
                                SEQUENCE LISTING

<110> Frendewey, David
      Droguett, Gustavo
      Gagliardi, Anthony
      Kuno, Junko
      Auerbach, Wojtek
      Valenzuela, David M.

<120> METHODS AND COMPOSITIONS FOR TARGETED
  GENETIC MODIFICATIONS AND METHODS OF USE
  
  

<130> 057766-463545

<150> US 62/017,582       
<151> 2014-06-26  

<150> US 62/017,627       
<151> 2014-06-26  

<160> 71

<170> FastSEQ for Windows Version 4.0

<210> 1
<211> 23
<212> DNA
<213> a target locus that is linked to a guide RNAArtifi

<220> 
<223> a target locus that is linked to a guide RNA
      (gRNA)
      

<220> 
<221> misc_feature   
<222> 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, 21
<223> n = A,T,C or G

<400> 1
gnnnnnnnnn nnnnnnnnnn ngg                                         23

<210> 2
<211> 80
<212> RNA
<213> Artificial Sequence

<220> 
<223> a guide RNA (gRNA)
      

<400> 2
guuuuagagc uagaaauagc aaguuaaaau aaggcuaguc cguuaucaac uugaaaaagu 60
ggcaccgagu cggugcuuuu                                             80

<210> 3
<211> 42
<212> RNA
<213> Artificial Sequence

<220> 
<223> a guide RNA (gRNA)
      

<400> 3
guuuuagagc uagaaauagc aaguuaaaau aaggcuaguc cg                    42

<210> 4
<211> 30
<212> RNA
<213> Artificial Sequence

<220> 
<223> a crRNA
      

<400> 4
guuuuagagc uagaaauagc aaguuaaaau                                  30

<210> 5
<211> 33
<212> RNA
<213> Artificial Sequence

<220> 
<223> a crRNA
      

<400> 5
guuuuagagc uagaaauagc aaguuaaaau aag                              33

<210> 6
<211> 26
<212> RNA
<213> Artificial Sequence

<220> 
<223> a crRNA
      

<400> 6
gaguccgagc agaagaagaa guuuua                                      26

<210> 7
<211> 12
<212> RNA
<213> Artificial Sequence

<220> 
<223> a tracrRNA

<400> 7
aaggcuaguc cg                                                     12

<210> 8
<211> 50
<212> RNA
<213> Artificial Sequence

<220> 
<223> a tracrRNA

<400> 8
aaggcuaguc cguuaucaac uugaaaaagu ggcaccgagu cggugcuuuu            50

<210> 9
<211> 23
<212> DNA
<213> Artificial Sequence

<220> 
<223> a target locus that is linked to a guide RNA
      (gRNA)
      

<220> 
<221> misc_feature   
<222> 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, 21
<223> n = A,T,C or G

<400> 9
gnnnnnnnnn nnnnnnnnnn ngg                                         23

<210> 10
<211> 23
<212> DNA
<213> Artificial Sequence

<220> 
<223> VG-1 gRNA target sequence
      

<400> 10
ccatgaatgc atttatggtg tgg                                         23

<210> 11
<211> 23
<212> DNA
<213> Artificial Sequence

<220> 
<223> VG-2 gRNA target sequence
      

<400> 11
ccgtggtgag aggcacaagt tgg                                         23

<210> 12
<211> 23
<212> DNA
<213> Artificial Sequence

<220> 
<223> VG-3 gRNA target sequence
      

<400> 12
gcaagcagct gggatgcagg tgg                                         23

<210> 13
<211> 20
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic sryTF1 primer

<400> 13
cgtggtgaga ggcacaagtt                                             20

<210> 14
<211> 19
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic sryTR1 primer

<400> 14
gagatcagca agcagctgg                                              19

<210> 15
<211> 22
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic sryTP1 probe

<400> 15
cccagcagaa tcccagcatg ca                                          22

<210> 16
<211> 18
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic sryTF2 primer

<400> 16
tggagggcca tgtcaagc                                               18

<210> 17
<211> 18
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic sryTR2 primer

<400> 17
acaagttggc ccagcaga                                               18

<210> 18
<211> 26
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic sryTP2 probe

<400> 18
tgaatgcatt tatggtgtgg tcccgt                                      26

<210> 19
<211> 20
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic sryTF3 primer

<400> 19
atgaatgcat ttatggtgtg                                             20

<210> 20
<211> 18
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic sryTR3 primer

<400> 20
aggtggaaaa gccttaca                                               18

<210> 21
<211> 23
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic sryTP3 probe

<400> 21
ccgtggtgag aggcacaagt tgg                                         23

<210> 22
<211> 19
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic sryTF4 primer

<400> 22
gtgtggtccc gtggtgaga                                              19

<210> 23
<211> 20
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic sryTR4 primer

<400> 23
agatcagcaa gcagctggga                                             20

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

<220> 
<223> Synthetic sryTP4 probe

<400> 24
aagttggccc agcagaatcc cagc                                        24

<210> 25
<211> 24
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic sryTF5 primer

<400> 25
catgcaaaat acagagatca gcaa                                        24

<210> 26
<211> 14
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic sryTR5 primer

<400> 26
ggaaaagcct taca                                                   14

<210> 27
<211> 15
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic sryTP5 probe

<400> 27
cagctgggat gcagg                                                  15

<210> 28
<211> 20
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic 648TUF primer

<400> 28
gatcagcaag cagctgggat                                             20

<210> 29
<211> 19
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic 648TUP probe

<400> 29
caggtggaaa agccttaca                                              19

<210> 30
<211> 73
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic

<400> 30
aattaccaca tcttttgcct attgccaccg cttgaggagt tgttggagaa gtctcattgg 60
aagaatcaga tga                                                    73

<210> 31
<211> 65
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic

<400> 31
aattaccaca tctttttgcc tattgtccaa atactggaga agtctcattg caacgaatca 60
gatga                                                             65

<210> 32
<211> 63
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic

<400> 32
aattaccaca tcttttgcct attgacaaaa tgttggagaa gtctcatggg aagaatcaaa 60
ttg                                                               63

<210> 33
<211> 90
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic

<400> 33
ctatcagata ggatatttta gagttttcat attgtatgga ggagttgttg gagaagtctc 60
attggaagaa tcagatgatg agatcttaat                                  90

<210> 34
<211> 70
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic

<400> 34
ctatcagata ggatatttta gagttgttgg agaagtctca tttggaagaa tcagatgatg 60
agatcttaat                                                        70

<210> 35
<211> 69
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic

<400> 35
ctatcagata ggatatttta gagttgttgg agaagtctca ttggaagaat cagatgatga 60
gatcttaat                                                         69

<210> 36
<211> 69
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic

<400> 36
ctatcacata ggatatttta gagttgttgg cgaagtctca ttggaagaat cagatgatga 60
gatcttaat                                                         69

<210> 37
<211> 69
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic

<400> 37
tcagatagga tattttagag ttttcatatt gtatggttat aggaggagtt gttggagaag 60
tctcattgg                                                         69

<210> 38
<211> 49
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic

<400> 38
tcagatagga tattttagag ttttcatatt gttggagaag tctcattgg             49

<210> 39
<211> 49
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic

<400> 39
tcagataggg tattttagag ttttcatatt gttggagaag tctcatggg             49

<210> 40
<211> 49
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic

<400> 40
tcccatagga tattttagag ttctcatatt gctgccgaag tctcattgc             49

<210> 41
<211> 38
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic

<400> 41
ttttagagtt tttcatattg ttgggagaag tctattgg                         38

<210> 42
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic KDM5D ZFN1 target sequence

<400> 42
ttaggtaggt agacagggat gttttctg                                    28

<210> 43
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic KDM5D ZFN2 target sequence

<400> 43
atccagtctc tgaaggaagc tctgacta                                    28

<210> 44
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic KDM5D ZFN3 target sequence

<400> 44
caaaagcttc agggggactc ttacactc                                    28

<210> 45
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic KDM5D ZFN4 target sequence

<400> 45
tttgagcagg ctacacagga gtatactt                                    28

<210> 46
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic KDM5D ZFN5 target sequence

<400> 46
aagcggtggc aataggcaaa agatgtgg                                    28

<210> 47
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic KDM5D ZFN6 target sequence

<400> 47
ctgaagtccc caagggagta tggagatg                                    28

<210> 48
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic KDM5D ZFN7 target sequence

<400> 48
agaaagcggt ggcaataggc aaaagatg                                    28

<210> 49
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic KDM5D ZFN8 target sequence

<400> 49
aagtccccaa gggagtatgg agatgccc                                    28

<210> 50
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic DDX3Y ZFN1 target sequence

<400> 50
actccaacga ctatgaccac tccgttca                                    28

<210> 51
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic DDX3Y ZFN2 target sequence

<400> 51
acagatcaga tgaagatgac tggtcaaa                                    28

<210> 52
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic DDX3Y ZFN3 target sequence

<400> 52
ctttcaagga aaaaaagaac aaaaccca                                    28

<210> 53
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic DDX3Y ZFN4 target sequence

<400> 53
ggtctgtgat aaggacagtt caggatgg                                    28

<210> 54
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic DDX3Y ZFN5 target sequence

<400> 54
taaatctgac tgagaatggg tagtagaa                                    28

<210> 55
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic DDX3Y ZFN6 target sequence

<400> 55
cagatggtcc aggagaggct ttgaaggc                                    28

<210> 56
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic DDX3Y ZFN7 target sequence

<400> 56
attgggcttc cctctggaat cacgagat                                    28

<210> 57
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic DDX3Y ZFN8 target sequence

<400> 57
tttcagtgat cgtggaagtg gatccagg                                    28

<210> 58
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic USP9Y ZFN1 target sequence

<400> 58
ctggtttgga aatcgtactg taaaagac                                    28

<210> 59
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic USP9Y ZFN2 target sequence

<400> 59
gcaaagaggt tgaggatttg gacatatt                                    28

<210> 60
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic USP9Y ZFN3 target sequence

<400> 60
gaggagttgt tggagaagtc tcattgga                                    28

<210> 61
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic USP9Y ZFN4 target sequence

<400> 61
atatgaacaa ggccaaggtg atgctcca                                    28

<210> 62
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic USP9Y ZFN5 target sequence

<400> 62
actcagaaga aggattagga atgctttg                                    28

<210> 63
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic USP9Y ZFN6 target sequence

<400> 63
atgcttagaa atgtatcagt tcatcttg                                    28

<210> 64
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic USP9Y ZFN7 target sequence

<400> 64
tccataagga ttttggaaaa agacacag                                    28

<210> 65
<211> 28
<212> DNA
<213> Artificial Sequence

<220> 
<223> Synthetic USP9Y ZFN8 target sequence

<400> 65
aggctgtgag tggatggaag tttgaaat                                    28

<210> 66
<211> 20
<212> RNA
<213> Artificial Sequence

<220> 
<223> Synthetic Kdm5dgA gRNA 1

<400> 66
uuugccgaau augcucucgu                                             20

<210> 67
<211> 20
<212> RNA
<213> Artificial Sequence

<220> 
<223> Synthetic Kdm5dgB gRNA 2

<400> 67
uugccgaaua ugcucucgug                                             20

<210> 68
<211> 20
<212> RNA
<213> Artificial Sequence

<220> 
<223> Synthetic Kdm5dgC gRNA 5

<400> 68
cgggcaucuc cauacucccu                                             20

<210> 69
<211> 20
<212> RNA
<213> Artificial Sequence

<220> 
<223> Synthetic Usp9ygA gRNA 1

<400> 69
uagcucguug uguagcaccu                                             20

<210> 70
<211> 20
<212> RNA
<213> Artificial Sequence

<220> 
<223> Synthetic Usp9ygB gRNA 1

<400> 70
uauaguuucu ucgggguaac                                             20

<210> 71
<211> 20
<212> RNA
<213> Artificial Sequence

<220> 
<223> Synthetic Usp9ygC gRNA 2

<400> 71
ggauacccuu cuauaggccc                                             20
