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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTTCTTTCCACTTCTGACTTCTCCAAGTCCAAACTCCAAAGTTCTCATCGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAGgtgagcaacccaaaaccgaagttcatttcttctcttttcgtccagagaccaatcatagtcgtagctcacgaaacaatcgaaaaaaatatcttgttcctgg...

Basic information

species Oryza sativa
transcript LOC_Os03g05390.1
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|88973492|gb|CI717920.1|CI717920
EST:     CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAG                         GATACACC
genomic: CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAGgtgagcaacc ... ttgtttgcagGATACACC
EST: gi|88670150|gb|CI724266.1|CI724266
EST:     CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAG                         GATACACC
genomic: CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAGgtgagcaacc ... ttgtttgcagGATACACC
EST: gi|88673593|gb|CI727706.1|CI727706
EST:     CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAG                         GATACACC
genomic: CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAGgtgagcaacc ... ttgtttgcagGATACACC
EST: gi|58666157|gb|CK054843.1|CK054843
EST:     CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAG                         GATACACC
genomic: CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAGgtgagcaacc ... ttgtttgcagGATACACC
EST: gi|88670805|gb|CI724921.1|CI724921
EST:     CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAG                         GATACACC
genomic: CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAGgtgagcaacc ... ttgtttgcagGATACACC
EST: gi|88416015|gb|CI594127.1|CI594127
EST:     CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCATGCCCCTACTCCGAG                         GATACACC
genomic: CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAGgtgagcaacc ... ttgtttgcagGATACACC
EST: gi|88972840|gb|CI717566.1|CI717566
EST:     CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAG                         GATACACC
genomic: CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAGgtgagcaacc ... ttgtttgcagGATACACC
EST: gi|58665102|gb|CK053788.1|CK053788
EST:     CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAG                         GATACACC
genomic: CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAGgtgagcaacc ... ttgtttgcagGATACACC
EST: gi|87009766|gb|CI310869.1|CI310869
EST:     CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAG                         GATACACC
genomic: CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAGgtgagcaacc ... ttgtttgcagGATACACC
EST: gi|88695197|gb|CI739235.1|CI739235
EST:     GCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAG                         GATACACC
genomic: GCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAGgtgagcaacc ... ttgtttgcagGATACACC
EST: gi|88362212|gb|CI608603.1|CI608603
EST:     CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGA-                         G-------
genomic: CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAGgtgagcaacc ... ttgtttgcagGATACACC
EST: gi|88671208|gb|CI723128.1|CI723128
EST:     CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAG                         GATACACC
genomic: CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAGgtgagcaacc ... ttgtttgcagGATACACC
EST: gi|88594485|gb|CI714443.1|CI714443
EST:     CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAG                         GATACACC
genomic: CGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAGgtgagcaacc ... ttgtttgcagGATACACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTTCTTTCCACTTCTGACTTCTCCAAGTCCAAACTCCAAAGTTCTCATCGTTGCGCGTGGCACTGTGGACTCTCCACTCTCCACGCCCCTACTCCGAGgtgagcaacccaaaaccgaagttcatttcttctcttttcgtccagagaccaatcatagtcgtagctcacgaaacaatcgaaaaaaatatcttgttcctgg

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