                         SEQUENCE LISTING

<110>  The Board of Trustees of the Leland Stanford Junior 
       University
 
<120>  HIGH-THROUGHPUT PRECISION GENOME EDITING

<130>  1057458

<140>  PCT/US17/50690
<141>  2017-09-08

<150>  US 62/385,783
<151>  2016-09-09

<160>  41    

<170>  PatentIn version 3.5

<210>  1
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic ADE1 forward primer

<400>  1
cattggtggc cagaggtaaa g                                                 21


<210>  2
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic ADE1 reverse primer

<400>  2
gtgaggagtt acactggcga c                                                 21


<210>  3
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic ADE1 guide sequence (20 bp)

<400>  3
caagtgcaaa gattatgcta                                                   20


<210>  4
<211>  921
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic ADE1 sequence

<400>  4
atgtcaatta cgaagactga actggacggt atattgccat tggtggccag aggtaaagtt       60

agagacatat atgaggtaga cgctggtacg ttgctgtttg ttgctacgga tcgtatctct      120

gcatatgacg ttattatgga aaacagcatt cctgaaaagg ggatcctatt gaccaaactg      180

tcagagttct ggttcaagtt cctgtccaac gatgttcgta atcatttggt cgacatcgcc      240

ccaggtaaga ctattttcga ttatctacct gcaaaattga gcgaaccaaa gtacaaaacg      300

caactagaag accgctctct attggttcac aaacataaac taattccatt ggaagtaatt      360

gtcagaggct acatcaccgg atctgcttgg aaagagtacg taaaaacagg tactgtgcat      420

ggtttgaaac aacctcaagg acttaaagaa tctcaagagt tcccagaacc aatcttcacc      480

ccatcgacca aggctgaaca aggtgaacat gacgaaaaca tctctcctgc ccaggccgct      540

gagctggtgg gtgaagattt gtcacgtaga gtggcagaac tggctgtaaa actgtactcc      600

aagtgcaaag attatgctaa ggagaagggc atcatcatcg cagacactaa attcgaattc      660

ggtattgacg aaaagaccaa tgaaattatt ctagtggacg aggtgctaac gccagactcc      720

tctagattct ggaacggtgc ctcttataag gtaggagaat cccaagattc ttacgataag      780

caatttttaa gagactggct tactgctaat aagttgaacg gtgttaacgg cgtcaaaatg      840

ccccaagaca ttgtcgacag gacaagggcc aaatatatag aggcttatga aacattgaca      900

gggtctaaat ggtctcacta a                                                921


<210>  5
<211>  720
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic eGFP sequence

<400>  5
atggtgagca agggcgagga gctgttcacc ggggtggtgc ccatcctggt cgagctggac       60

ggcgacgtaa acggccacaa gttcagcgtg tccggcgagg gcgagggcga tgccacctac      120

ggcaagctga ccctgaagtt catctgcacc accggcaagc tgcccgtgcc ctggcccacc      180

ctcgtgacca ccctgaccta cggcgtgcag tgcttcagcc gctaccccga ccacatgaag      240

cagcacgact tcttcaagtc cgccatgccc gaaggctacg tccaggagcg caccatcttc      300

ttcaaggacg acggcaacta caagacccgc gccgaggtga agttcgaggg cgacaccctg      360

gtgaaccgca tcgagctgaa gggcatcgac ttcaaggagg acggcaacat cctggggcac      420

aagctggagt acaactacaa cagccacaac gtctatatca tggccgacaa gcagaagaac      480

ggcatcaagg tgaacttcaa gatccgccac aacatcgagg acggcagcgt gcagctcgcc      540

gaccactacc agcagaacac ccccatcggc gacggccccg tgctgctgcc cgacaaccac      600

tacctgagca cccagtccgc cctgagcaaa gaccccaacg agaagcgcga tcacatggtc      660

ctgctggagt tcgtgaccgc cgccgggatc actctcggca tggacgagct gtacaagtaa      720


<210>  6
<211>  45
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic Fusion linker sequence

<400>  6
ggtggaggag gctctggtgg aggcggtagc ggaggcggag ggtcg                       45


<210>  7
<211>  50
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic ADE1 homology arm

<400>  7
tagagtggca gaactggctg taaaactgta ctccaagtgc aaagattatg                  50


<210>  8
<211>  38
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic Donor sequence

<400>  8
gttcacactc actagagtga cgaacaatac acgttagc                               38


<210>  9
<211>  50
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic ADE1 homology arm

<400>  9
ctaaggagaa gggcatcatc atcgcagaca ctaaattcga attcggtatt                  50


<210>  10
<211>  1716
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic ADE2 sequence

<400>  10
atggattcta gaacagttgg tatattagga gggggacaat tgggacgtat gattgttgag       60

gcagcaaaca ggctcaacat taagacggta atactagatg ctgaaaattc tcctgccaaa      120

caaataagca actccaatga ccacgttaat ggctcctttt ccaatcctct tgatatcgaa      180

aaactagctg aaaaatgtga tgtgctaacg attgagattg agcatgttga tgttcctaca      240

ctaaagaatc ttcaagtaaa acatcccaaa ttaaaaattt acccttctcc agaaacaatc      300

agattgatac aagacaaata tattcaaaaa gagcatttaa tcaaaaatgg tatagcagtt      360

acccaaagtg ttcctgtgga acaagccagt gagacgtccc tattgaatgt tggaagagat      420

ttgggttttc cattcgtctt gaagtcgagg actttggcat acgatggaag aggtaacttc      480

gttgtaaaga ataaggaaat gattccggaa gctttggaag tactgaagga tcgtcctttg      540

tacgccgaaa aatgggcacc atttactaaa gaattagcag tcatgattgt gagatctgtt      600

aacggtttag tgttttctta cccaattgta gagactatcc acaaggacaa tatttgtgac      660

ttatgttatg cgcctgctag agttccggac tccgttcaac ttaaggcgaa gttgttggca      720

gaaaatgcaa tcaaatcttt tcccggttgt ggtatatttg gtgtggaaat gttctattta      780

gaaacagggg aattgcttat taacgaaatt gccccaaggc ctcacaactc tggacattat      840

accattgatg cttgcgtcac ttctcaattt gaagctcatt tgagatcaat attggatttg      900

ccaatgccaa agaatttcac atctttctcc accattacaa cgaacgccat tatgctaaat      960

gttcttggag acaaacatac aaaagataaa gagctagaaa cttgcgaaag agcattggcg     1020

actccaggtt cctcagtgta cttatatgga aaagagtcta gacctaacag aaaagtaggt     1080

cacataaata ttattgcctc cagtatggcg gaatgtgaac aaaggctgaa ctacattaca     1140

ggtagaactg atattccaat caaaatctct gtcgctcaaa agttggactt ggaagcaatg     1200

gtcaaaccat tggttggaat catcatggga tcagactctg acttgccggt aatgtctgcc     1260

gcatgtgcgg ttttaaaaga ttttggcgtt ccatttgaag tgacaatagt ctctgctcat     1320

agaactccac ataggatgtc agcatatgct atttccgcaa gcaagcgtgg aattaaaaca     1380

attatcgctg gagctggtgg ggctgctcac ttgccaggta tggtggctgc aatgacacca     1440

cttcctgtca tcggtgtgcc cgtaaaaggt tcttgtctag atggagtaga ttctttacat     1500

tcaattgtgc aaatgcctag aggtgttcca gtagctaccg tcgctattaa taatagtacg     1560

aacgctgcgc tgttggctgt cagactgctt ggcgcttatg attcaagtta tacaacgaaa     1620

atggaacagt ttttattaaa gcaagaagaa gaagttcttg tcaaagcaca aaagttagaa     1680

actgtcggtt acgaagctta tctagaaaac aagtaa                               1716


<210>  11
<211>  50
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic ADE2 homology arm

<400>  11
tggaaatgtt ctatttagaa acaggggaat tgcttattaa cgaaattgcc                  50


<210>  12
<211>  50
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic ADE2 homology arm

<400>  12
tgaaggcctc acaactctgg acattatacc attgatgctt gcgtcacttc                  50


<210>  13
<211>  18
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic Guide 3 0.74

<400>  13
attaacgaaa ttgcccca                                                     18


<210>  14
<211>  1338
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic Retron Ec86 sequence

<400>  14
taactatgat aagattccgt atgcgcaccc ttagcgagag gtttatcatt aaggtcaacc       60

tctggatgtt gtttcggcat cctgcattga atctgagtta ctgtctgttt tccttgttgg      120

aacggagagc atcgcctgat gctctccgag ccaaccagga aacccgtttt ttctgacgta      180

agggtgcgca actttcatga aatccgctga atatttgaac acttttagat tgagaaatct      240

cggcctacct gtcatgaaca atttgcatga catgtctaag gcgactcgca tatctgttga      300

aacacttcgg ttgttaatct atacagctga ttttcgctat aggatctaca ctgtagaaaa      360

gaaaggccca gagaagagaa tgagaaccat ttaccaacct tctcgagaac ttaaagcctt      420

acaaggatgg gttctacgta acattttaga taaactgtcg tcatctcctt tttctattgg      480

atttgaaaag caccaatcta ttttgaataa tgctaccccg catattgggg caaactttat      540

actgaatatt gatttggagg attttttccc aagtttaact gctaacaaag tttttggagt      600

gttccattct cttggttata atcgactaat atcttcagtt ttgacaaaaa tatgttgtta      660

taaaaatctg ctaccacaag gtgctccatc atcacctaaa ttagctaatc taatatgttc      720

taaacttgat tatcgtattc agggttatgc aggtagtcgg ggcttgatat atacgagata      780

tgccgatgat ctcaccttat ctgcacagtc tatgaaaaag gttgttaaag cacgtgattt      840

tttattttct ataatcccaa gtgaaggatt ggttattaac tcaaaaaaaa cttgtattag      900

tgggcctcgt agtcagagga aagttacagg tttagttatt tcacaagaga aagttgggat      960

aggtagagaa aaatataaag aaattagagc aaagatacat catatatttt gcggtaagtc     1020

ttctgagata gaacacgtta ggggatggtt gtcatttatt ttaagtgtgg attcaaaaag     1080

ccataggaga ttaataactt atattagcaa attagaaaaa aaatatggaa agaacccttt     1140

aaataaagcg aagacctaat ggtcttcgtt ttaaaactaa agctcatagg ttgaaaaatt     1200

gagcacttct tcgtccaacc agttatttag ttcctgcaat cgtttctgca ggggcatcaa     1260

ttcgtttctt acgaatacct tgctagcctt ctccacatcc ccaaaccccc cgacattatt     1320

aggcataatt cccatcat                                                   1338


<210>  15
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic Plasmid start sequence

<400>  15
taactatgat aagattccgt                                                   20


<210>  16
<211>  12
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic Inverted repeat sequence

<400>  16
tgcgcaccct ta                                                           12


<210>  17
<211>  12
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic Second inverted repeat

<400>  17
taagggtgcg ca                                                           12


<210>  18
<211>  82
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic msr locus

<400>  18
atgcgcaccc ttagcgagag gtttatcatt aaggtcaacc tctggatgtt gtttcggcat       60

cctgcattga atctgagtta ct                                                82


<210>  19
<211>  86
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic msd locus

<400>  19
tctgagttac tgtctgtttt ccttgttgga acggagagca tcgcctgatg ctctccgagc       60

caaccaggaa acccgttttt tctgac                                            86


<210>  20
<211>  41
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic Replaceable region

<400>  20
tgttggaacg gagagcatcg cctgatgctc tccgagccaa c                           41


<210>  21
<211>  963
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic Ec86 reverse transcriptase (optimized)

<400>  21
atgaaatccg ctgaatattt gaacactttt agattgagaa atctcggcct acctgtcatg       60

aacaatttgc atgacatgtc taaggcgact cgcatatctg ttgaaacact tcggttgtta      120

atctatacag ctgattttcg ctataggatc tacactgtag aaaagaaagg cccagagaag      180

agaatgagaa ccatttacca accttctcga gaacttaaag ccttacaagg atgggttcta      240

cgtaacattt tagataaact gtcgtcatct cctttttcta ttggatttga aaagcaccaa      300

tctattttga ataatgctac cccgcatatt ggggcaaact ttatactgaa tattgatttg      360

gaggattttt tcccaagttt aactgctaac aaagtttttg gagtgttcca ttctcttggt      420

tataatcgac taatatcttc agttttgaca aaaatatgtt gttataaaaa tctgctacca      480

caaggtgctc catcatcacc taaattagct aatctaatat gttctaaact tgattatcgt      540

attcagggtt atgcaggtag tcggggcttg atatatacga gatatgccga tgatctcacc      600

ttatctgcac agtctatgaa aaaggttgtt aaagcacgtg attttttatt ttctataatc      660

ccaagtgaag gattggttat taactcaaaa aaaacttgta ttagtgggcc tcgtagtcag      720

aggaaagtta caggtttagt tatttcacaa gagaaagttg ggataggtag agaaaaatat      780

aaagaaatta gagcaaagat acatcatata ttttgcggta agtcttctga gatagaacac      840

gttaggggat ggttgtcatt tattttaagt gtggattcaa aaagccatag gagattaata      900

acttatatta gcaaattaga aaaaaaatat ggaaagaacc ctttaaataa agcgaagacc      960

taa                                                                    963


<210>  22
<211>  6
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic Sequence between second inverted repeat sequence and 
       Ec86 reverse transcriptase sequence

<400>  22
actttc                                                                   6


<210>  23
<211>  179
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic Sequence located 3' of EC86 reverse transcriptase 
       sequence

<400>  23
tggtcttcgt tttaaaacta aagctcatag gttgaaaaat tgagcacttc ttcgtccaac       60

cagttattta gttcctgcaa tcgtttctgc aggggcatca attcgtttct tacgaatacc      120

ttgctagcct tctccacatc cccaaacccc ccgacattat taggcataat tcccatcat       179


<210>  24
<211>  669
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic Cassette sequence

<400>  24
gttcctggcc ttttgctggc cttttgctct taattaagta tatgtgttat gtagtatact       60

ctttcttcaa caattaaata ctctcggtag ccaagttggt ttaaggcgca agactgtaat      120

ttatcactac gaaatcttga gatcgggcgt tcgactcgcc cccgggagag atggccggca      180

tggtcccagc ctcctcgctg gcgccggctg ggcaacacct tcgggtggcg aatgggactt      240

tatgcgcacc cttagcgaga ggtttatcat taaggtcaac ctctggatgt tgtttcggca      300

tcctgcattg aatctgagtt actgtctgtt ttcctctctg acaattactt ccaatggaat      360

tagtttatgt ttgtgaacca atagagatca gtcttctagt tgcgttttgt actttggttc      420

gctcaatttt gcaggaggaa acccgttttt tctgacgtaa gggtgcgcag tttgtgaacc      480

aatagagagg ttttagagct agaaatagca agttaaaata aggctagtcc gttatcaact      540

tgaaaaagtg gcaccgagtc ggtgcttttt ttattttttg tcactattgt tatgtaaaat      600

gccacctctg acagtatgga acgcaaactt ctgtctagtg gataggaact cttgttgttc      660

tttgctagc                                                              669


<210>  25
<211>  9
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic Start sequence (5' of Pci1-Up)

<400>  25
gttcctggc                                                                9


<210>  26
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic Pci1-Up sequence (primer binding site)

<400>  26
cttttgctgg ccttttgctc                                                   20


<210>  27
<211>  8
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic Sequence between Pci1-Up and tRNA-Tyr

<400>  27
ttaattaa                                                                 8


<210>  28
<211>  132
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic tRNA-Tyr

<400>  28
gtatatgtgt tatgtagtat actctttctt caacaattaa atactctcgg tagccaagtt       60

ggtttaaggc gcaagactgt aatttatcac tacgaaatct tgagatcggg cgttcgactc      120

gcccccggga ga                                                          132


<210>  29
<211>  72
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic HDV ribozyme

<400>  29
gatggccggc atggtcccag cctcctcgct ggcgccggct gggcaacacc ttcgggtggc       60

gaatgggact tt                                                           72


<210>  30
<211>  121
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic msd locus

<400>  30
ctctgacaat tacttccaat ggaattagtt tatgtttgtg aaccaataga gatcagtctt       60

ctagttgcgt tttgtacttt ggttcgctca attttgcagg aggaaacccg ttttttctga      120

c                                                                      121


<210>  31
<211>  23
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic msd locus (portion overlaping the vector, not including
       donor)

<400>  31
tctgagttac tgtctgtttt cct                                               23


<210>  32
<211>  94
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic Vector sequence

<400>  32
atgcgcaccc ttagcgagag gtttatcatt aaggtcaacc tctggatgtt gtttcggcat       60

cctgcattga atctgagtta ctgtctgttt tcct                                   94


<210>  33
<211>  100
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic Donor DNA1

<400>  33
ctctgacaat tacttccaat ggaattagtt tatgtttgtg aaccaataga gatcagtctt       60

ctagttgcgt tttgtacttt ggttcgctca attttgcagg                            100


<210>  34
<211>  34
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic Constant synthesis sequence

<400>  34
aggaaacccg ttttttctga cgtaagggtg cgca                                   34


<210>  35
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic Guide2 sequence

<400>  35
gtttgtgaac caatagagag                                                   20


<210>  36
<211>  82
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic sgRNA coding sequence

<400>  36
gttttagagc tagaaatagc aagttaaaat aaggctagtc cgttatcaac ttgaaaaagt       60

ggcaccgagt cggtgctttt tt                                                82


<210>  37
<211>  75
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic SNR52 terminator

<400>  37
tttatttttt gtcactattg ttatgtaaaa tgccacctct gacagtatgg aacgcaaact       60

tctgtctagt ggata                                                        75


<210>  38
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic RPR1 terminator

<400>  38
ggaactcttg ttgttcttt                                                    19


<210>  39
<211>  6
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic End sequence (3' of RPR1 terminator)

<400>  39
gctagc                                                                   6


<210>  40
<211>  15
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic Partial ADE1 amino acid sequence (N-terminal to edit 
       site)

<400>  40

Pro Ala Lys Leu Ser Glu Pro Lys Tyr Lys Thr Gln Leu Glu Asp 
1               5                   10                  15  


<210>  41
<211>  17
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic Partial ADE1 amino acid sequence (C-terminal to edit 
       site)

<400>  41

Ser Leu Leu Val His Lys His Lys Leu Ile Pro Leu Glu Val Ile Val 
1               5                   10                  15      


Arg 
    


