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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agattgtggtaggatttagctgctacatggaacagacatattcttgagtgtttttcctttagctgccgctatttcatgatctgtctacttttggatatagGTCATTGATGTAGCAACTTCTCTTGCCAAAGTTGCGGATGTCGATAGAAATCTTGGGAACGAAAGCATGGCAGTTGAGGGTTTTGAGGAAGCAATTAAAT

Basic information

species Oryza sativa
transcript LOC_Os02g55200.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g55200.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G049672_T01 (Zea mays), 3'ss of exon 6
agattgtggtaggatttagctgctacatggaacagacata---ttcttgagtgtttt-tcctttagctgccgctatttcatgatctgtctacttttggatatagGTCATTGATGTAGCAACTTCTCTTGCCAAAGTTGCGGATGTCGATAGAAATCTTGGGAACGAAAGCATGGCAGTTGAGGGTTTTGAGGAAGCAATTAAAT
    |  |  | |       ||||     | | |  | ||    |||    |   |  | | | |  ||||    | |  | |  ||     ||||| ||||||||||||||| | |||||||||||||| |||||||||||||| |||||||||||||| |||||||| |  |||||||||||||||||||||||||||  ||
----tcagccaaggccatcttgctttcaaggataagcttagggctctcagatccgtaatacctgaagtgccatattattttaacttgcaatattttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAATCTTGGTAACGAAAGTACCGCAGTTGAGGGTTTTGAGGAAGCAATTCGAT
















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|29657742|gb|CB654017.1|CB654017
EST:     TGGACGTTCGCAGAAGTGCAGTAAAAGAACACTCAGCTGTGGCTTCCCAG                         GTCATTGATGTAGCAACTTCTCTTGCCAAAGTTGCGGATGTCGATAGAAAT
genomic: TGGACGTTCGCAGAAGTGCAGTAAAAGAACACTCAGCTGTGGCTTCCCAGgtgattactg ... ttggatatagGTCATTGATGTAGCAACTTCTCTTGCCAAAGTTGCGGATGTCGATAGAAAT
EST: gi|89189931|gb|CI049470.1|CI049470
EST:     AAGAACACTCAGCTGTGGCTTCCCAG                         GTCATTGATGTAGCAACTTCTCTTGCCAAAGTTGCGGATGTCGATAGAAAT
genomic: AAGAACACTCAGCTGTGGCTTCCCAGgtgattactg ... ttggatatagGTCATTGATGTAGCAACTTCTCTTGCCAAAGTTGCGGATGTCGATAGAAAT
EST: gi|2427558|gb|C72021.1|C72021
EST:     GGACGTTCGCAGANGTGCAGTAAAAGGACCACTCAGCTGTGGCTTCCCAG                         GTCATTGATGTAG-AACTTCTCTTGCCAAAGTTCCGGATGTCGATAGAAA
genomic: GGACGTTCGCAGAAGTGCAGTAAAAGAAC-ACTCAGCTGTGGCTTCCCAGgtgattactg ... ttggatatagGTCATTGATGTAGCAACTTCTCTTGCCAAAGTTGCGGATGTCGATAGAAA
EST: gi|86597624|gb|CI274615.1|CI274615
EST:     GTTCGCAGAAGTGCAGTAAAAGAACACTCAGCTGTGGCTTCCCAG                         GTCATTGATGTAGCAACTTCTCTTGCCAAAGTTGCGGATGTCGATAGAAAT
genomic: GTTCGCAGAAGTGCAGTAAAAGAACACTCAGCTGTGGCTTCCCAGgtgattactg ... ttggatatagGTCATTGATGTAGCAACTTCTCTTGCCAAAGTTGCGGATGTCGATAGAAAT
EST: gi|58589478|gb|CF987786.1|CF987786
EST:     TGGGCGTTCGCAGAAGTGCAGTAAAAGAACACTCAGCTGTGGCTTCCCAG                         GTCATTGATGTAGCAACTTCTCTTGCCAAAGTTGCGGATGTCGATAGAAAT
genomic: TGGACGTTCGCAGAAGTGCAGTAAAAGAACACTCAGCTGTGGCTTCCCAGgtgattactg ... ttggatatagGTCATTGATGTAGCAACTTCTCTTGCCAAAGTTGCGGATGTCGATAGAAAT
EST: gi|29659820|gb|CB656095.1|CB656095
EST:     TGGACGTTCGCAGAAGTGCAGTAAAAGAACACTCAGCTGTGGCTTCCCAG                         GTCATTGATGTAGCAACTTCTCTTGCCAAAGTTGCGGATGTCGATAGAAAT
genomic: TGGACGTTCGCAGAAGTGCAGTAAAAGAACACTCAGCTGTGGCTTCCCAGgtgattactg ... ttggatatagGTCATTGATGTAGCAACTTCTCTTGCCAAAGTTGCGGATGTCGATAGAAAT
EST: gi|9865344|gb|AU101094.1|AU101094
EST:     TGGACGTTCGCAGAAGTGCAGTAAAAGAACACTCAGCTGTGGCTTCCCAG                         GTCATTGATGTAGCAACTTCTCTTGCCAAAGTTGCGGATGTCGATAGAAAT
genomic: TGGACGTTCGCAGAAGTGCAGTAAAAGAACACTCAGCTGTGGCTTCCCAGgtgattactg ... ttggatatagGTCATTGATGTAGCAACTTCTCTTGCCAAAGTTGCGGATGTCGATAGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtgtttttcctttagctgccgctatttcatgatctgtctacttttggatatagGTCATTGATGTAGCAACTTCTCTTGCCAAAGTTGCGGATGTCGATAGAAATCTTGGGAACGAAAGCATGGCAGTTGAGGGTTTTGAGGAAGCAATTAAAT
                                      tctactttt  CT-rich tract
                        tatttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agattgtggtaggatttagctgctacatggaacagacatattcttgagtgtttttcctttagctgccgctatttcatgatctgtctacttttggatatagGTCATTGATGTAGCAACTTCTCTTGCCAAAGTTGCGGATGTCGATAGAAATCTTGGGAACGAAAGCATGGCAGTTGAGGGTTTTGAGGAAGCAATTAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA