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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcccaatctccccctcctccccgaaccccaactcccgaggatcgattgagtgaaattttgtggattttggatgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGATCAGCTACCTGACGGGACCGCTGGGGGAGTCGACGGCGGGGGCGGCGGC

Basic information

species Oryza sativa
transcript LOC_Os01g65100.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65100.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G400602_T01 (Zea mays), 3'ss of exon 1
-----gtacgcccaatctccccctcctccccgaaccccaactcccgaggatcgatt--gagtgaaat--tttgtggattttggatgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGATCAGCTACCTGACGGGACCGCTGGGGGAGTCGACGGCGGGGGCGGCGGC
     |  | |||  ||  | |      | ||  | |  |||   | ||  ||     | ||  | |  |     |   | ||||| |   |||||||||||| ||||||||||||||||||||||| |||||||||||||||||||||||||||||||| ||||| ||||| || || ||||| ||||||||
gtacggcgccccctgtcctcgctgggcacgcgcgcacacactgatgcggcgcgggccggggttgactaatcgagaggggtcggatgggtgcagGGGTGGAGATAGCGGAGAGGTTCGCGTACCACGGGGTGTCGGCGAACCTGATCAGCTACCTGACGGGGCCGCTCGGGGAATCCACCGCGGGCGCGGCGGC
















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|29658133|gb|CB654408.1|CB654408
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGACATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|88452998|gb|CI574545.1|CI574545
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|29617558|gb|CB622570.1|CB622570
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|29660045|gb|CB656320.1|CB656320
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|87023816|gb|CI288169.1|CI288169
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|88326976|gb|CI676089.1|CI676089
EST:     GGCCTCCCGCGCCTCCACCGGCCGNTGGTCCGCCGTAATGTTCGTNCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACTACGGTGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|29677445|gb|CB673720.1|CB673720
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|88309678|gb|CI656419.1|CI656419
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGNGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|88765227|gb|CI774321.1|CI774321
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|88576350|gb|CI670495.1|CI670495
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|88410323|gb|CI575921.1|CI575921
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|29681953|gb|CB678228.1|CB678228
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|86888738|gb|CI307796.1|CI307796
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|29657453|gb|CB653728.1|CB653728
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|29633992|gb|CB639001.1|CB639001
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|58587513|gb|CF985821.1|CF985821
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|86901070|gb|CI306259.1|CI306259
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|29674560|gb|CB670835.1|CB670835
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|88388197|gb|CI627736.1|CI627736
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|29657215|gb|CB653490.1|CB653490
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|88354398|gb|CI624788.1|CI624788
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|88370001|gb|CI680683.1|CI680683
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTTAC-ACGGCGTGTCGGCGAACCTG
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGT-ACCACGGCGTGTCGGCGAACCTG
EST: gi|88426172|gb|CI574055.1|CI574055
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCAAGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|88410871|gb|CI578677.1|CI578677
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGAGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
EST: gi|29681781|gb|CB678056.1|CB678056
EST:     GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCG                         GGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA
genomic: GGCCTCCCGCGCCTCCACCGGCCGCTGGTCCGCCGCAATGTTCGTCCTCGgtacgcccaa ... atgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccccaactcccgaggatcgattgagtgaaattttgtggattttggatgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGATCAGCTACCTGACGGGACCGCTGGGGGAGTCGACGGCGGGGGCGGCGGC
                         tgaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcccaatctccccctcctccccgaaccccaactcccgaggatcgattgagtgaaattttgtggattttggatgtgaaaagGGGTGGAGATCGCGGAGAGGTTCGCGTACCACGGCGTGTCGGCGAACCTGATCAGCTACCTGACGGGACCGCTGGGGGAGTCGACGGCGGGGGCGGCGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT