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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTATACTGATTCTAAGACTTTGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAGgtatgttgtatacctggactttcattgctgtgtgaaccttttcatttatggagatgcttgtaaaacagcactgtgaatctcccatctttcatttatattt...

Basic information

species Oryza sativa
transcript LOC_Os12g03470.3
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03470.3 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G006130_T04 (Zea mays), 5'ss of exon 13
GTCTATACTGATTCTAAGACTTTGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAGgtatgttgtatacctggactttc-----attgctgtgtgaaccttttcatttatggagatgcttgtaaaacagcactgtgaatctcccatctttcatttatattt
|||||||||||||||||||||||||||   |||| |||  ||||||| ||| ||||||||| ||| || |||||| ||  ||   ||    ||       | |  | || ||      || || | |   |  | | ||   || |  |  |    |||   | |||| || |    
GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGAACATCTCGTAGTGGACCTAAGgtaagtcttaagtctcattttcacaaggactcttatgagacagccctctttcacgaccagtcattta---catcgatcagggattcctggcattcacttgtga--

upper sequence: LOC_Os12g03470.3 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G006130_T05 (Zea mays), 5'ss of exon 12
GTCTATACTGATTCTAAGACTTTGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAGgtatgttgtatacctggactttca----ttgctgtgtgaaccttttcatttatggagatgcttgtaaaacagcactgtgaatctcccatctttcatttatattt
|||||||||||||||||||||||||||   |||| |||  ||||||| ||| |||| |||| ||| || |||||| ||   |  |      |  ||     |  | || ||      || || | |   |  | | ||   || |  |  |    |||   | |||| ||      
GTCTATACTGATTCTAAGACTTTGTTTAACATGAGGAGCACATTTGACAGAACATCACGTAGTGGACCTAAGgtaagtctaagtctcattttcacaaggactcttatgagactgccctctttcacgaccagtcattta---catcgatcagggattcctggcattcacttgggag-

upper sequence: LOC_Os12g03470.3 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G077299_T03 (Zea mays), 5'ss of exon 12
GTCTATACTGATTCTAAGACTTTGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAGgtatgttgt-atacctggactttcattgctgtgtgaaccttttcatttatggagatgcttgtaaaacagcactgtgaatctcccatctttcatttatattt
||||||| ||||||||||||||||||    ||||||||  ||||||| ||| ||||||||| ||| ||||||||| ||| | ||  |   |     |||  ||||  |    | || ||  || ||  || | || |       || || |     |  ||||  ||    | 
GTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAGgtaagttctgattacataagaaaaattcttgtgaaatagctctctttcgtg-agtagcatttacattgtatttgggatttcttgacatttctcttgggatg

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|29667817|gb|CB664092.1|CB664092
EST:     TGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAG                         GCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCANGTAGAGGAAGT
genomic: TGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAGgtatgttgta ... ttggttgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGT
EST: gi|29627660|gb|CB632671.1|CB632671
EST:     ATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAG                         GCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGT
genomic: ATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAGgtatgttgta ... ttggttgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGT
EST: gi|699908|gb|D46199.1|D46199
EST:     TGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAG                         GCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGT
genomic: TGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAGgtatgttgta ... ttggttgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGT
EST: gi|33381874|gb|CF197217.1|CF197217
EST:     TGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAG                         GCTTTTGTCAGTGAATATGCTGTTTGGAGNNGTGATGC
genomic: TGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAGgtatgttgta ... ttggttgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGC
EST: gi|33654398|gb|CF277012.1|CF277012
EST:     TGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAG                         GCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGT
genomic: TGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAGgtatgttgta ... ttggttgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGT
EST: gi|58690391|gb|CK079078.1|CK079078
EST:     TGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAG                         GCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGT
genomic: TGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAGgtatgttgta ... ttggttgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGT
EST: gi|29667818|gb|CB664093.1|CB664093
EST:     ATGAAGAGTGCATCTGATAGATCATCTCGTAATGGGCCCAAG                         GCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGT
genomic: ATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAGgtatgttgta ... ttggttgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGT
EST: gi|29686128|gb|CB682403.1|CB682403
EST:     TGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAG                         GCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAAGTAGAGGAAGT
genomic: TGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAGgtatgttgta ... ttggttgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTATACTGATTCTAAGACTTTGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAGgtatgttgtatacctggactttcattgctgtgtgaaccttttcatttatggagatgcttgtaaaacagcactgtgaatctcccatctttcatttatattt

- - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - AGATCA