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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaatttaccccttttaaatcaaaatcaaaacaagcataatttatctgattttgcccctatggtctgaatgcttccatatcaaattctcaataccttcagGCCTGGGAGCTGTACGAGAACAACAACCCTCTGGGCATTGTAGACCCAAATCTCAGAGAATTCAACAGGGCGGAGGTGCTCCGGGCCATCCACGTCGCCC

Basic information

species Oryza sativa
transcript LOC_Os04g52600.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52600.1 (Oryza sativa), 3'ss of exon 23
lower sequence: GRMZM2G155837_T02 (Zea mays), 3'ss of exon 19
ctaatttaccccttttaaatcaaaatcaaaacaagcataatttatc---tgattttgcccctatg-gtctgaatgct-tccatatcaaattctcaataccttcagGCCTGGGAGCTGTACGAGAACAACAACCCTCTGGGCATTGTAGACCCAAATCTCAGAGAATTCAACAGGGCGGAGGTGCTCCGGGCCATCCACGTCGCCC
 |||| ||   |   | ||||   | |  || |  ||||| | |      ||  | || ||   | ||| |  ||   |   || | |||  |     | |||||| |||| | ||||||||  | ||| ||||||||| |||  | ||||| || |||  |||||||||||| |  ||||||||||| ||||||||||| ||||
ataatatagatc---tgaatctgtaccgtaata--cataactgaagaaacgaagtcgctccagcgtgtcaggttgtaatttctagctaatcttgtgcgctttcagGTCTGGCAACTGTACGAAGAAAACCACCCTCTGGACATGCTCGACCCGAAGCTCGCAGAATTCAACAGCGACGAGGTGCTCCGTGCCATCCACGTGGCCC
















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|29680824|gb|CB677099.1|CB677099
EST:     CGAACTACGATGATACACTTGAAGAAGATAAGATTTACATTTTCGAATGG                         GCCTGGGAGCTGTACGAGAACAACAACCCTCTGGGCATTGT
genomic: CGAACTACGATGATACACTTGAAGAAGATAAGATTTACATTTTCGAATGGgtaagctcag ... ataccttcagGCCTGGGAGCTGTACGAGAACAACAACCCTCTGGGCATTGT
EST: gi|29661697|gb|CB657972.1|CB657972
EST:     CGAACTACGATGATACACTTGAAGAAGATAAGATTTACATTTTCGAATGG                         GCCTGGGAGCTGTACGAGAACAACAACCCTCTGGGCATTGTAGACCCAAAT
genomic: CGAACTACGATGATACACTTGAAGAAGATAAGATTTACATTTTCGAATGGgtaagctcag ... ataccttcagGCCTGGGAGCTGTACGAGAACAACAACCCTCTGGGCATTGTAGACCCAAAT
EST: gi|29661052|gb|CB657327.1|CB657327
EST:     CGAACTACGATGATACACTTGAAGAAGATAAGATTTACATTTTCGAATGG                         GCCTGGGAGCTGTACGAGAACAACAACCCTCTGGGCATTGTAGACCCAAAT
genomic: CGAACTACGATGATACACTTGAAGAAGATAAGATTTACATTTTCGAATGGgtaagctcag ... ataccttcagGCCTGGGAGCTGTACGAGAACAACAACCCTCTGGGCATTGTAGACCCAAAT
EST: gi|58592421|gb|CF990729.1|CF990729
EST:     CGAACTACGATGATACACTTGAAGAAGATAAGATTTACATTTTCGAATGG                         GCCTGGGAGCTGTACGAGAACAACAACCGCTCTGGGCATTGTAGACCCAAA
genomic: CGAACTACGATGATACACTTGAAGAAGATAAGATTTACATTTTCGAATGGgtaagctcag ... ataccttcagGCCTGGGAGCTGTACGAGAACAACAACC-CTCTGGGCATTGTAGACCCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgattttgcccctatggtctgaatgcttccatatcaaattctcaataccttcagGCCTGGGAGCTGTACGAGAACAACAACCCTCTGGGCATTGTAGACCCAAATCTCAGAGAATTCAACAGGGCGGAGGTGCTCCGGGCCATCCACGTCGCCC
 atctgat  putative branch site (score: 4)
                                              taccttc  putative PPT
                               atatcaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaatttaccccttttaaatcaaaatcaaaacaagcataatttatctgattttgcccctatggtctgaatgcttccatatcaaattctcaataccttcagGCCTGGGAGCTGTACGAGAACAACAACCCTCTGGGCATTGTAGACCCAAATCTCAGAGAATTCAACAGGGCGGAGGTGCTCCGGGCCATCCACGTCGCCC

- - - - - - - - aaatcaa
- - - - - - - - - - - - - - - -caagcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatgc