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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCGGGATCCGGATCGGGCCTCAAGGACTTCCCCTACACCATCGGCGAGCCCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctcctcccttcccctcaccgctcgatcgggggcgcggatcgatttgatagatccccatgagatggggcggcggagatatgcgagagcgtgccg...

Basic information

species Oryza sativa
transcript LOC_Os01g60440.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60440.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AC218972.3_FGT001 (Zea mays), 5'ss of exon 1
CGCGGGATCCGGATCGGGCCTCAAGGACTTCCCCTACACCATCGGCGAGCCCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctcctcccttcccctcaccgctcgatcgggggcgcggatcgatttgatagatccccatgagatggggcggcggagatatgcgagagcgtgccg-
|||||||||||||||||| |||||||||||||||||||||||||||||||||||||| || || |||||||| ||||  ||||||||||| |||||||||||||||| ||| |      || |||      | | |         ||    | | |  |  |  ||   ||    | ||        |  |  ||   || 
CGCGGGATCCGGATCGGGACTCAAGGACTTCCCCTACACCATCGGCGAGCCCTACGCATCGGCTTGGGGCTCATGGAAACACCACCGCGGTACCTCCAAGgtacgct-tccgcatcattccacactttcacacccgatcgatcagtcccccttagatgtatcgttgttttgttttgtcgactgccgactggtacggttcgg

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G098078_T01 (Zea mays), 5'ss of exon 1
CGCGGGATCCGGATCGGGCCTCAAGGACTTCCCCTACACCATCGGCGAGCCCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc-------ctcccttcccctcacc-gctcgatcgggggcgcggatcgatttgatagatccccatgagatggggcggcggagatatgcgagagcgtgccg
|||||||||||||||||| ||||||||||||||||||||||| || ||| | ||||| ||||| ||||| || ||||| ||||||||||| ||||||||||||||||  |        || |  |  | |||| | |||||| |   | |   | ||| ||                | |   ||||  | |  ||   |        
CGCGGGATCCGGATCGGGGCTCAAGGACTTCCCCTACACCATTGGTGAGACATACGCATCCGCCTGGGGTTCATGGACACACCACCGCGGTACCTCCAAGgtacgcttccgcatcatttcaccccttcccacccgatcgatcagacccccccttggatgtgtcgttgttttgcttcgtcgactggcgcggttcggcagaa--------

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv13s0067g03110.t01 (Vitis vinifera), 5'ss of exon 1
CGCGGGATCCGGATCGGGCCTCAAGGACTTCCCCTACACCATCGGCGAGCCCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctcctcccttcccctcaccgctcgatcgggggcgcggatcgatttgatagatccccatgagatggggcggcggagatatgcg--agagcgtgccg
 || ||||| ||| | |||||||| ||  | ||||||| |||||||||||||||| | ||||| |||||||| ||||| |||   || |||||||| |||||    | |||   ||  |  || |   ||  |        | | | ||| |   |  |     ||   ||    ||  |   |||| |   || |  |   
AGCTGGATCTGGAGCCGGCCTCAAAGATCTGCCCTACAACATCGGCGAGCCCTACTCATCCGCCTGGGGCTCCTGGACTCACTCTCGTGGCACCTCTAAGgtcatttttccgagctctctatctcttatcagttttcatttctgct-gatatacgatgttttggtggtttgatttggttgttttatgggttggaactcgta-

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|88731434|gb|CI755047.1|CI755047
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|58674671|gb|CK063358.1|CK063358
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|88402539|gb|CI598766.1|CI598766
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|117245083|gb|CT843332.1|CT843332
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|88407897|gb|CI588926.1|CI588926
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: C-TACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|58695768|gb|CK084455.1|CK084455
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|58695973|gb|CK084660.1|CK084660
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|25804372|gb|CA760333.1|CA760333
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|88693922|gb|CI737960.1|CI737960
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|88396204|gb|CI595752.1|CI595752
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|58690937|gb|CK079624.1|CK079624
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|29636110|gb|CB641119.1|CB641119
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|88422483|gb|CI571465.1|CI571465
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|88427152|gb|CI586700.1|CI586700
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|29622867|gb|CB627878.1|CB627878
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|88721252|gb|CI744551.1|CI744551
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCA
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCA
EST: gi|58658376|gb|CK047056.1|CK047056
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGGCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|88364351|gb|CI612300.1|CI612300
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|58665117|gb|CK053803.1|CK053803
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|88401421|gb|CI585977.1|CI585977
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCAACGCGGCACCTCCAAG                         GATGATGGGTCGCC-GTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|88415228|gb|CI584051.1|CI584051
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|88391809|gb|CI603328.1|CI603328
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|29676650|gb|CB672925.1|CB672925
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|88391301|gb|CI595555.1|CI595555
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|88389249|gb|CI598047.1|CI598047
EST:     C-TACGCCTCCGGGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCCATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|88364900|gb|CI614518.1|CI614518
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|88410810|gb|CI578616.1|CI578616
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|88410217|gb|CI575815.1|CI575815
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|88395237|gb|CI611154.1|CI611154
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|88431589|gb|CI576780.1|CI576780
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
EST: gi|29623070|gb|CB628081.1|CB628081
EST:     CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAG                         GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG
genomic: CCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAG

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: 72 (upstream exon), 65 (downstream exon)
Score: 53

CGCGGGATCCGGATCGGGCCTCAAGGACTTCCCCTACACCATCGGCGAGCCCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctc ... ttttctgcagGATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACA




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCGGGATCCGGATCGGGCCTCAAGGACTTCCCCTACACCATCGGCGAGCCCTACGCCTCCGCGTGGGGCTCGTGGACGCACCACCGCGGCACCTCCAAGgtacgctctcctcccttcccctcaccgctcgatcgggggcgcggatcgatttgatagatccccatgagatggggcggcggagatatgcgagagcgtgccg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggggcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcggcg