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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGGAGAAAGCTCAAGGGAAACTATCATGGATGCCAACTCCAGTTTAAATGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAGgtatgttaggatttgatccacttcatgtcctcatcctttattatgtcagaactgcatgtgtttttgagttgtaattcagagtttcaaatgttgacataag...

Basic information

species Oryza sativa
transcript LOC_Os05g11550.2
intron # 2
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|58663416|gb|CK052102.1|CK052102
EST:     TGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAG                         CAAACAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCTAA
genomic: TGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAGgtatgttagg ... ttttctgcagCAAACAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCTAA
EST: gi|88722240|gb|CI745750.1|CI745750
EST:     TGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAG                         CAAACAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCT
genomic: TGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAGgtatgttagg ... ttttctgcagCAAACAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCT
EST: gi|88402728|gb|CI613176.1|CI613176
EST:     TGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAG                         CAAATAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCTAA
genomic: TGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAGgtatgttagg ... ttttctgcagCAAACAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCTAA
EST: gi|58672770|gb|CK061456.1|CK061456
EST:     TGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAG                         CAAACAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCTAA
genomic: TGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAGgtatgttagg ... ttttctgcagCAAACAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCTAA
EST: gi|88356730|gb|CI619216.1|CI619216
EST:     TGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAG                         CAAACAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCTAA
genomic: TGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAGgtatgttagg ... ttttctgcagCAAACAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCTAA
EST: gi|29630243|gb|CB635252.1|CB635252
EST:     TGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAG                         CAAACAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCTAA
genomic: TGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAGgtatgttagg ... ttttctgcagCAAACAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCTAA
EST: gi|58671706|gb|CK060392.1|CK060392
EST:     TGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAG                         CAAACAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCTAA
genomic: TGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAGgtatgttagg ... ttttctgcagCAAACAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCTAA
EST: gi|29676952|gb|CB673227.1|CB673227
EST:     TGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAG                         CAAACAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCTAA
genomic: TGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAGgtatgttagg ... ttttctgcagCAAACAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCTAA
EST: gi|29681334|gb|CB677609.1|CB677609
EST:     TGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAG                         CAAACAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCTAA
genomic: TGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAGgtatgttagg ... ttttctgcagCAAACAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCTAA
EST: gi|66920389|gb|CX107237.1|CX107237
EST:     TGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAG                         CAAACAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCTAA
genomic: TGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAGgtatgttagg ... ttttctgcagCAAACAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCTAA
EST: gi|88692699|gb|CI736274.1|CI736274
EST:     TGAGCAAAAGTCTGAGGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAG                         CAAACAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCTAA
genomic: TGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAGgtatgttagg ... ttttctgcagCAAACAAGTTCTCCCTGGCTATAGAGCTCTATAGTCAAGCCATTGAGCTAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGGAGAAAGCTCAAGGGAAACTATCATGGATGCCAACTCCAGTTTAAATGAGCAAAAGTCTGAAGAACTCAAGCTTAAAGCAAATGATGCCTTTAAAGgtatgttaggatttgatccacttcatgtcctcatcctttattatgtcagaactgcatgtgtttttgagttgtaattcagagtttcaaatgttgacataag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA