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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGAGATGAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgcccaactcctttccctctctcctctcctctccgatctccgcctcgccctcggggcattgctggggagggatgcggtggcgctggcgctggc...

Basic information

species Oryza sativa
transcript LOC_Os01g16030.2
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|88339997|gb|CI650444.1|CI650444
EST:     AGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: AGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88694598|gb|CI738636.1|CI738636
EST:     GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88760986|gb|CI770542.1|CI770542
EST:     GAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: GAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88570416|gb|CI661789.1|CI661789
EST:     GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88353172|gb|CI654438.1|CI654438
EST:     GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGGTTG                      
genomic: GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAA----Ggttggtacgc ... attgttt
EST: gi|88357962|gb|CI650698.1|CI650698
EST:     GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|163929270|gb|EG711031.1|EG711031
EST:     GATGAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: GATGAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|117234117|gb|CT842356.1|CT842356
EST:     ATGAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: ATGAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88302447|gb|CI668293.1|CI668293
EST:     GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGGTTG                      
genomic: GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAA----Ggttggtacgc ... attgttt
EST: gi|88347834|gb|CI635927.1|CI635927
EST:     GAGAGAGGCCAGGCGCGCGCACGAGATCGATCTCCAGCAAGGTTG                      
genomic: GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAA----Ggttggtacgc ... attgttt
EST: gi|88453678|gb|CI683368.1|CI683368
EST:     GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88341662|gb|CI641414.1|CI641414
EST:     GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88454148|gb|CI693823.1|CI693823
EST:     GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88341576|gb|CI641328.1|CI641328
EST:     GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88454038|gb|CI691003.1|CI691003
EST:     GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88570756|gb|CI662129.1|CI662129
EST:     GAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: GAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88410309|gb|CI575907.1|CI575907
EST:     GATGAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: GATGAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88735809|gb|CI757384.1|CI757384
EST:     GAGGCCANGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: GAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|2310839|gb|C26994.1|C26994
EST:     CGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTNCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: CGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88572261|gb|CI663832.1|CI663832
EST:     GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88742204|gb|CI765712.1|CI765712
EST:     GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACCGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88734570|gb|CI758078.1|CI758078
EST:     GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88349175|gb|CI678148.1|CI678148
EST:     GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88305327|gb|CI653053.1|CI653053
EST:     GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88572018|gb|CI663589.1|CI663589
EST:     AGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: AGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88664650|gb|CI700897.1|CI700897
EST:     GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88369043|gb|CI677620.1|CI677620
EST:     GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88571110|gb|CI662483.1|CI662483
EST:     GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGGTTG                      
genomic: GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAA----Ggttggtacgc ... attgttt
EST: gi|66915825|gb|CX102673.1|CX102673
EST:     CACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: CACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88762783|gb|CI772339.1|CI772339
EST:     GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
EST: gi|88333173|gb|CI641016.1|CI641016
EST:     GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGGTTG                      
genomic: GAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAA----Ggttggtacgc ... attgttt
EST: gi|396941528|gb|HO188737.1|HO188737
EST:     ACGAGATCGATCTCCAGCAAG                         GTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC
genomic: ACGAGATCGATCTCCAGCAAGgttggtacgc ... attgtttaagGTCTTGCACAACTGCGGCAAGATGGGCCTCACTTTCACGAAGCTTTTCAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGAGATGAGAGAGGCCACGCGCGCGCACGAGATCGATCTCCAGCAAGgttggtacgcccaactcctttccctctctcctctcctctccgatctccgcctcgccctcggggcattgctggggagggatgcggtggcgctggcgctggc

 GGAGAT
- GAGATG
- - - -  GAGAGG
- - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggggagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtggcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcgctg