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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatctaaacagagcctaatagctattttagcatactgttcgatcgttttgcctattttagcttactgttcgatagttttgccgatgatctgatccagcagGGGCTGCGCGGCAACCTCTACGCCACCGCGGCGCCGAGGATGTTGGCCGGCGCCGCCGCAGCGTGCCAGGAGCTGAAGAAGCGGGCAATGGCTAGCCCCG

Basic information

species Oryza sativa
transcript LOC_Os02g56940.3
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|86507862|gb|CI150495.1|CI150495
EST:     AGACCGTCAACGGCGGCGCGAACTCTCCGGACCTCACCCTCATCACCAAGCAG                       
genomic: AGACCGTCAACGGCGGCGCGAACTCTCCGGACCTCACCCTCATCACC-A--AGgtagctataa ... gatccagc
EST: gi|88985723|gb|CI033052.1|CI033052
EST:     CTCTCCGGACCTCACCCTCATCACCAAG                         GGGCTGCGCGGCAACCTCTACGCCACCGCGGCGCCGAGGATGTTGGCCGGC
genomic: CTCTCCGGACCTCACCCTCATCACCAAGgtagctataa ... gatccagcagGGGCTGCGCGGCAACCTCTACGCCACCGCGGCGCCGAGGATGTTGGCCGGC
EST: gi|15853323|gb|BI806119.1|BI806119
EST:     CGGCGCGAACTCTCCGGACCTCACCCTCATCACCAAG                         GGGCTGCGCGGCAACCTCTACGCCACCGCGGCGCCGAGGATGTTGGCCGGC
genomic: CGGCGCGAACTCTCCGGACCTCACCCTCATCACCAAGgtagctataa ... gatccagcagGGGCTGCGCGGCAACCTCTACGCCACCGCGGCGCCGAGGATGTTGGCCGGC
EST: gi|86871627|gb|CI331004.1|CI331004
EST:     AGACCGTCAACGGCGGCGCGAACTCTCCGGACCTCACCCTCATCACCAAGCAG                       
genomic: AGACCGTCAACGGCGGCGCGAACTCTCCGGACCTCACCCTCATCACC-A--AGgtagctataa ... gatccagc
EST: gi|88440444|gb|CI549325.1|CI549325
EST:     CTCACCCTCATCACCAAGCAG                       
genomic: CTCACCCTCATCACC-A--AGgtagctataa ... gatccagc
EST: gi|89170410|gb|CI039687.1|CI039687
EST:     AGACCGTCAACGGCGGCGCGAACTCTCCGGACCTCACCCTCATCACCAAG                         GGGCTGCGCGGCAACCTCTACGCCACCGCGGCGCCGAGGATGTTGGCCGGC
genomic: AGACCGTCAACGGCGGCGCGAACTCTCCGGACCTCACCCTCATCACCAAGgtagctataa ... gatccagcagGGGCTGCGCGGCAACCTCTACGCCACCGCGGCGCCGAGGATGTTGGCCGGC
EST: gi|88434955|gb|CI549152.1|CI549152
EST:     CGTCAACGGCGGCGCGAACTTTCCGGACCTCACCCTCATCACCAAGCAG                       
genomic: CGTCAACGGCGGCGCGAACTCTCCGGACCTCACCCTCATCACC-A--AGgtagctataa ... gatccagc
EST: gi|86534306|gb|CI174512.1|CI174512
EST:     CCGTCAACGGCGGCGCGAACTCTCCGGACCTCACCCTCATCACCAAG                         GGTCTGCGCGGCAACCTTTACGCCACCGCGGCGCCGAGGATGTTGGCCGGC
genomic: CCGTCAACGGCGGCGCGAACTCTCCGGACCTCACCCTCATCACCAAGgtagctataa ... gatccagcagGGGCTGCGCGGCAACCTCTACGCCACCGCGGCGCCGAGGATGTTGGCCGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgcctattttagcttactgttcgatagttttgccgatgatctgatccagcagGGGCTGCGCGGCAACCTCTACGCCACCGCGGCGCCGAGGATGTTGGCCGGCGCCGCCGCAGCGTGCCAGGAGCTGAAGAAGCGGGCAATGGCTAGCCCCG
       tatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatctaaacagagcctaatagctattttagcatactgttcgatcgttttgcctattttagcttactgttcgatagttttgccgatgatctgatccagcagGGGCTGCGCGGCAACCTCTACGCCACCGCGGCGCCGAGGATGTTGGCCGGCGCCGCCGCAGCGTGCCAGGAGCTGAAGAAGCGGGCAATGGCTAGCCCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - -aaacagag
- - - - - - - - - - - - - - agcatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccgatg