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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagtctaaaatgtctgtccaactgcatggctctcttgcagtccaactatctcattgggattcttatcgatctatatcctgtcag

Basic information

species Oryza sativa
transcript LOC_Os11g33240.2
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 17
TGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagtctaaaa--tgtctgtccaactgcatg-gctctcttgcagtccaactatctcattgggattcttatcgatctatatcctgtcag
||| || |||||||||||||| |||||||| || ||||| ||| ||||||| |||||||||||  ||||| | ||||| |||||||||||||||||||||||  ||||  ||  | ||| || || |||||   || ||||| ||| |||| || | |     | | ||  || |  |           
TGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTTTCCAACTGgtccgtctggaacctttctatctaattgcatttactttcttg-agttcaacaattttaaaaataatatt-ccgttgcag----------

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 15
TGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagtctaaaa--tgtctgtccaactgcatg-gctctcttgcagtccaactatctcat-tgggattcttatcgatctatatcctgtcag
||| || |||||||||||||| |||| ||| || ||||| |||  ||| || |||||||||||  ||||||| ||||| |||||||| ||||||||||||||  ||||| |   | |||||| || |||||  ||| ||||| |||  ||| || | |  |  ||| ||        || |         
TGGATTTGGTCATGGAGTTCTGCGTAGGACGGACCCACGGTATCTATGCCAAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTGgtccgtctagatcctctctgtctaattgcatttgctttcttg-agttgaacgattttagatacgatactccgtacgttacag--------

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G063851_T05 (Zea mays), 5'ss of exon 2
TGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagtctaaaatgtct-gtccaactgcatggctctcttgcagtccaactatctcattgggattcttatcgatctatatcctgtcag
||| || |||||||||||||| ||||||||||| ||||| ||| ||||||| |||||||||||  ||||| | |||||  ||||||||||||||||| ||||  ||||  ||  | |  || || | |||     | ||  |||  |||  | | |   | | |||| | | |  |           
TGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTTTCCAATTGgtccgtctggaaccttttatctaatttcatttacttttttgagttgaacggttttaaatgtaatctt-tggttacag----------

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA08G16770.1 (Glycine max), 5'ss of exon 16
TGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgt--------------tagtctaaaatgtctgtccaactgcatggctctcttgcagtccaactat--ctcattgggattcttatcgatctatatcctgtcag---------------
||| |  || ||||| ||| ||||  |||| |||||| |||| ||||||||||||||||||||||||||| | |||||| | ||||||  ||||||  ||||              || |  || ||     |     || |  ||| ||||||    || | |   |||| | | | | | ||   |  || | ||                    
TGGATATGGACATGGGGTTTTACGCCAGACAGATCCAAGATACACATGTCAGAGGGAGTTTGCTTTGAAGCATTTGCCTAATGATCCATATTTCCAGTTGgtaatcacttatttcctaattcaagattgtgttttctttggagtgctttcttgcgacacagccaaagctcacttgtaatttaatttcttcatgttctaatgcaactgaccctttcag

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA15G42300.2 (Glycine max), 5'ss of exon 16
TGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagtctaaaatgtctgtc-caactgcatggctctcttgcagt-----ccaactatctcattgggattcttatcgatctatatcctgtcag
||| |  || ||||| ||| ||||  |||| |||||| |||| ||||||||||||||||||||||||||| | |||||| | ||||||  |||||| ||||| |      | |  || |  |||     ||  |   ||| |||     |   | |            ||   |  | ||  | ||| ||||
TGGATATGGACATGGGGTTTTACGCCAGACAGATCCAAGATACACATGTCAGAGGGAGTTTGCTTTGAAGCATTTGCCTAATGATCCATATTTCCAGCTGgtaatcacttatttcctatttcaagattgtgttttctttggagtgctttcttgcgacacagccaaagctcacttgtaactg-accctttcag

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 16
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 16
TGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagt-ctaaaatgtctgtccaactgcatggctctcttgcagtccaactatctcattgggattcttatcgatcta---tatcctgtcag
||| || || ||||||||| | ||||| || |||||| ||||||  ||||| ||||||||||| |||||| |||||||||| |||||||| ||||| ||||||| | || |||   |||   ||   ||  | | | ||  | |       ||   ||     |      ||  |    || | |  |||
TGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGTTCCAGCTGgttattacttaaagccctgattaaagacaatggtttgtt-tatttttgtgttccagttcatccttgagctgacttggtttaccattacag

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|163929405|gb|EG713830.1|EG713830
EST:     AGAGGGAGTTTGCTTTGAAG-ACTTGCCTGAGGATCCACTTTTCCAACTG                         GTCTCCAAGTTGTATGAAGTTGTGCCTCCAATCCTCACTGAGCTTGGCAAG
genomic: AGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagtctaa ... atcctgtcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCAATCCTCACTGAGCTTGGCAAG
EST: gi|86504183|gb|CI146816.1|CI146816
EST:     AGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTG                         GTCTCCAAGTTGTATGAAGTTGTGCCTCCAATCCTCACTGAGCTTGGCAAG
genomic: AGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagtctaa ... atcctgtcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCAATCCTCACTGAGCTTGGCAAG
EST: gi|86500499|gb|CI143132.1|CI143132
EST:     ACTTTTCCAACTG                         GTCTCCAAGTTGTATGAAGTTGTGCCTCCAATCGTCACTGAGCTTGGCAAG
genomic: ACTTTTCCAACTGgttagtctaa ... atcctgtcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCAATCCTCACTGAGCTTGGCAAG
EST: gi|86480028|gb|CI122661.1|CI122661
EST:     GCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTG                         GTCTCCAAGTTGTATGAAGTTGTGCCTCCAATCCTCACTGAGCTTGGCAAG
genomic: GCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagtctaa ... atcctgtcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCAATCCTCACTGAGCTTGGCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTTTCCAACTGgttagtctaaaatgtctgtccaactgcatggctctcttgcagtccaactatctcattgggattcttatcgatctatatcctgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT