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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCGGAAGAGAATATCTGCAGCTTGATCAGTTCCAAAACTGAGATATATCTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcgatcgctttgctttaatttgcactatttaatttgtccatgccactgacagattcctcctcttggcag

Basic information

species Oryza sativa
transcript LOC_Os01g38229.4
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|88401684|gb|CI588625.1|CI588625
EST:     CTGCAGCTTGATCAGTTCCAAAAATTTAGCTGGGCACGCACTACCGGCAG                         CAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
EST: gi|2427665|gb|C72128.1|C72128
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACC-G--G                         CAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
EST: gi|88370128|gb|CI585133.1|CI585133
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAG                         CAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
EST: gi|88735124|gb|CI758632.1|CI758632
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAG                         CAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
EST: gi|88299856|gb|CI577358.1|CI577358
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAG                         CAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
EST: gi|88730185|gb|CI753800.1|CI753800
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAG                         CAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
EST: gi|88745808|gb|CI769168.1|CI769168
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAG                         CAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
EST: gi|88405610|gb|CI588816.1|CI588816
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAG                         CAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
EST: gi|88312710|gb|CI587618.1|CI587618
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAG                         CAGTTCAAGTGACAAACCAATTTGAATTGCGGCTAGCGCCAGCACAGGCAT
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAG-GACAAACCAATTTGAA-GGCGGCTAGCGCCAGCACAGGCAT
EST: gi|33676436|gb|CF304675.1|CF304675
EST:     AAAACTTTAGCTGGGCACGCACTACCGGCAG                         CAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
genomic: AAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
EST: gi|33676380|gb|CF304619.1|CF304619
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAG                         CAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
EST: gi|29635968|gb|CB640977.1|CB640977
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAG                         CAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
EST: gi|88741944|gb|CI764449.1|CI764449
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAG                         CAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
EST: gi|88730157|gb|CI753772.1|CI753772
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAG                         CAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
EST: gi|88735330|gb|CI758838.1|CI758838
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAG                         CAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
EST: gi|88367669|gb|CI568441.1|CI568441
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAG                         CAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
EST: gi|88410785|gb|CI578591.1|CI578591
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAG                         CAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
EST: gi|88744080|gb|CI767440.1|CI767440
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAG                         CAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
EST: gi|88444063|gb|CI594436.1|CI594436
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACC-G--G                         CAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
EST: gi|572225|gb|D41736.1|D41736
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAG                         CAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCA-CACAGGCATGC
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
EST: gi|88762537|gb|CI772093.1|CI772093
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAG                         CAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
EST: gi|88386177|gb|CI570812.1|CI570812
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAG                         CAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ctcttggcagCAGTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTCGGAAGAGAATATCTGCAGCTTGATCAGTTCCAAAACTGAGATATATCTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcgatcgctttgctttaatttgcactatttaatttgtccatgccactgacagattcctcctcttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT