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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatattagtcatccaacctcacatgcgctctctctctctctctctcgtaaatatttccatggtttactttattaccattctatattttgttaattcctcgtttattgttattcttattgatag

Basic information

species Oryza sativa
transcript LOC_Os01g16970.3
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16970.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G052875_T02 (Zea mays), 5'ss of exon 11
GTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatattagtcatccaacctcacatgcgctctctctctctctctctcgtaaatatttccatggtttactttattaccattctatattttgttaattcctcgtttattgttattcttattgatag
| || || ||||||||||||| ||||||||||||||||||||||| |||||| || ||||| |||||||| |||||||| ||    ||    | |  ||| | | | | |      |||  ||  |||  ||     | | | |||    || ||  ||||  |  || |                
GCAAAGACAAGGAGTTCTATTCCTTTTATGATCAGTGCTTTGAGACCAAGGAAGGAAAgtatgtatatta-tcatccaatcttttttgtctgccccttctgtttttattgc-----tttttattatttggtt-----ctaatttatgaactggta--tccttatggatag----------------

upper sequence: LOC_Os01g16970.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AC213600.3_FGT002 (Zea mays), 5'ss of exon 11
GTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatat-tagtcatccaacctcacatgcgctctctctctctctctctcgtaaatatttccatggtttactttattaccattctatattttgttaattcctcgtttattgttattcttattgatag
|||| || ||||||||||||| ||||||||||||||| ||||||| |||||| || ||||| |||||| |   |||||||  |    ||  |  ||| ||| | | | | |      |||  ||  |||  ||     | | | | |    || ||  ||||  |  || |                
GTAATGACAAGGAGTTCTATTCCTTTTATGATCAGTGTTTTGAGACCAAGGAAGGGAAgtatgtatatgttagcatccaatatttactgtccgttctttctgtttttattgc-----tttttattatttggtt-----ctaatttgtgaactgcta--tccttatggatag----------------
















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|33679534|gb|CF307773.1|CF307773
EST:     TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAA                         GTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
genomic: TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatat ... ttattgatagGTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
EST: gi|33679492|gb|CF307731.1|CF307731
EST:     TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAA                         GTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
genomic: TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatat ... ttattgatagGTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
EST: gi|29627610|gb|CB632621.1|CB632621
EST:     AAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAA                         GTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
genomic: AAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatat ... ttattgatagGTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
EST: gi|33679522|gb|CF307761.1|CF307761
EST:     TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAA                         GTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
genomic: TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatat ... ttattgatagGTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
EST: gi|33679756|gb|CF307995.1|CF307995
EST:     TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAA                         GTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
genomic: TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatat ... ttattgatagGTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
EST: gi|29614303|gb|CB619316.1|CB619316
EST:     AAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAA                         GTATGTTTACAAGGTATGTCCGTTCAAGAAAGCTTCGCAGGTTGAAGGACA
genomic: AAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatat ... ttattgatagGTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
EST: gi|33679967|gb|CF308206.1|CF308206
EST:     TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAA                         GTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
genomic: TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatat ... ttattgatagGTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
EST: gi|33679350|gb|CF307589.1|CF307589
EST:     TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAA                         GTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
genomic: TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatat ... ttattgatagGTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
EST: gi|29622278|gb|CB627289.1|CB627289
EST:     AAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAA                         GTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
genomic: AAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatat ... ttattgatagGTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
EST: gi|33679589|gb|CF307828.1|CF307828
EST:     TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAA                         GTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
genomic: TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatat ... ttattgatagGTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
EST: gi|29627609|gb|CB632620.1|CB632620
EST:     AAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAA                         GTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
genomic: AAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatat ... ttattgatagGTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
EST: gi|88371457|gb|CI602635.1|CI602635
EST:     AAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAA                         GTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
genomic: AAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatat ... ttattgatagGTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
EST: gi|33679903|gb|CF308142.1|CF308142
EST:     TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAA                         GTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
genomic: TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatat ... ttattgatagGTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
EST: gi|33679526|gb|CF307765.1|CF307765
EST:     TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAA                         GTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
genomic: TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatat ... ttattgatagGTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
EST: gi|33680003|gb|CF308242.1|CF308242
EST:     TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAA                         GTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
genomic: TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatat ... ttattgatagGTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
EST: gi|29627670|gb|CB632681.1|CB632681
EST:     AAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAA                         GTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
genomic: AAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatat ... ttattgatagGTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
EST: gi|58589761|gb|CF988069.1|CF988069
EST:     AAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAA                         GTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
genomic: AAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatat ... ttattgatagGTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
EST: gi|33679947|gb|CF308186.1|CF308186
EST:     TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAA                         GTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
genomic: TCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatat ... ttattgatagGTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
EST: gi|29627671|gb|CB632682.1|CB632682
EST:     AAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAA                         GTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA
genomic: AAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatat ... ttattgatagGTATGTTTACAAGGTATGTCCATTCAAGAAAGCTTCGCAGGTTGAAGGACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAAgtacgtatattagtcatccaacctcacatgcgctctctctctctctctctcgtaaatatttccatggtttactttattaccattctatattttgttaattcctcgtttattgttattcttattgatag

- - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - -  AAGGAG