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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGATCTGGAAAACCCATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagtttttgctcaattcaggtgcactgctatggaaattcatagttaagtgcatgttcttttatcagtacggatggtggctaaacttatatttctcttctgataatattaataatgtcttccgatgtttattccag

Basic information

species Oryza sativa
transcript LOC_Os06g37180.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 6
CCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGATCTGGAAAACCCATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagtttttgctcaattcaggtgcactgctatggaa-attcatagttaagtgcatgttct--------------tttatcagtacggat-----ggtggc--taaacttatatttctcttctgataatat-taataatgtcttccgatgtttattccag
||||||||||| |||||||||||||||||||||||||| ||||||||||| ||||| |||||||| || || || || || |||||||||||||||||||||||||  || ||   |||| |  | ||||| |  ||   |||| || ||||||||||| |              ||||  ||||  |||      | |||  ||||   ||   ||  |  | | | | | |||| ||||  || ||| ||| || |||
CCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTACCTGAAGCCTACTTGGATATCTCTGgtaagtaatttct-ggttcaagcacgctgctctacaatgctcatggtgaagtgcatgttgtggagagtagtaggttttagaagtattgattgattagcggcattaaatcaatgagtccatctttaaagtttgtaatcatgtactctgat-tttgttgcag

upper sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G094497_T02 (Zea mays), 5'ss of exon 5
CCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGATCTGGAAAACCCATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagtttttgctcaattcaggtgcactgctatggaa-attcatagttaagtgcatgttct--------------tttatcagtac-ggatggt--ggctaaacttatatttctcttctgataatat-taataatgtcttccgatgtttattccag
|||||||||||||||||||||||||||||||||||||| ||||||||||| ||||| |||||||| || || ||||| || |||||||||||||||||||||||||  || ||   |||  |    ||||| |  || | |||| |||||||||||| | |              ||||   |||  || |  |   | ||||   ||   ||  |  | | | | | |||  ||||  || ||| |||  | |||
CCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTGCCCGAAGCCTACTTGGATATCTCTGgtaagtaatttct-ggttctagcatgctgctctacaatactcatggttaagtgcatgctgtcgtgcagagtaggttttagacgtattggttaattgagttaaatcaatgagtccatctttaaattttgtaaatatgtactctgat-tttgctgcag

upper sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA09G38110.2 (Glycine max), 5'ss of exon 6
CCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGATCTGGAAAACCCATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagtttttgctcaattcaggtgcactgctatggaaattcatagttaagtgcatgttcttttatcagtacggatggtggctaaacttatatttctcttctgataatattaataatgtcttccgatgtttattccag
|| || ||| | || |||||||| ||||| || ||||| ||||||||||| ||||||||||| ||||| || || || ||||| |||||||| || || ||||     || ||    || || |    | |||| | ||  ||  |||  |     || ||| ||   ||       |   | |                                                     
CCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAGgtataaaatttct----tctgggga---ggtatgaatatgtatgtttatctttgccttttttaat--atatcccccataattcag----------------------------------------------------

upper sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA18G48280.1 (Glycine max), 5'ss of exon 6
CCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGATCTGGAAAACCCATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagtttttgctcaattcaggtgcactgctatggaaattcatagttaagtgcatgttcttttatcagtacggatggtggctaaacttatatttctcttctgataatattaataatgtcttccgatgtttattccag
 | || ||| | || |||||||| ||||| || ||||| ||||||||||| ||||||||||| ||||| ||||| || ||||| |||||||| || || ||||  |  || ||    || || |    | | || | || |||  ||   |   ||   |||||    |       ||   | |                                                     
-CAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATTTTACCTGAGGCTTACTTGGACATATCAGGtatataatttct----tctgggga---ggtctgaatatgcatgtttt--tctttgcctttttaaatattttccctgtaattcagg---------------------------------------------------

upper sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA20G24070.1 (Glycine max), 5'ss of exon 7
CCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGATCTGGAAAACCCATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagtttttgctcaattcaggtgcactgctatggaaattcatagttaagtgcatgttcttttatcagtacggatggtggctaaacttatatttctcttctgataatattaataatgtcttccgatgtttattccag
||||||||||| || |||||||| ||||| |||||||| ||||||||||| ||||||||||| ||||| ||||| || ||||| ||| ||||||| |||||||    |||    |||||   |||| || | |  || |  ||  | | |||   ||| |||   |   |   ||  |  | | | ||                                                 
CCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGTTCTGGAAAACCAATTGATAATGGTCCACCAATTTTACCTGAGGCTTACCTGGATATTTCTGgta----ttta---aattcctttgcagtgttctacaattgtatgttgatgtgtgagttttttccccctaat--atcttcccaatatttcag----------------------------------------------

upper sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA10G42940.2 (Glycine max), 5'ss of exon 6
CCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGATCTGGAAAACCCATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagtttttgctcaattcaggtgcactgctatggaa-attcatagttaagtgcatgttcttttatcagtacggatggtggctaaacttatatttctcttctgataatattaataatgtcttccgatgtttattccag
||||||||||| || |||||||| ||||| |||||||| ||||||||||| ||||||||||| ||||| ||||| || ||||| ||| ||||||| |||||||  |||    ||  ||   |||  || | || | |  || ||   | | |   |   |  | ||   | |  |   || |                                                        
CCTGTCTCACTAGACATGCTTGGACGCATATTTAATGGCTCTGGAAAACCAATTGATAATGGTCCACCAATTTTACCTGAGGCTTACCTGGATATTTCTGgta--tttaacttcctttgcagtgttctacaattgtatgttgatgtgtgaatttttaccccctaatatcttcccaatatgtcag------------------------------------------------------

upper sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 5'ss of exon 6
CCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGATCTGGAAAACCCATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagtttttgctcaattcaggtgcactgctatggaaattcatagttaagtgcatgttcttttatcagtacggatggtggctaaacttatatttctcttctgataatattaataatgtcttccgatgtttattccag
||||| ||| | || |||||||||||||| ||||| || || ||||| || |||||||||||||| |||||| ||||||| || ||| | ||||| || ||| ||      || |    |     | | | || || ||   |     | ||    ||| ||| |   ||   |||     |   ||||||||  |                                         
CCTGTATCATTGGACATGCTTGGGCGCATATTTAACGGTTCAGGAAAGCCGATTGATAATGGCCCTCCTATTCTGCCAGAAGCATACCTTGATATTTCAGgtgagca---actaagaggacaattatt-ccattgagatctctgaagcaatgt---ttcatttgttcttaaaaatgtcaatt--ccttatattgatag---------------------------------------

upper sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 5'ss of exon 6
CCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGATCTGGAAAACCCATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagtttttgctcaattcaggtgcactgctatggaaattcatagttaagtgcatgttcttttatcagtacggatggtggctaaacttatatttctcttctgataatattaataatgtcttccgatgtttattccag
||||| ||| | || |||||||| ||||| ||||| || || ||||| || |||||||||||||| ||||||||||||||||| ||| | ||||| |||||| ||  ||  ||    ||| ||  | ||   |   ||   | ||  ||     |||| ||  ||   | |||  | |   |    |||||                                              
CCTGTGTCATTGGACATGCTTGGCCGCATATTTAACGGCTCGGGAAAGCCAATTGATAATGGCCCTCCTATTTTGCCAGAGGCATACCTTGATATTTCTGgtgagcattgact-gcctcaagtcaattgtactctgaagaga-aggaaaaaatctgtt-ttaaattgtttcggtcgataatt---tttatag---------------------------------------------

upper sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT4G38510.5 (Arabidopsis thaliana), 5'ss of exon 7
CCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGATCTGGAAAACCCATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagtttttgctcaattcaggtgcactgctatggaaattcatagttaagtgcatgttcttttatcagtacggatggtggctaaacttatatttctcttctgataatattaataatgtcttccgatgtttattccag
||||| ||  | ||||||||||| ||||| || ||||| || || || |||||||| || || |||||||| ||||| ||||| ||||||||||| |||||| || |  |      |   |   ||    ||    |  ||||| | ||   ||              ||    |     ||| |||| | ||||||                                        
CCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGTTCAGGGAAGCCCATTGACAACGGTCCACCTATATTGCCTGAGGCGTACTTGGATATTTCTGgtgagctgctttagcctcttgtcacataattac--tatctcataataaaacacaca----------gatataatt-----ctagacttttgtttctccag-------------------------------------

upper sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 5'ss of exon 6
CCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGATCTGGAAAACCCATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagtttttgctcaattcaggtgcactgctatggaaattcatagttaagtgcatgttcttttatcagtacggatggtggctaaacttatatttctcttctgataatattaataatgtcttccgatgtttattccag
||||| ||||| ||||||||||| |||||||||||||| |||||||||||||||||||||||||| || ||| |||||||||| ||| | ||||| |||||| |||  |      |      ||   |  ||   |||   |  |  |||   || || | ||||| | |   ||  |    |||||  |  || ||||   |||                                
CCTGTATCACTGGATATGCTTGGCCGCATTTTTAATGGTTCTGGAAAACCCATTGATAATGGCCCCCCAATTCTGCCAGAGGCTTACCTAGATATTTCTGgtcagtaatgctaggaagataatgatttattaccaaaagctagggaaaag---attttatgttatctggatatataat----aaactcttccttgtctttc-atag-------------------------------

upper sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 5'ss of exon 6
CCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGATCTGGAAAACCCATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagtttttgctcaattcaggtgcactg-ctatggaaattcatagttaagtgcatgttcttttatcagta-cggatggtggctaaacttatatttctcttctgataatattaataatgtcttccgatgtttattccag
||||||||| | |||||||||||||| || |||||||| || || ||||||||||||||||| || ||||| ||||||||||| ||||||||||| |||||| |||||||    |  |    |    |  | ||  ||| |||    | |      |   ||  | ||||  | |||  ||  ||  ||| |  ||  ||| |   |                                
CCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGTTCAGGGAAACCCATTGATAATGGGCCTCCTATATTGCCAGAGGCTTACTTGGATATTTCTGgtgagttttttaggaggtggtattatttaaccattaaaactcacctctgaactttagagtttacaacagtggcagatcctg--tactctttttctttccttttttcag-------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|29633929|gb|CB638938.1|CB638938
EST:     CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTG                         GAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
genomic: CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagttttt ... tttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
EST: gi|42591928|gb|CK738414.1|CK738414
EST:     CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTG                         GAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
genomic: CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagttttt ... tttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
EST: gi|2309809|gb|C25964.1|C25964
EST:     CATTGATAATGGCCCACCTATTTTGCCAGAGGC-TACTTGGATATCTCTG                         GAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
genomic: CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagttttt ... tttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
EST: gi|428226|gb|D24374.1|D24374
EST:     CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTG                         GAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
genomic: CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagttttt ... tttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
EST: gi|29668004|gb|CB664279.1|CB664279
EST:     CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTG                         GAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
genomic: CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagttttt ... tttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
EST: gi|29641774|gb|CB646781.1|CB646781
EST:     CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTG                         GAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
genomic: CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagttttt ... tttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
EST: gi|33793646|gb|CF322707.1|CF322707
EST:     CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTG                         GAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
genomic: CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagttttt ... tttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
EST: gi|56550172|gb|CX056276.1|CX056276
EST:     CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTG                         GAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
genomic: CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagttttt ... tttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
EST: gi|29631355|gb|CB636364.1|CB636364
EST:     CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTG                         GAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
genomic: CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagttttt ... tttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
EST: gi|29683215|gb|CB679490.1|CB679490
EST:     CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTG                         GAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
genomic: CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagttttt ... tttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
EST: gi|29630856|gb|CB635865.1|CB635865
EST:     CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTG                         GAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
genomic: CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagttttt ... tttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
EST: gi|29617703|gb|CB622715.1|CB622715
EST:     CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTG                         GAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
genomic: CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagttttt ... tttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
EST: gi|29675287|gb|CB671562.1|CB671562
EST:     CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTG                         GAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
genomic: CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagttttt ... tttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
EST: gi|29669854|gb|CB666129.1|CB666129
EST:     CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTG                         GAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
genomic: CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagttttt ... tttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
EST: gi|29630446|gb|CB635455.1|CB635455
EST:     CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTG                         GAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
genomic: CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagttttt ... tttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
EST: gi|29681069|gb|CB677344.1|CB677344
EST:     CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTG                         GAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
genomic: CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagttttt ... tttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
EST: gi|29642143|gb|CB647150.1|CB647150
EST:     CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTG                         GAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA
genomic: CATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagttttt ... tttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 70 (upstream exon), 75 (downstream exon)
Score: 120

CCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGATCTGGAAAACCCATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACTTGGATATCTCTGgtaagttttt ... tttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAACAGGGATATCAACCATTGATGTCATGAACTCCATTGCTCGAGGCCAAAA




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