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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatacagctagctatctctaacctttgtgctgtgctgagcacattccatttcccagtttaaaagaatcaccttttttttcttcttcctttcctccctagCTTGTTGCAGCTGCTGCTCCAAGTAGTGTGTGGCGATCCTTAGTTTTTTGCACTTAGGGAGGGTGCACTCTGCTGATCCTCTTTTACTTGGTTCAGTATC

Basic information

species Oryza sativa
transcript LOC_Os04g54474.2
intron # 2
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|88765567|gb|CI774661.1|CI774661
EST:     GAGCTTTACCCTGGCTATCTTGAAGACCATTTTAACATCCACAAGCTTAG                         CTTGTTGCAGCTGCTGCTCCAAGTAGTGTGTGGCGATCCTTAGTTTTTTGC
genomic: GAGCTTTACCCTGGCTATCTTGAAGACCATTTTAACATCCACAAGCTTAGgtgtgtattc ... tcctccctagCTTGTTGCAGCTGCTGCTCCAAGTAGTGTGTGGCGATCCTTAGTTTTTTGC
EST: gi|88761390|gb|CI770946.1|CI770946
EST:     GAGCTTTACCCTGGCTATCTTGAAGACCATTTTAACATCCACAAGCTTAG                         CTTGTTGCAGCTGCTGCTCCAAGTAGTGTGTGGCGATCCTTAGTTTTTTGC
genomic: GAGCTTTACCCTGGCTATCTTGAAGACCATTTTAACATCCACAAGCTTAGgtgtgtattc ... tcctccctagCTTGTTGCAGCTGCTGCTCCAAGTAGTGTGTGGCGATCCTTAGTTTTTTGC
EST: gi|88762353|gb|CI771909.1|CI771909
EST:     GAGCTTTACCCTGGCTATCTTGAAGACCATTTTAACATCCACAAGCTTAG                         CTTGTTGCAGCTGCTGCTCCAAGTAGTGTGTGGCGATCCTTAGTTTTTTGC
genomic: GAGCTTTACCCTGGCTATCTTGAAGACCATTTTAACATCCACAAGCTTAGgtgtgtattc ... tcctccctagCTTGTTGCAGCTGCTGCTCCAAGTAGTGTGTGGCGATCCTTAGTTTTTTGC
EST: gi|88761383|gb|CI770939.1|CI770939
EST:     GAGCTTTACCCTGGCTATCTTGAAGACCATTTTAACATCCACAAGCTTAG                         CTTGTTGCAGCTGCTGCTCCAAGTAGTGTGTGGCGATCCTTAGTTTTTTGC
genomic: GAGCTTTACCCTGGCTATCTTGAAGACCATTTTAACATCCACAAGCTTAGgtgtgtattc ... tcctccctagCTTGTTGCAGCTGCTGCTCCAAGTAGTGTGTGGCGATCCTTAGTTTTTTGC
EST: gi|88764644|gb|CI773762.1|CI773762
EST:     GAGCTTTACCCTGGCTATCTTGAAGACCATTTTAACATCCACAAGCTTAG                         CTTGTTGCAGCTGCTGCTCCAAGTAGTGTGTGGCGATCCTTAGTTTTTTGC
genomic: GAGCTTTACCCTGGCTATCTTGAAGACCATTTTAACATCCACAAGCTTAGgtgtgtattc ... tcctccctagCTTGTTGCAGCTGCTGCTCCAAGTAGTGTGTGGCGATCCTTAGTTTTTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatttcccagtttaaaagaatcaccttttttttcttcttcctttcctccctagCTTGTTGCAGCTGCTGCTCCAAGTAGTGTGTGGCGATCCTTAGTTTTTTGCACTTAGGGAGGGTGCACTCTGCTGATCCTCTTTTACTTGGTTCAGTATC
                      tcaccttttttttctt  CT-rich tract
                           ttttttttcttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatacagctagctatctctaacctttgtgctgtgctgagcacattccatttcccagtttaaaagaatcaccttttttttcttcttcctttcctccctagCTTGTTGCAGCTGCTGCTCCAAGTAGTGTGTGGCGATCCTTAGTTTTTTGCACTTAGGGAGGGTGCACTCTGCTGATCCTCTTTTACTTGGTTCAGTATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
gcataca
- - - - - - - - - - - - - -gtgctgt
- - - - - - - - - - - - - - - - - - - - cacattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagaa