaaag atgctgaaga tcagttgggt
     6121 gcacgagtgg gttacatcga actggatctc aacagcggta agatccttga gagttttcgc
     6181 cccgaagaac gttttccaat gatgagcact tttaaagttc tgctatgtgg cgcggtatta
     6241 tcccgtgttg acgccgggca agagcaactc ggtcgccgca tacactattc tcagaatgac
     6301 ttggttgagt actcaccagt cacagaaaag catcttacgg atggcatgac agtaagagaa
     6361 ttatgcagtg ctgccataac catgagtgat aacactgcgg ccaacttact tctgacaacg
     6421 atcggaggac cgaaggagct aaccgctttt ttgcacaaca tgggggatca tgtaactcgc
     6481 cttgatcgtt gggaaccgga gctgaatgaa gccataccaa acgacgagcg tgacaccacg
     6541 atgcctgtag caatggcaac aacgttgcgc aaactattaa ctggcgaact acttactcta
     6601 gcttcccggc aacaattaat agactggatg gaggcggata aagttgcagg accacttctg
     6661 cgctcggccc ttccggctgg ctggtttatt gctgataaat ctggagccgg tgagcgtggg
     6721 tctcgcggta tcattgcagc actggggcca gatggtaagc cctcccgtat cgtagttatc
     6781 tacacgacgg ggagtcaggc aactatggat gaacgaaata gacagatcgc tgagataggt
     6841 gcctcactga ttaagcattg gtaactgtca gaccaagttt actcatatat actttagatt
     6901 gatttaaaac ttcattttta atttaaaagg atctaggtga agatcctttt tgataatctc
     6961 atgaccaaaa tcccttaacg tgagttttcg ttccactgag cgtcagaccc cgtagaaaag
     7021 atcaaaggat cttcttgaga tccttttttt ctgcgcgtaa tctgctgctt gcaaacaaaa
     7081 aaaccaccgc taccagcggt ggtttgtttg ccggatcaag agctaccaac tctttttccg
     7141 aaggtaactg gcttcagcag agcgcagata ccaaatactg ttcttctagt gtagccgtag
     7201 ttaggccacc acttcaagaa ctctgtagca ccgcctacat acctcgctct gctaatcctg
     7261 ttaccagtgg ctgctgccag tggcgataag tcgtgtctta ccgggttgga ctcaagacga
     7321 tagttaccgg ataaggcgca gcggtcgggc tgaacggggg gttcgtgcac acagcccagc
     7381 ttggagcgaa cgacctacac cgaactgaga tacctacagc gtgagctatg agaaagcgcc
     7441 acgcttcccg aagggagaaa ggcggacagg tatccggtaa gcggcagggt cggaacagga
     7501 gagcgcacga gggagcttcc agggggaaac gcctggtatc tttatagtcc tgtcgggttt
     7561 cgccacctct gacttgagcg tcgatttttg tgatgctcgt caggggggcg gagcctatgg
     7621 aaaaacgcca gcaacgcggc ctttttacgg ttcctggcct tttgctggcc ttttgctcac
     7681 atgttctttc ctgcgttatc ccctgattct gtggataacc gtattaccgc ctttgagtga
     7741 gctgataccg ctcgccgcag ccgaacgacc gagcgcagcg agtcagtgag cgaggaagcg
     7801 gaagagcgcc caatacgcaa accgcctctc cccgcgcgtt ggccgattca ttaatgcagc
     7861 aagctcatgg ctgactaatt ttttttattt atgcagaggc cgaggccgcc tcggcctctg
     7921 agctattcca gaagtagtga ggaggctttt ttggaggcct aggcttttgc aaaaagctcc
     7981 ccgtggcacg acaggtttcc cgactggaaa gcgggcagtg agcgcaacgc aattaatgtg
     8041 agttagctca ctcattaggc accccaggct ttacacttta tgcttccggc tcgtatgttg
     8101 tgtggaattg tgagcggata acaatttcac acaggaaaca gctatgacat gattacgaat
     8161 ttcacaaata aagcattttt ttcactgcat tctagttgtg gtttgtccaa actcatcaat
     8221 gtatcttatc atgtctggat caactggata actcaagcta accaaaatca tcccaaactt
     8281 cccaccccat accctattac cactgccaat tacctgtggt ttcatttact ctaaacctgt
     8341 gattcctctg aattattttc attttaaaga aattgtattt gttaaatatg tactacaaac
     8401 ttagtagt
//
