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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagcatagtaaacaaaaattaaagtttgactaactcaaagttttagattggatgaaactactctgtattattgtcttagtggaatttgctgttgcatagGTTGGGGATGGAATAAATGATGCACCATCTTTAGCAGCTGCTGATGTGGGAGTAGCTATGCGAACAAACTCAAAAGAGAGTGCTGCCTCTGACGCGGCTT

Basic information

species Oryza sativa
transcript LOC_Os03g08070.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g08070.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM5G855347_T03 (Zea mays), 3'ss of exon 4
-tgagcatagtaaacaa--aaattaaagtttgactaactcaaagttttagattggatgaaactactctgtattattgtcttagtggaatttgctgttgcatagGTTGGGGATGGAATAAATGATGCACCATCTTTAGCAGCTGCTGATGTGGGAGTAGCTATGCGAACAAACTCAAAAGAGAGTGCTGCCTCTGACGCGGCTT
  | |   ||||    |  | ||     |||    |  | |   ||||    || ||| |  | |     |  |||| ||| || | | | |||||||  |||||||| ||||||||||| ||||| || ||||||||||| || ||||| ||| |||| ||||||||  | ||||||||||  ||||||||||| || ||||
tcgtgtcaagtacttgactacatgtctattttttaactttactttttttacctgcatgga--ttcctaacaacattgactt-gttgtactcgctgttgtctagGTTGGTGATGGAATAAACGATGCCCCGTCTTTAGCAGCCGCAGATGTTGGAATAGCCATGCGAACTCATTCAAAAGAGAACGCTGCCTCTGATGCAGCTT
















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|116875530|gb|EC366038.1|EC366038
EST:     AGGCAGGCATTATAACTGCATTGCAAGGAGAGGGACGTCGGGTTGCAATG                         GTTGGGGATGGAATAAATGATGCACCATCTTTAGCAGCTGCTGATGTGGGA
genomic: AGGCAGGCATTATAACTGCATTGCAAGGAGAGGGACGTCGGGTTGCAATGgtaatgctct ... tgttgcatagGTTGGGGATGGAATAAATGATGCACCATCTTTAGCAGCTGCTGATGTGGGA
EST: gi|116875017|gb|EC365525.1|EC365525
EST:     AGGCAGGCATTATAACTGCATTGCAAGGAGAGGGACGTCGGGTTGCAATG                         GTTGGGGATGGAATAAATGATGCACCATCTTTAGCAGCTGCTGATGTGGGA
genomic: AGGCAGGCATTATAACTGCATTGCAAGGAGAGGGACGTCGGGTTGCAATGgtaatgctct ... tgttgcatagGTTGGGGATGGAATAAATGATGCACCATCTTTAGCAGCTGCTGATGTGGGA
EST: gi|29622947|gb|CB627958.1|CB627958
EST:     AGGCAGGCATTATAACTGCATTGCAAGGAGAGGGACGTCGGGTTGCAATG                         GTTGGGGATGGAATAAATGATGCACCATCTTTAGCAGCTGCTGATGTGGGA
genomic: AGGCAGGCATTATAACTGCATTGCAAGGAGAGGGACGTCGGGTTGCAATGgtaatgctct ... tgttgcatagGTTGGGGATGGAATAAATGATGCACCATCTTTAGCAGCTGCTGATGTGGGA
EST: gi|29662866|gb|CB659141.1|CB659141
EST:     AGGCAGGCATTATAACTGCATTGCAAGGAGAGGGACGTCGGGTTGCAATG                         GTTGGGGATGGAATAAATGATGCACCATCTTTAGCAGCTGCTGATGTGGGA
genomic: AGGCAGGCATTATAACTGCATTGCAAGGAGAGGGACGTCGGGTTGCAATGgtaatgctct ... tgttgcatagGTTGGGGATGGAATAAATGATGCACCATCTTTAGCAGCTGCTGATGTGGGA
EST: gi|116875544|gb|EC366052.1|EC366052
EST:     AGGCAGGCATTATAACTGCATTGCAAGGAGAGGGACGTCGGGTTGCAATG                         GTTGGGGATGGAATAAATGATGCACCATCTTTAGCAGCTGCTGATGTGGGA
genomic: AGGCAGGCATTATAACTGCATTGCAAGGAGAGGGACGTCGGGTTGCAATGgtaatgctct ... tgttgcatagGTTGGGGATGGAATAAATGATGCACCATCTTTAGCAGCTGCTGATGTGGGA
EST: gi|116875028|gb|EC365536.1|EC365536
EST:     AGGCAGGCATTATAACTGCATTGCAAGGAGAGGGACGTCGGGTTGCAATG                         GTTGGGGATGGAATAAATGATGCACCATCTTTAGCAGCTGCTGATGTGGGA
genomic: AGGCAGGCATTATAACTGCATTGCAAGGAGAGGGACGTCGGGTTGCAATGgtaatgctct ... tgttgcatagGTTGGGGATGGAATAAATGATGCACCATCTTTAGCAGCTGCTGATGTGGGA
EST: gi|87027726|gb|CI274290.1|CI274290
EST:     AGGAGAGGGACGTCGGNTTGCAATG                         GTTGGGGATGGAATAAATGATGCACCATCTTTAGCAGCTGCTGATGTGGGA
genomic: AGGAGAGGGACGTCGGGTTGCAATGgtaatgctct ... tgttgcatagGTTGGGGATGGAATAAATGATGCACCATCTTTAGCAGCTGCTGATGTGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattggatgaaactactctgtattattgtcttagtggaatttgctgttgcatagGTTGGGGATGGAATAAATGATGCACCATCTTTAGCAGCTGCTGATGTGGGAGTAGCTATGCGAACAAACTCAAAAGAGAGTGCTGCCTCTGACGCGGCTT
                   tgtattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagcatagtaaacaaaaattaaagtttgactaactcaaagttttagattggatgaaactactctgtattattgtcttagtggaatttgctgttgcatagGTTGGGGATGGAATAAATGATGCACCATCTTTAGCAGCTGCTGATGTGGGAGTAGCTATGCGAACAAACTCAAAAGAGAGTGCTGCCTCTGACGCGGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC