                         SEQUENCE LISTING

<110>  Whitehead Institute for Biomedical Research
       Young, Richard A
       Sigova, Alla A
       Abraham, Brian J
 
<120>  Transcription Factor Trapping by RNA in Gene Regulatory Elements

<130>  151262-00005

<150>  62266805
<151>  2015-12-14

<160>  54    

<170>  PatentIn version 3.5

<210>  1
<211>  30
<212>  RNA
<213>  Artificial Sequence

<220>
<223>  RNA oligonucleotide

<400>  1
cucuucucuc uuaaaauggc ugccugucug                                        30


<210>  2
<211>  30
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  2
gagaagagag aattttaccg acggacagac                                        30


<210>  3
<211>  30
<212>  RNA
<213>  Artificial Sequence

<220>
<223>  RNA oligonucleotide

<400>  3
cccgccuccc caggccuacg cgcugagcuc                                        30


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

<220>
<223>  DNA oligonucleotide

<400>  4
ctcttctctc ttaaaatggc tgcctgtctg                                        30


<210>  5
<211>  23
<212>  RNA
<213>  Mus musculus

<400>  5
ggugaauuuc uuccuggcag auc                                               23


<210>  6
<211>  20
<212>  RNA
<213>  Photinus pyralis

<400>  6
ggacaucacu uacgcugagu                                                   20


<210>  7
<211>  33
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Sequence used for trimming GRO-seq reads

<400>  7
tggaattctc gggtgccaag gaactccagt cac                                    33


<210>  8
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA adapter with 5rApp on 5' end and 3ddC on 3' end

<400>  8
tggaattctc gggtgccaag g                                                 21


<210>  9
<211>  65
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide with Sp-C18 (hexaethyleneglycol) after GAGTGT
       and after CACTCA


<220>
<221>  misc_feature
<222>  (2)..(5)
<223>  n is A, C, G, or T

<400>  9
annnnagatc ggaagagcgt cgtgtaggga aagagtgtca ctcaccttgg cacccgagaa       60

ttcca                                                                   65


<210>  10
<211>  53
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  10
aatgatacgg cgaccaccga gatctacact ctttccctac acgacgctct tcc              53


<210>  11
<211>  55
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  11
caagcagaag acggcatacg agatcgtgat cggtccttgg cacccgagaa ttcca            55


<210>  12
<211>  55
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  12
caagcagaag acggcatacg agatacatcg cggtccttgg cacccgagaa ttcca            55


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

<220>
<223>  DNA oligonucleotide

<400>  13
aatgatacgg cgaccacc                                                     18


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

<220>
<223>  DNA oligonucleotide

<400>  14
caagcagaag acggcatac                                                    19


<210>  15
<211>  30
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  15
ctctttccct acacgacgct cttccgatct                                        30


<210>  16
<211>  25
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  16
tggaattctc gggtgccaag gaccg                                             25


<210>  17
<211>  30
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  17
tcgctccccg gccatcttgg cggctggtgt                                        30


<210>  18
<211>  30
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  18
acaccagccg ccaagatggc cggggagcga                                        30


<210>  19
<211>  30
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  19
aggcagtggc tagctcacgt ccctggatcg                                        30


<210>  20
<211>  30
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  20
cgatccaggg acgtgagcta gccactgcct                                        30


<210>  21
<211>  30
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  21
cagacaggca gccattttaa gagagaagag                                        30


<210>  22
<211>  30
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  22
cccgcctccc caggcctacg cgctgagctc                                        30


<210>  23
<211>  30
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  23
gagctcagcg cgtaggcctg gggaggcggg                                        30


<210>  24
<211>  40
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  24
ggtgggaggg agactgccct ttgtcatgta gaaggagctt                             40


<210>  25
<211>  40
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  25
aagctccttc tacatgacaa agggcagtct ccctcccacc                             40


<210>  26
<211>  40
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  26
acgtgcaggg agactgccct ttgtcatgta gaagcagttg                             40


<210>  27
<211>  40
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  27
caactgcttc tacatgacaa agggcagtct ccctgcacgt                             40


<210>  28
<211>  30
<212>  RNA
<213>  Artificial Sequence

<220>
<223>  RNA oligonucleotide

<400>  28
cagacaggca gccauuuuaa gagagaagag                                        30


<210>  29
<211>  60
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA/RNA chimeric oligonucleotide (first 30 nucleotides are DNA, 
       second 30 nucleotides are RNA)

<400>  29
tcgctccccg gccatcttgg cggctggtgt cucuucucuc uuaaaauggc ugccugucug       60


<210>  30
<211>  60
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA/RNA chimeric oligonucleotide (first 30 nucleotides are DNA, 
       second 30 nucleotides are RNA)

<400>  30
acaccagccg ccaagatggc cggggagcga cucuucucuc uuaaaauggc ugccugucug       60


<210>  31
<211>  20
<212>  DNA
<213>  Mus musculus

<400>  31
gtactggctg ctcaaatgtc                                                   20


<210>  32
<211>  21
<212>  DNA
<213>  Mus musculus

<400>  32
gtgatgtagg tataattagc c                                                 21


<210>  33
<211>  21
<212>  DNA
<213>  Mus musculus

<400>  33
ttgcatgttg ttcctcggag c                                                 21


<210>  34
<211>  21
<212>  DNA
<213>  Mus musculus

<400>  34
ccatgtatgg ttacggggat c                                                 21


<210>  35
<211>  20
<212>  DNA
<213>  Mus musculus

<400>  35
gctgaaagac cacagctccc                                                   20


<210>  36
<211>  21
<212>  DNA
<213>  Mus musculus

<400>  36
ttgggtgttg agaataggtc c                                                 21


<210>  37
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  37
ggcaaacttt cggttcagtg g                                                 21


<210>  38
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  38
ttttcctccc ccaagacagg                                                   20


<210>  39
<211>  23
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  39
cccaccttgt gttcaaatgc tga                                               23


<210>  40
<211>  22
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  40
acgcttttct tctgccttct gc                                                22


<210>  41
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  41
aaccatcagg aaggcatcag g                                                 21


<210>  42
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  42
agctgatagg cactctgggt a                                                 21


<210>  43
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  43
gatctccgta caagcaggag g                                                 21


<210>  44
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  44
actcacctaa atctgcctgc c                                                 21


<210>  45
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  45
agatgccaga ggtcaccttt g                                                 21


<210>  46
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  46
caagaggatt tgtggggctc t                                                 21


<210>  47
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  47
tacacgtgtg cgccagaaga g                                                 21


<210>  48
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  48
tctaggagcc cagccccttt t                                                 21


<210>  49
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  49
ctccattgtc ctagggatgc c                                                 21


<210>  50
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  50
actttattca cggggctcca g                                                 21


<210>  51
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  51
actgacttcc tccaaggcca c                                                 21


<210>  52
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA oligonucleotide

<400>  52
tgaatgcttg gtccccagtg t                                                 21


<210>  53
<211>  9
<212>  PRT
<213>  Homo sapiens


<220>
<221>  MISC_FEATURE
<222>  (1)..(9)
<223>  X is any amino acid

<400>  53

Leu Xaa Xaa Leu Xaa Xaa Leu Xaa Leu 
1               5                   


<210>  54
<211>  8
<212>  PRT
<213>  Homo sapiens


<220>
<221>  MISC_FEATURE
<222>  (2)..(2)
<223>  X is V or I

<220>
<221>  MISC_FEATURE
<222>  (4)..(4)
<223>  X is any amino acid

<400>  54

Asp Xaa Glu Xaa Asn Pro Gly Pro 
1               5               


