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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctttttaggaaacattaagatactttgaaatgtgaaagaagtctgttgagaacaaataagggatggtgtcagtatcaattggtattcttattccatcaacaatctacttaattatgttttatattacttgtggctgcagGCTTACTCTATCGAAGTTTGCCGAGCTGAACATCAAGCTCTGGGCCTATCAATT

Basic information

species Oryza sativa
transcript LOC_Os11g04030.1
intron # 5
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|29680054|gb|CB676329.1|CB676329
EST:     CCACGAGATTCCTTCTTGGTGCTCTGAATGGATTGCTTGCACCAATAAAG                         GCTTACTCTATCGAAGTTTGCCGAGCTGAACATCAAGCTCTGGGCCTATCA
genomic: CCACGAGATTCCTTCTTGGTGCTCTGAATGGATTGCTTGCACCAATAAAGgtaccttttt ... gtggctgcagGCTTACTCTATCGAAGTTTGCCGAGCTGAACATCAAGCTCTGGGCCTATCA
EST: gi|29674310|gb|CB670585.1|CB670585
EST:     CCACGAGATTCCTTCTTGGTGCTCTGAATGGATTGCTTGCACCAATAAAG                         GCTTACTCTATCGAAGTTTGCCGAGCTGAACATCAAGCTCTGGGCCTATCA
genomic: CCACGAGATTCCTTCTTGGTGCTCTGAATGGATTGCTTGCACCAATAAAGgtaccttttt ... gtggctgcagGCTTACTCTATCGAAGTTTGCCGAGCTGAACATCAAGCTCTGGGCCTATCA
EST: gi|29644401|gb|CB649408.1|CB649408
EST:     CCACGAGATTCCTTCTTGGTGCTCTGAATGGATTGCTTGCACCAATAAAG                         GCTTACTCTATCGAAGTTTGCCGAGCTGAACATCAAGCTCTGGGCCTATCA
genomic: CCACGAGATTCCTTCTTGGTGCTCTGAATGGATTGCTTGCACCAATAAAGgtaccttttt ... gtggctgcagGCTTACTCTATCGAAGTTTGCCGAGCTGAACATCAAGCTCTGGGCCTATCA
EST: gi|33677870|gb|CF306109.1|CF306109
EST:     CCACGAGATTCCTTCTTGGTGCTCTGAATGGATTGCTTGCACCAATAAAG                         GCTTACTCTATCGAAGTTTGCCGAGCTGAACATCAAGCTCTGGGCCTATCA
genomic: CCACGAGATTCCTTCTTGGTGCTCTGAATGGATTGCTTGCACCAATAAAGgtaccttttt ... gtggctgcagGCTTACTCTATCGAAGTTTGCCGAGCTGAACATCAAGCTCTGGGCCTATCA
EST: gi|88411903|gb|CI571395.1|CI571395
EST:     CCACGAGATTCCTTCTTGGTGCTCTGAATGGATTGCTTGCACCAATAAAG                         GCTTACTCTATCGAAGTTTGCCGAGCTGAACATCAAGCTCTGGGCCTATCA
genomic: CCACGAGATTCCTTCTTGGTGCTCTGAATGGATTGCTTGCACCAATAAAGgtaccttttt ... gtggctgcagGCTTACTCTATCGAAGTTTGCCGAGCTGAACATCAAGCTCTGGGCCTATCA
EST: gi|29682083|gb|CB678358.1|CB678358
EST:     CCACGAGATTCCTTCTTGGTGCTCTGAATGGATTGCTTGCACCAATAAAG                         GCTTACTCTATCGAAGTTTGCCGAGCTGAACATCAAGCTCTGGGCCTATCA
genomic: CCACGAGATTCCTTCTTGGTGCTCTGAATGGATTGCTTGCACCAATAAAGgtaccttttt ... gtggctgcagGCTTACTCTATCGAAGTTTGCCGAGCTGAACATCAAGCTCTGGGCCTATCA
EST: gi|29679865|gb|CB676140.1|CB676140
EST:     CCACGAGATTCCTTCTTGGTGCTCTGAATGGATTGCTTGCACCAATAAAG                         GCTTACTCTATCGAAGTTTGCCGAGCTGAACATCAAGCTCTGGGCCTATCA
genomic: CCACGAGATTCCTTCTTGGTGCTCTGAATGGATTGCTTGCACCAATAAAGgtaccttttt ... gtggctgcagGCTTACTCTATCGAAGTTTGCCGAGCTGAACATCAAGCTCTGGGCCTATCA
EST: gi|33678908|gb|CF307147.1|CF307147
EST:     CCACGAGATTCCTTCTTGGTGCTCTGAATGGATTGCTTGCACCAATAAAG                         GCTTACTCTATCGAAGTTTGCCGAGCTGAACATCAAGCTCTGGGCCTATCA
genomic: CCACGAGATTCCTTCTTGGTGCTCTGAATGGATTGCTTGCACCAATAAAGgtaccttttt ... gtggctgcagGCTTACTCTATCGAAGTTTGCCGAGCTGAACATCAAGCTCTGGGCCTATCA
EST: gi|29678070|gb|CB674345.1|CB674345
EST:     CCACGAGATTCCTTCTTGGTGCTCTGAATGGATTGCTTGCACCAATAAAG                         GCTTACTCTATCGAAGTTTGCCGAGCTGAACATCAAGCTCTGGGCCTATCA
genomic: CCACGAGATTCCTTCTTGGTGCTCTGAATGGATTGCTTGCACCAATAAAGgtaccttttt ... gtggctgcagGCTTACTCTATCGAAGTTTGCCGAGCTGAACATCAAGCTCTGGGCCTATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttattccatcaacaatctacttaattatgttttatattacttgtggctgcagGCTTACTCTATCGAAGTTTGCCGAGCTGAACATCAAGCTCTGGGCCTATCAATT
                     acttaat  putative branch site (score: 4)
             aacaatctacttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacctttttaggaaacattaagatactttgaaatgtgaaagaagtctgttgagaacaaataagggatggtgtcagtatcaattggtattcttattccatcaacaatctacttaattatgttttatattacttgtggctgcagGCTTACTCTATCGAAGTTTGCCGAGCTGAACATCAAGCTCTGGGCCTATCAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT