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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGGATCCCTATTGGAAGGAAAATAGACCTTGCAGCCTATAACAGCTATGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaattaacaatctatccaaataaaataagtacttcattttttataaaattcttagcttttatctgatcatattgcag

Basic information

species Oryza sativa
transcript LOC_Os01g53880.4
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g53880.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G057067_T01 (Zea mays), 5'ss of exon 3
GATGGGATCCCTATTGGAAGGAAAATAGACCTTGCAGCCTATAACAGCTATGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgta-gaaattaac-aatctatccaaataaaataagtacttcattt--tttataaaattcttagcttttatctgatcatattgcag----------------
|| |||||||| || ||||||||| ||||||||||||||||  ||||||| ||  |||||||    |  |||||| | || ||||| || ||||||||||||  ||||| | | ||||  |   ||  ||| |  |||||   ||  ||| || ||||  |||   || ||      |  ||                   
GACGGGATCCCCATCGGAAGGAAAGTAGACCTTGCAGCCTACGACAGCTACGAGAGGCTATCACTGGGCGTCAAAGAGCTTTTCCACGGTTTTCTTCAAGgtgcgaaatcagccaatcagttagaacgaaacagttacttggattcatttttagaatttctagagatt-tcgagctgtggtgggcctaaagttatagggtc
















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|29675176|gb|CB671451.1|CB671451
EST:     TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|86842279|gb|CI335208.1|CI335208
EST:     TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|29672643|gb|CB668918.1|CB668918
EST:     TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|29679028|gb|CB675303.1|CB675303
EST:     TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|88830109|gb|CI074781.1|CI074781
EST:     AGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: AGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|4715467|gb|AU056584.1|AU056584
EST:     TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|88831238|gb|CI082048.1|CI082048
EST:     GGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: GGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|88831004|gb|CI080428.1|CI080428
EST:     GTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: GTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|29643256|gb|CB648263.1|CB648263
EST:     TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|29675174|gb|CB671449.1|CB671449
EST:     TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|29639753|gb|CB644762.1|CB644762
EST:     TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|89177420|gb|CI250869.1|CI250869
EST:     TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGGATCCCTATTGGAAGGAAAATAGACCTTGCAGCCTATAACAGCTATGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaattaacaatctatccaaataaaataagtacttcattttttataaaattcttagcttttatctgatcatattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG