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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTACTGTAGCTGGTGCCAATAATGAGGCTGAAGCAGCTAAAATTGCTCGTTCAGTGGCATCTTCCTCCCTGGTTAAAgtatgatactgtttagcagcaaaattttgctaattaggagaggattgacacccctctgtcattcgttagcccagaaagcctgagttgttaaattattttttatcag

Basic information

species Oryza sativa
transcript LOC_Os03g17120.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17120.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G044237_T03 (Zea mays), 5'ss of exon 13
GTTACTGTAGCTGGTGCCAATAATGAGGCTGAAGCAGCTAAAATTGCTCGTTCAGTGGCATCTTCCTCCCTGGTTAAAgtatgatact-gtttagcagcaaaattttgctaattaggag----aggattgacacccctctgtcattcgttagcccagaaagcctgagttgttaaattattttttatcag
|||||||||  ||| ||||| || ||||| ||||| |||||||||||||||||||| |||||||| ||  ||||||||||||| |  | ||||| |    || || ||| | | |  ||    ||      ||  | ||| |   ||  |  ||||||| ||| || |  ||| ||| |||| |  |||
GTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAAgtatgttgatagtttatctagcaatttctgcaattcaatagtatcagccaaagcagtcttcttttcatccatcccccagaaggccagaatgattatatt-ttttgtgacag
















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|27546388|gb|CA767223.2|CA767223
EST:     CTGAAGCAGCTAAAATTGCTCGTTCAGTGGCATCTTCCTCCCTGGTTAAA                         GCCGCTGTATTTGGAAGAGACCCAAACTGGGGACGTATTGCTTGTTCTGTC
genomic: CTGAAGCAGCTAAAATTGCTCGTTCAGTGGCATCTTCCTCCCTGGTTAAAgtatgatact ... tttttatcagGCCGCTGTATTTGGAAGAGACCCAAACTGGGGACGTATTGCTTGTTCTGTC
EST: gi|86494844|gb|CI137477.1|CI137477
EST:     CTGAAGCAGCTAAAATTGCTCGTTCAGTGGCATCTTCCTCNCTGGTTAAA                         GCCGCTGTATTTGGAAGAGACCCAAACTGGGGACGTATTGCTTGTTCTGTC
genomic: CTGAAGCAGCTAAAATTGCTCGTTCAGTGGCATCTTCCTCCCTGGTTAAAgtatgatact ... tttttatcagGCCGCTGTATTTGGAAGAGACCCAAACTGGGGACGTATTGCTTGTTCTGTC
EST: gi|87020790|gb|CI269507.1|CI269507
EST:     TGAAGCAGCTAAAATTGCTCGTTCAGTGGCATCTTCTCTCCCTGGTTAAA                         GCCGCTGTATTTGGAAGAGACCCAAACTGGGGACGTATTGCTTGTTCTGTC
genomic: TGAAGCAGCTAAAATTGCTCGTTCAGTGGCATCTTC-CTCCCTGGTTAAAgtatgatact ... tttttatcagGCCGCTGTATTTGGAAGAGACCCAAACTGGGGACGTATTGCTTGTTCTGTC
EST: gi|86499008|gb|CI141641.1|CI141641
EST:     CTGAAGCAGCTAAAATTGCTCGTTCAGTGGCATCTTCCTCCCTGGTTAAA                         GCCGCTGTATTTGGAAGAGACCCAAACTGGGGACGTATTGCTTGTTCTGTC
genomic: CTGAAGCAGCTAAAATTGCTCGTTCAGTGGCATCTTCCTCCCTGGTTAAAgtatgatact ... tttttatcagGCCGCTGTATTTGGAAGAGACCCAAACTGGGGACGTATTGCTTGTTCTGTC
EST: gi|29613227|gb|CB618240.1|CB618240
EST:     CTGAAGCAGCTAAAATTGCTCGTTCAGTGGCATCTTCCTCCCTGGTTAAA                         GCCGCTGTATTTGGAAGAGACCCAAACTGGGGACGTATTGCTTGTTCTGTC
genomic: CTGAAGCAGCTAAAATTGCTCGTTCAGTGGCATCTTCCTCCCTGGTTAAAgtatgatact ... tttttatcagGCCGCTGTATTTGGAAGAGACCCAAACTGGGGACGTATTGCTTGTTCTGTC
EST: gi|29670993|gb|CB667268.1|CB667268
EST:     CTGAAGCAGCTAAAATTGCTCGTTCAGTGGCATCTTCCTCCCTGGTTAAA                         GCCGCTGTATTTGGAAGAGACCCAAACTGGGGACGTATTGCTTGTTCTGTC
genomic: CTGAAGCAGCTAAAATTGCTCGTTCAGTGGCATCTTCCTCCCTGGTTAAAgtatgatact ... tttttatcagGCCGCTGTATTTGGAAGAGACCCAAACTGGGGACGTATTGCTTGTTCTGTC
EST: gi|87012910|gb|CI297137.1|CI297137
EST:     CTGAAGCAGCTAAAATTGCTCGTTCAGTGGCATCTTCCTCCCTGGTTAAA                         GCCGCTGTATTTGGAAGAGACCCAAACTGGGGACGTATTGCTTGTTCTGTC
genomic: CTGAAGCAGCTAAAATTGCTCGTTCAGTGGCATCTTCCTCCCTGGTTAAAgtatgatact ... tttttatcagGCCGCTGTATTTGGAAGAGACCCAAACTGGGGACGTATTGCTTGTTCTGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTACTGTAGCTGGTGCCAATAATGAGGCTGAAGCAGCTAAAATTGCTCGTTCAGTGGCATCTTCCTCCCTGGTTAAAgtatgatactgtttagcagcaaaattttgctaattaggagaggattgacacccctctgtcattcgttagcccagaaagcctgagttgttaaattattttttatcag

- - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - -  GCAGCT