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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgcgtaataagaccttttttttatgtttttgtttcccaaattttgctgtctggaaataatttcttgaaagggttggctttgatcgtttgctcgtgcagGAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAGCGCGTGGCGGTGAAGTACTACAGCGATGACTGGCCCTCTTTGTCCTCGA

Basic information

species Oryza sativa
transcript LOC_Os01g62150.2
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|33656563|gb|CF279177.1|CF279177
EST:     GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATG                         GAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
genomic: GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATGgtaatttcct ... gctcgtgcagGAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
EST: gi|33688268|gb|CF316507.1|CF316507
EST:     GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATG                         GAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
genomic: GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATGgtaatttcct ... gctcgtgcagGAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
EST: gi|88729722|gb|CI753232.1|CI753232
EST:     GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATG                         GAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
genomic: GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATGgtaatttcct ... gctcgtgcagGAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
EST: gi|58686756|gb|CK075443.1|CK075443
EST:     GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATG                         GAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
genomic: GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATGgtaatttcct ... gctcgtgcagGAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
EST: gi|88390456|gb|CI607492.1|CI607492
EST:     GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATG                         GAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
genomic: GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATGgtaatttcct ... gctcgtgcagGAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
EST: gi|33657559|gb|CF280173.1|CF280173
EST:     GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATG                         GAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
genomic: GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATGgtaatttcct ... gctcgtgcagGAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
EST: gi|88386053|gb|CI570688.1|CI570688
EST:     GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATG                         GAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
genomic: GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATGgtaatttcct ... gctcgtgcagGAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctgtctggaaataatttcttgaaagggttggctttgatcgtttgctcgtgcagGAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAGCGCGTGGCGGTGAAGTACTACAGCGATGACTGGCCCTCTTTGTCCTCGA
                                 ctttgat  putative branch site (score: 5)
                                          tttgctc  putative PPT
          aaataatttcttgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgcgtaataagaccttttttttatgtttttgtttcccaaattttgctgtctggaaataatttcttgaaagggttggctttgatcgtttgctcgtgcagGAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAGCGCGTGGCGGTGAAGTACTACAGCGATGACTGGCCCTCTTTGTCCTCGA

- - - - - - - - - - - ttatgtt
- - - - - - - - - - - - - - - ttgtttc
- - - - - - - - - - - - - - - - - - - - - - -tgctgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - gaaataa