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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctctttgttattttttgtcttgattatatttttcgtatttattgtttaatttctttcagttcttcagtattcagcaaagctaataatttgatattgcagGCGGCATATCCTTTTACTAGTGGAGGCCTGACAGAATTATATAAAGACTGCTGAAAATGTCTGAGTTCCTTGACCTTGAGGCACAAGATGGGATAAGGAT

Basic information

species Oryza sativa
transcript LOC_Os09g28610.1
intron # 1
splice site 3'
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|88317402|gb|CI628051.1|CI628051
EST:     GCCTCCTCCACCGACTCCGGCCGCCGCTGCCTGCGGCGCGGTGCTGTCAG                         GCGGCATATCCTTTTACTAGTGGAGGCCTGACAGAATTATATAAAGACTGT
genomic: GCCTCCTCCACCGACTCCGGCCGCCGCTGCCTGCGGCGCGGTGCTGTCAGgtcagtagca ... gatattgcagGCGGCATATCCTTTTACTAGTGGAGGCCTGACAGAATTATATAAAGACTGC
EST: gi|88317442|gb|CI628091.1|CI628091
EST:     GCCTCCTCCACCGACTCCGGCCGCCGCTGCCTGCGGCGCGGTGCTGTCAG                         GCGGCATATCCTTTTACTAGTGGAGGCCTGACAGAATTATATAAAGACTGC
genomic: GCCTCCTCCACCGACTCCGGCCGCCGCTGCCTGCGGCGCGGTGCTGTCAGgtcagtagca ... gatattgcagGCGGCATATCCTTTTACTAGTGGAGGCCTGACAGAATTATATAAAGACTGC
EST: gi|88347305|gb|CI632590.1|CI632590
EST:     GCCTCCTCCACCGACTCCGGCCGCCGCTGCCTGCGGCGCGGTGCTGTCAG                         GCGGCATATCCTTTTACTAGTGGAGGCCTGACAGAATTATATAAAGACTGC
genomic: GCCTCCTCCACCGACTCCGGCCGCCGCTGCCTGCGGCGCGGTGCTGTCAGgtcagtagca ... gatattgcagGCGGCATATCCTTTTACTAGTGGAGGCCTGACAGAATTATATAAAGACTGC
EST: gi|88398128|gb|CI585631.1|CI585631
EST:     GCCTCCTCCACCGACTCCGGCCGCCGCTGCCTGCGGCGCGGTGCTGTCAG                         GCGGCATATCCTTTTACTAGTGGAGGCCTGACAGAATTATATAAAGACTGC
genomic: GCCTCCTCCACCGACTCCGGCCGCCGCTGCCTGCGGCGCGGTGCTGTCAGgtcagtagca ... gatattgcagGCGGCATATCCTTTTACTAGTGGAGGCCTGACAGAATTATATAAAGACTGC
EST: gi|88337072|gb|CI628158.1|CI628158
EST:     GCCTCCTCCACCGACTCCGGCCGCCGCTGCCTGCGGCGCGGTGCTGTCAG                         GCGGCATATCCTTTTACTAGTGGAGGCCTGACAGAATTATATAAAGACTGC
genomic: GCCTCCTCCACCGACTCCGGCCGCCGCTGCCTGCGGCGCGGTGCTGTCAGgtcagtagca ... gatattgcagGCGGCATATCCTTTTACTAGTGGAGGCCTGACAGAATTATATAAAGACTGC
EST: gi|88317406|gb|CI628055.1|CI628055
EST:     GCCTCCTCCACCGACTCCGGCCGCCGCTGCCTGCGGCGCGGTGCTGTCAG                         GCGGCATATCCTTTTACTAGTGGAGGCCTGACAGAATTATATAAAGACTGC
genomic: GCCTCCTCCACCGACTCCGGCCGCCGCTGCCTGCGGCGCGGTGCTGTCAGgtcagtagca ... gatattgcagGCGGCATATCCTTTTACTAGTGGAGGCCTGACAGAATTATATAAAGACTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaatttctttcagttcttcagtattcagcaaagctaataatttgatattgcagGCGGCATATCCTTTTACTAGTGGAGGCCTGACAGAATTATATAAAGACTGCTGAAAATGTCTGAGTTCCTTGACCTTGAGGCACAAGATGGGATAAGGAT
                                    taataatttgatatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctctttgttattttttgtcttgattatatttttcgtatttattgtttaatttctttcagttcttcagtattcagcaaagctaataatttgatattgcagGCGGCATATCCTTTTACTAGTGGAGGCCTGACAGAATTATATAAAGACTGCTGAAAATGTCTGAGTTCCTTGACCTTGAGGCACAAGATGGGATAAGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - tgtcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagcaaa