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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcacccgtacgcagcatcctctcttccatcccctctctaccccgcaccttttctcttcgccttaacccttagctgaaaccgcatgccgcagGTTTGGCCCGGCTCTGAAGTAAGCAGGATTCTGAATCTGAGAACGAGGAGTTGGATTGGGGGACTATGGCTCAGATCCCCAATCTCGACAATGCTCCTCT

Basic information

species Oryza sativa
transcript LOC_Os04g14654.1
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|88453003|gb|CI574550.1|CI574550
EST:     CAGCAGCGGGCGCCGCCGACCTGCTGCTTCCGCCCGCATCCTCGTCGCCG                         GTTTGGCCCGGCTCTGAAGTAAGCAGGATTCTGAATCTGAGAACGAGGAGT
genomic: CAGCAGCGGGCGCCGCCGACCTGCTGCTTCCGCCCGCATCCTCGTCGCCGgtgagcaccc ... catgccgcagGTTTGGCCCGGCTCTGAAGTAAGCAGGATTCTGAATCTGAGAACGAGGAGT
EST: gi|88301457|gb|CI597150.1|CI597150
EST:     CAGCAGCGGGCGCCGCCGACCTGCTGCTTCCGCCCGCATCCTCGTCGCCG                         GTTTGGCCCGGCTCTGAAGTAAGCAGGATTCTGAATCTGAGAACGAGGAGT
genomic: CAGCAGCGGGCGCCGCCGACCTGCTGCTTCCGCCCGCATCCTCGTCGCCGgtgagcaccc ... catgccgcagGTTTGGCCCGGCTCTGAAGTAAGCAGGATTCTGAATCTGAGAACGAGGAGT
EST: gi|88760782|gb|CI770338.1|CI770338
EST:     CAGCAGCGGGCGCCGCCGACCTGCTGCTTCCGCCCGCATCCTCGTCGCCG                         GTTTGGCCCGGCTCTGAAGTAAGCAGGATTCTGAATCTGAGAACGAGGAGT
genomic: CAGCAGCGGGCGCCGCCGACCTGCTGCTTCCGCCCGCATCCTCGTCGCCGgtgagcaccc ... catgccgcagGTTTGGCCCGGCTCTGAAGTAAGCAGGATTCTGAATCTGAGAACGAGGAGT
EST: gi|88738544|gb|CI762052.1|CI762052
EST:     CAGCAGCGGGCGCCGCCGACCTGCTGCTTCCGCCCGCATCCTCGTCGCCG                         GTTTGGCCCGGCTCTGAAGTAAGCAGGATTCTGAATCTGAGAACGAGGAGT
genomic: CAGCAGCGGGCGCCGCCGACCTGCTGCTTCCGCCCGCATCCTCGTCGCCGgtgagcaccc ... catgccgcagGTTTGGCCCGGCTCTGAAGTAAGCAGGATTCTGAATCTGAGAACGAGGAGT
EST: gi|88350673|gb|CI617528.1|CI617528
EST:     CAGCAGCGGGCGCCGCCGACCTGCTGCTTCCGCCCGCATCCTCGTCGCCG                         GTTTGGCCCGGCTCTGAAGTAAGCAGGATTCTGAATCTGAGAACGAGGAGT
genomic: CAGCAGCGGGCGCCGCCGACCTGCTGCTTCCGCCCGCATCCTCGTCGCCGgtgagcaccc ... catgccgcagGTTTGGCCCGGCTCTGAAGTAAGCAGGATTCTGAATCTGAGAACGAGGAGT
EST: gi|88723438|gb|CI746948.1|CI746948
EST:     CAGCAGCGGGCGCCGCCGACCTGCTGCTTCCGCCCGCATCCTCGTCGCCG                         GTTTGGCCCGGCTCTGAAGTAAGCAGGATTCTGAATCTGAGAACGAGGAGT
genomic: CAGCAGCGGGCGCCGCCGACCTGCTGCTTCCGCCCGCATCCTCGTCGCCGgtgagcaccc ... catgccgcagGTTTGGCCCGGCTCTGAAGTAAGCAGGATTCTGAATCTGAGAACGAGGAGT
EST: gi|29635893|gb|CB640902.1|CB640902
EST:     CAGCAGCGGGCGCCGCCGACCTGCTGCTTCCGCCCGCATCCTCGTCGCCG                         GTTTGGCCCGGCTCTGAAGTAAGCAGGATTCTGAATCTGAGAACGAGGAGT
genomic: CAGCAGCGGGCGCCGCCGACCTGCTGCTTCCGCCCGCATCCTCGTCGCCGgtgagcaccc ... catgccgcagGTTTGGCCCGGCTCTGAAGTAAGCAGGATTCTGAATCTGAGAACGAGGAGT
EST: gi|117229564|gb|CT859877.1|CT859877
EST:     CAGCAGCGGGGGCCGCCGACCTGCTGCTTCCGCCCGCATCCTCGTCGCCG                         GTTTGGCCCGGCTCTGAAGTAAGCAGGATTCTGAATCTGAGAACGAGGAGT
genomic: CAGCAGCGGGCGCCGCCGACCTGCTGCTTCCGCCCGCATCCTCGTCGCCGgtgagcaccc ... catgccgcagGTTTGGCCCGGCTCTGAAGTAAGCAGGATTCTGAATCTGAGAACGAGGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaccccgcaccttttctcttcgccttaacccttagctgaaaccgcatgccgcagGTTTGGCCCGGCTCTGAAGTAAGCAGGATTCTGAATCTGAGAACGAGGAGTTGGATTGGGGGACTATGGCTCAGATCCCCAATCTCGACAATGCTCCTCT
                       ccttaac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcacccgtacgcagcatcctctcttccatcccctctctaccccgcaccttttctcttcgccttaacccttagctgaaaccgcatgccgcagGTTTGGCCCGGCTCTGAAGTAAGCAGGATTCTGAATCTGAGAACGAGGAGTTGGATTGGGGGACTATGGCTCAGATCCCCAATCTCGACAATGCTCCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC