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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTGgttagttcaaatttacagcatctttgtctgacataatttgcaaagtgtttaattaactgtctgacatgatggttcattag

Basic information

species Oryza sativa
transcript LOC_Os03g17980.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G107867_T04 (Zea mays), 5'ss of exon 7
GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTGgttagttcaaatttacagcatctttgt-ctgacataatttgcaaagtgtttaattaactgtctgac-atgatggttc-attag------------------------
||||||||||||||||||||||| ||||||||||| ||  |||| || ||||||||| | || ||||| |||||||||||  |||||||| || ||| ||| || ||  ||  | | | ||  |    || ||||| || |     |||  ||  |    | |||||                        
GCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATGgttagtacacattaacaacacctgggtgttcaaaaaagatcttgagggtttatttgatctattgatgattctaacactattagatgtttgaatggttgcctctccag
















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|29672731|gb|CB669006.1|CB669006
EST:     GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTG                         GAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
genomic: GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTGgttagttcaa ... ggttcattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
EST: gi|29673828|gb|CB670103.1|CB670103
EST:     GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTG                         GAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
genomic: GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTGgttagttcaa ... ggttcattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
EST: gi|58666104|gb|CK054790.1|CK054790
EST:     GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCGTTG                         GAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATA
genomic: GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTGgttagttcaa ... ggttcattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATA
EST: gi|29616520|gb|CB621532.1|CB621532
EST:     GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCGTTG                         GAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
genomic: GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTGgttagttcaa ... ggttcattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
EST: gi|218478287|gb|FG959067.1|FG959067
EST:     GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCGTTG                         GAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
genomic: GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTGgttagttcaa ... ggttcattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
EST: gi|29663427|gb|CB659702.1|CB659702
EST:     GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTG                         GAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
genomic: GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTGgttagttcaa ... ggttcattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
EST: gi|218493226|gb|FG956765.1|FG956765
EST:     GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCGTTG                         GAGAGGAA-TTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
genomic: GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTGgttagttcaa ... ggttcattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
EST: gi|29614996|gb|CB620009.1|CB620009
EST:     GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCGTTG                         GAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
genomic: GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTGgttagttcaa ... ggttcattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
EST: gi|29672696|gb|CB668971.1|CB668971
EST:     GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTG                         GAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
genomic: GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTGgttagttcaa ... ggttcattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTGgttagttcaaatttacagcatctttgtctgacataatttgcaaagtgtttaattaactgtctgacatgatggttcattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG