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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttctatttatacttctgtttatttaattgttgtttcgaattgttagactagactgtaatggcatgcagtctgcgatgattcaaagtgtatttgtttaagcaaattaacagcttcttctgggccgtgtgtaacatatatcattttccaattaacttttcgattttgcagATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAATCCCCGGTGGGTGGATGGTGAGCTATTGGTGCTCAATGGCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g01790.1
intron # 9
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|29677187|gb|CB673462.1|CB673462
EST:     AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTG                         ATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
genomic: AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTGgtaatttcta ... gattttgcagATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
EST: gi|8856498|gb|AU093816.1|AU093816
EST:     AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTG                         ATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
genomic: AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTGgtaatttcta ... gattttgcagATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
EST: gi|86595065|gb|CI260304.1|CI260304
EST:     TGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTG                         ATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
genomic: TGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTGgtaatttcta ... gattttgcagATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
EST: gi|29623733|gb|CB628744.1|CB628744
EST:     AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTG                         ATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
genomic: AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTGgtaatttcta ... gattttgcagATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
EST: gi|58696013|gb|CK084700.1|CK084700
EST:     AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTG                         ATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
genomic: AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTGgtaatttcta ... gattttgcagATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
EST: gi|25802741|gb|CA758702.1|CA758702
EST:     AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTG                         ATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
genomic: AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTGgtaatttcta ... gattttgcagATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
EST: gi|29624183|gb|CB629194.1|CB629194
EST:     AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTG                         ATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
genomic: AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTGgtaatttcta ... gattttgcagATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
EST: gi|29624596|gb|CB629607.1|CB629607
EST:     AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTG                         ATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
genomic: AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTGgtaatttcta ... gattttgcagATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
EST: gi|29630522|gb|CB635531.1|CB635531
EST:     AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTG                         ATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
genomic: AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTGgtaatttcta ... gattttgcagATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
EST: gi|27921302|gb|CB097110.1|CB097110
EST:     AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTG                         ATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
genomic: AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTGgtaatttcta ... gattttgcagATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
EST: gi|29622850|gb|CB627861.1|CB627861
EST:     AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTG                         ATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
genomic: AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTGgtaatttcta ... gattttgcagATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
EST: gi|29622533|gb|CB627544.1|CB627544
EST:     AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTG                         ATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
genomic: AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTGgtaatttcta ... gattttgcagATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
EST: gi|29617659|gb|CB622671.1|CB622671
EST:     AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTG                         ATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
genomic: AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTGgtaatttcta ... gattttgcagATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
EST: gi|22305855|gb|BQ907077.1|BQ907077
EST:     GGGCCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTG                         ATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
genomic: GGG-CAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTGgtaatttcta ... gattttgcagATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
EST: gi|29624598|gb|CB629609.1|CB629609
EST:     AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTG                         ATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
genomic: AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTGgtaatttcta ... gattttgcagATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
EST: gi|29669220|gb|CB665495.1|CB665495
EST:     AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTG                         ATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
genomic: AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTGgtaatttcta ... gattttgcagATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
EST: gi|15855354|gb|BI808166.1|BI808166
EST:     CCCTGAAGAATTTGGTGTG                         ATTGTCTAGCTATAAAGGTCAA-GGAGAATTGCACA-CCTGGCTTC-AAAA
genomic: CCCTGAAGAATTTGGTGTGgtaatttcta ... gattttgcagATTG-CTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAA
EST: gi|29621884|gb|CB626895.1|CB626895
EST:     AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTG                         ATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
genomic: AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTGgtaatttcta ... gattttgcagATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT
EST: gi|29625044|gb|CB630055.1|CB630055
EST:     AGGGCAAACGTTTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTG                         ATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGTTTCAAAAAT
genomic: AGGGCAAACGTCTTGAGAACCGTGGTGCATACCCTGAAGAATTTGGTGTGgtaatttcta ... gattttgcagATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctgggccgtgtgtaacatatatcattttccaattaacttttcgattttgcagATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAATCCCCGGTGGGTGGATGGTGAGCTATTGGTGCTCAATGGCAAG
                                 aattaac  putative branch site (score: 2)
                                       cttttcg  CT-rich tract
               taacatatatcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttctatttatacttctgtttatttaattgttgtttcgaattgttagactagactgtaatggcatgcagtctgcgatgattcaaagtgtatttgtttaagcaaattaacagcttcttctgggccgtgtgtaacatatatcattttccaattaacttttcgattttgcagATTGCTAGCTATAAAGGTCAAGGGAGAATTGCACAGCCTGGCTTCAAAAATCCCCGGTGGGTGGATGGTGAGCTATTGGTGCTCAATGGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA