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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCACCTGCCCTCCTCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAGgtggcggcgctgcccttcccccttgttcttcttccttgcatctgcttccctcccgttttgcttctaattgtatttctctttcgtttccgcag

Basic information

species Oryza sativa
transcript LOC_Os07g12650.4
intron # 1
splice site 5'
intron type U2

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|88722319|gb|CI745829.1|CI745829
EST:     TCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAG                         ATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
genomic: TCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAGgtggcggcgc ... gtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
EST: gi|13806613|gb|AU181586.1|AU181586
EST:     CTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAG                         ATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
genomic: CTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAGgtggcggcgc ... gtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
EST: gi|88358899|gb|CI619403.1|CI619403
EST:     TCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAG                         ATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
genomic: TCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAGgtggcggcgc ... gtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
EST: gi|88357562|gb|CI623616.1|CI623616
EST:     TCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAG                         ATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
genomic: TCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAGgtggcggcgc ... gtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
EST: gi|88332492|gb|CI651652.1|CI651652
EST:     TCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAG                         ATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
genomic: TCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAGgtggcggcgc ... gtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
EST: gi|88339791|gb|CI649048.1|CI649048
EST:     TCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAG                         ATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
genomic: TCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAGgtggcggcgc ... gtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
EST: gi|218485304|gb|FG956287.1|FG956287
EST:     CCGCTCTCCCAAG                         ATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
genomic: CCGCTCTCCCAAGgtggcggcgc ... gtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
EST: gi|427734|gb|D23869.1|D23869
EST:     CGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAG                         ATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
genomic: CGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAGgtggcggcgc ... gtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCCACCTGCCCTCCTCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAGgtggcggcgctgcccttcccccttgttcttcttccttgcatctgcttccctcccgttttgcttctaattgtatttctctttcgtttccgcag

- - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - CGCCGCCG