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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttcaaagattgcaactgttgttgcctatgcataatttgccagtctgttttggcctaccgatctgacttttattgtcttcgtgtattttatttgtgcagCAGTCTATTAGAGATGGATCTACAACCTTGAGAACTGTCAAAGATGTTGGCATAGATTCATCACTGAGTGCCTCTCCTTCTCGTTGGCCTATTGATTTTG

Basic information

species Oryza sativa
transcript LOC_Os08g43400.4
intron # 11
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|313083968|gb|HO213751.1|HO213751
EST:     AGAAGACTGATAGTGACCATGAGGATGAACTTGATGAGTATCAGGATCAG                         CAGTCTATTAGAGATGGATCTACAACCTTGAGAACTGTCAAAGATGTTGGC
genomic: AGAAGACTGATAGTGACCATGAGGATGAACTTGATGAGTATCAGGATCAGgtaatcatgt ... atttgtgcagCAGTCTATTAGAGATGGATCTACAACCTTGAGAACTGTCAAAGATGTTGGC
EST: gi|33793306|gb|CF322532.1|CF322532
EST:     AGAAGACTGATAGTGACCATGAGGATGAACTTGATGAGTATCAGGATCAG                         CAGTCTATTAGAGATGGATCTACAACCTTGAGAACTGTCAAAGATGTTGGC
genomic: AGAAGACTGATAGTGACCATGAGGATGAACTTGATGAGTATCAGGATCAGgtaatcatgt ... atttgtgcagCAGTCTATTAGAGATGGATCTACAACCTTGAGAACTGTCAAAGATGTTGGC
EST: gi|29657638|gb|CB653913.1|CB653913
EST:     AGAAGACTGATAGTGACCATGAGGATGAACTTGATGAGTATCAGGATCAG                         CAGTCTATTAGAGATGGATCTACAACCTTGAGAACTGTCAAAGATGTTGGC
genomic: AGAAGACTGATAGTGACCATGAGGATGAACTTGATGAGTATCAGGATCAGgtaatcatgt ... atttgtgcagCAGTCTATTAGAGATGGATCTACAACCTTGAGAACTGTCAAAGATGTTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttttggcctaccgatctgacttttattgtcttcgtgtattttatttgtgcagCAGTCTATTAGAGATGGATCTACAACCTTGAGAACTGTCAAAGATGTTGGCATAGATTCATCACTGAGTGCCTCTCCTTCTCGTTGGCCTATTGATTTTG
                atctgac  putative branch site (score: 3)
                                         ttttattt  putative PPT
                                     tgtattttatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttcaaagattgcaactgttgttgcctatgcataatttgccagtctgttttggcctaccgatctgacttttattgtcttcgtgtattttatttgtgcagCAGTCTATTAGAGATGGATCTACAACCTTGAGAACTGTCAAAGATGTTGGCATAGATTCATCACTGAGTGCCTCTCCTTCTCGTTGGCCTATTGATTTTG

- - - - gattgca
- - - - - - - - - - tgttgcc
- - - - - - - - - - - - - - atgcata
- - - - - - - - - - - - - - - - - - - - - - - tgttttg