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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTACACTAAAAGAGGAAGAACTAGCAGATCTGAAGGACCAGTTCGATGCAATTGATGTTGATAAAAGTGGATCAATTAGTATTGAGGAAATGCGGCATgtaagttcttactggatattcttaatgaaaatgcactttggcacataattgaagtctctgattgtcttttttatgtttcaatag

Basic information

species Oryza sativa
transcript LOC_Os02g03410.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g03410.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G053868_T02 (Zea mays), 5'ss of exon 9
AAGTACACTAAAAGAGGAAGAACTAGCAGATCTGAAGGACCAGTTCGATGCAATTGATGTTGATAAAAGTGGATCAATTAGTATTGAGGAAATGCGGCATgtaagttcttactggatattcttaatgaaaatgcactttggcacataattg----aagtctctgattgtcttttttatgtttcaatag
 || || || || |||||||| ||| ||||||||||||| ||||| |||||||||||| | |||||||||||||| |||||||| ||||||||||| |||||| |||||   | |   ||  | |||||||||| ||| |   |  || |       |   ||||||    | |  |||||||  |||
GAGCACCCTTAACGAGGAAGAGCTATCAGATCTGAAGGATCAGTTTGATGCAATTGATATCGATAAAAGTGGATCGATTAGTATCGAGGAAATGCGTCATgtaggttct-gttagtgtttgctgatgaaaatgc-cttagatcctgaactactctgcggtgctgattaatctgtgcatgtttcggtag
















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|87024700|gb|CI259415.1|CI259415
EST:     CAATTGATGTTGATAAAAGTGGATCAATTAGTATTGAGGAAATGCGGCAT                         GCCCTTGCAAAGGATCTTCCTTGGAGATTGAAGGGCCCCCGTGTTCTCGAG
genomic: CAATTGATGTTGATAAAAGTGGATCAATTAGTATTGAGGAAATGCGGCATgtaagttctt ... gtttcaatagGCCCTTGCAAAGGATCTTCCTTGGAGATTGAAGGGCCCCCGTGTTCTCGAG
EST: gi|29680387|gb|CB676662.1|CB676662
EST:     CAATTGATGTTGATAAAAGTGGATCAATTAGTATTGAGGAAATGCGGCAT                         GCCCTTGCAAAGGATCTTCCTTGGAGATTGAAGGGCCCCCGTGTTCTCGAG
genomic: CAATTGATGTTGATAAAAGTGGATCAATTAGTATTGAGGAAATGCGGCATgtaagttctt ... gtttcaatagGCCCTTGCAAAGGATCTTCCTTGGAGATTGAAGGGCCCCCGTGTTCTCGAG
EST: gi|44675829|gb|CR289263.1|CR289263
EST:     CAATTGATGTTGATAAAAGTGGATCAATTAGTATTGAGGAAATGCGGCAT                         GCCCTTGCAAAGGATCTTCCTTGGAGATTGAAGGGCCCCCGTGTTCTCGAG
genomic: CAATTGATGTTGATAAAAGTGGATCAATTAGTATTGAGGAAATGCGGCATgtaagttctt ... gtttcaatagGCCCTTGCAAAGGATCTTCCTTGGAGATTGAAGGGCCCCCGTGTTCTCGAG
EST: gi|88576337|gb|CI670482.1|CI670482
EST:     CAATTGATGTTGATAAAAGTGGATCAATTAGTATTGAGGAAATGCGGCAT                         GCCCTTGCAAAGGATCTTCCTTGGAGATTGAAGGGCCCCCGTGTTCTCGAG
genomic: CAATTGATGTTGATAAAAGTGGATCAATTAGTATTGAGGAAATGCGGCATgtaagttctt ... gtttcaatagGCCCTTGCAAAGGATCTTCCTTGGAGATTGAAGGGCCCCCGTGTTCTCGAG
EST: gi|29657421|gb|CB653696.1|CB653696
EST:     CAATTGATGTTGATAAAAGTGGATCAATTAGTATTGAGGAAATGCGGCAT                         GCCCTTGCAAAGGATCTTCCTTGGAGATTGAAGGGCCCCGGTGTTCTCGAG
genomic: CAATTGATGTTGATAAAAGTGGATCAATTAGTATTGAGGAAATGCGGCATgtaagttctt ... gtttcaatagGCCCTTGCAAAGGATCTTCCTTGGAGATTGAAGGGCCCCCGTGTTCTCGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGTACACTAAAAGAGGAAGAACTAGCAGATCTGAAGGACCAGTTCGATGCAATTGATGTTGATAAAAGTGGATCAATTAGTATTGAGGAAATGCGGCATgtaagttcttactggatattcttaatgaaaatgcactttggcacataattgaagtctctgattgtcttttttatgtttcaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA