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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttttccagagcaaagcgctggttattaccctacaaagaacatgttattttgagaagtaatgagaacaggtgatttagctgcaaagtgttctgttgcagGTATGAACGTTTCCTCAAGATAATGATTTTGAGTGTATTAAAGCAAACACAAAGACCTGTGAAATTCTGGTTCATAAAGAATTATCTATCTCCACAGTTC

Basic information

species Oryza sativa
transcript LOC_Os02g44510.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g44510.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G846198_T01 (Zea mays), 3'ss of exon 3
ctttttccagagcaaagcgctggttattaccctacaaagaacatgttattttgagaagtaatgagaacaggtgatttagctgcaaagtgttctgttgcagGTATGAACGTTTCCTCAAGATAATGATTTTGAGTGTATTAAAGCAAACACAAAGACCTGTGAAATTCTGGTTCATAAAGAATTATCTATCTCCACAGTTC
 |||  || ||     ||         ||  |   |   ||||      | ||| |||  ||||| ||| ||  |||||||||    | |  |||||||||||||| ||||||||||| |||||||||||||||||  ||||  | ||||| || || ||||| || |||||||| ||||||||||||||||||||||||
atttcacctgaagtttgcaacatactgtattcgctacccaacaaacatgtctgaaaagcgatgaggacatgtagtttagctgcgcgttttcttgttgcagGTATGAGCGTTTCCTCAAAATAATGATTTTGAGTGTTCTAAAAAAGACACAGAGGCCAGTGAAGTTTTGGTTCATTAAGAATTATCTATCTCCACAGTTC
















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|58658861|gb|CK047541.1|CK047541
EST:     GCAAGACAAGGGGAGACAATCAACATTTTCTCTGTTGCTTCTGGGCATCT                         GTATGAACGTTTCCTCAAGATAATGATTTTGAGTGTATTAAAGCAAACACA
genomic: ACAAGACAAGGGGAGACAATCAACATTTTCTCTGTTGCTTCTGGGCATCTgtaagtgccc ... tctgttgcagGTATGAACGTTTCCTCAAGATAATGATTTTGAGTGTATTAAAGCAAACACA
EST: gi|58609426|gb|CK037459.1|CK037459
EST:     AGGGGAGACAATCAACATTTTCTCTGTTGCTTCTGGGCATCT                         GTATGAACGTTTCCTCGAGATAATGATTTTGAGTGTATTAAAGCAAACACA
genomic: AGGGGAGACAATCAACATTTTCTCTGTTGCTTCTGGGCATCTgtaagtgccc ... tctgttgcagGTATGAACGTTTCCTCAAGATAATGATTTTGAGTGTATTAAAGCAAACACA
EST: gi|58654435|gb|CK043115.1|CK043115
EST:     GCAAGACAAGGGGAGACAATCAACATTTTCTCTGTTGCTTCTGGGCATCT                         GTATGAACGTTTCCTCAAGATAATGATTTTGAGTGTAT
genomic: ACAAGACAAGGGGAGACAATCAACATTTTCTCTGTTGCTTCTGGGCATCTgtaagtgccc ... tctgttgcagGTATGAACGTTTCCTCAAGATAATGATTTTGAGTGTAT
EST: gi|29624544|gb|CB629555.1|CB629555
EST:     GCAAGACAAGGGGAGACAATCAACATTTTCTCTGTTGCTTCTGGGCATCT                         GTATGAACGTTTCCTCAAGATAATGATTTTGAGTGTATTAAAGCAAACACA
genomic: ACAAGACAAGGGGAGACAATCAACATTTTCTCTGTTGCTTCTGGGCATCTgtaagtgccc ... tctgttgcagGTATGAACGTTTCCTCAAGATAATGATTTTGAGTGTATTAAAGCAAACACA
EST: gi|33794022|gb|CF322901.1|CF322901
EST:     ACAAGACAAGGGGAGACAATCAACATTTTCTCTGTTGCTTCTGGGCATCT                         GTATGAACGTTTCCTCAAGATAATGATTTTGAGTGTATTAAAGCAAACACA
genomic: ACAAGACAAGGGGAGACAATCAACATTTTCTCTGTTGCTTCTGGGCATCTgtaagtgccc ... tctgttgcagGTATGAACGTTTCCTCAAGATAATGATTTTGAGTGTATTAAAGCAAACACA
EST: gi|58689586|gb|CK078273.1|CK078273
EST:     GCAAGACAAGGGGAGACAATCAACATTTTCTCTGTTGCTTCTGGGCATCT                         GTATGAACGTTTCCTCAAGATAATGATTTTGAGTGTATTAAAGCAAACACA
genomic: ACAAGACAAGGGGAGACAATCAACATTTTCTCTGTTGCTTCTGGGCATCTgtaagtgccc ... tctgttgcagGTATGAACGTTTCCTCAAGATAATGATTTTGAGTGTATTAAAGCAAACACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattttgagaagtaatgagaacaggtgatttagctgcaaagtgttctgttgcagGTATGAACGTTTCCTCAAGATAATGATTTTGAGTGTATTAAAGCAAACACAAAGACCTGTGAAATTCTGGTTCATAAAGAATTATCTATCTCCACAGTTC
                                            ttctgtt  CT-rich tract
          aagtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttttccagagcaaagcgctggttattaccctacaaagaacatgttattttgagaagtaatgagaacaggtgatttagctgcaaagtgttctgttgcagGTATGAACGTTTCCTCAAGATAATGATTTTGAGTGTATTAAAGCAAACACAAAGACCTGTGAAATTCTGGTTCATAAAGAATTATCTATCTCCACAGTTC

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