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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtcacacacactacaagaacagctttgcaatgttgtcacattttgtaagaatcacatttttcgtgttcgttgatgccttccttacaatgcaacgacagCTTGGAACGACGCCGTGGAGGAGGCGTGCCAGAACGGCATCGGCGTGATCGCGGAGCCGAGCGGCAGCATGAGGGACGGCGACGCCGTCGACTGCTGCAA

Basic information

species Oryza sativa
transcript LOC_Os08g10570.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g10570.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G368902_T01 (Zea mays), 3'ss of exon 11
ctgtcacacacactacaagaa-cagctttgcaatgttgtcacattttgtaagaatcacatttttcgtgttcgttgatgccttcct----tacaatgcaacga--cagCTTGGAACGACGCCGTGGAGGAGGCGTGCCAGAACGGCATCGGCGTGATCGCGGAGCCGAGCGGCAGCATGAGGGACGGCGACGCCGTCGACTGCTGCAA
        |   ||    ||| | | ||    |||     |    | |||| |||      | |  | ||  ||   |  || ||    |  | || || ||  |||||||||||||||| ||||||||||||||||||  |||| | |  |||||||| |||||  ||||||||||  |||||   |||||||| || ||||||||
-------gctggctgtgtgaatctgattctggatgcaacgaagaatagtaaaaatgcagcgtctgttatttattagcgtgttgctgaactggactggaatgatgcagCTTGGAACGACGCGGTGGAGGAGGCGTGCCAGCGCGGCGTGGCGGTGATCGCAGAGCCCGGCGGCAGCATCCGGGACCAGGACGCCGTGGAGTGCTGCAA
















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|87020611|gb|CI267332.1|CI267332
EST:     AGAGGAGGCCAAAGGAGCTGCTTTGGCCAGTGATGCATTCTTCCCATTCG                         CTTGGAACGACGCCGTGGAGGAGGCGTGCCAGAACGGCATCGGCGTGATCG
genomic: AGAGGAGGCCAAAGGAGCTGCTTTGGCCAGTGATGCATTCTTCCCATTCGgtaagaacaa ... gcaacgacagCTTGGAACGACGCCGTGGAGGAGGCGTGCCAGAACGGCATCGGCGTGATCG
EST: gi|86506616|gb|CI149249.1|CI149249
EST:     AGAGGAGGCCAAAGGAGCTGCTTTGGCCAGTGATGCATTCTTCCCATTCG                         CTTGGAACGACGCCGTGGAGGAGGCGTGCCAGAACGGCATCGGCGTGATCG
genomic: AGAGGAGGCCAAAGGAGCTGCTTTGGCCAGTGATGCATTCTTCCCATTCGgtaagaacaa ... gcaacgacagCTTGGAACGACGCCGTGGAGGAGGCGTGCCAGAACGGCATCGGCGTGATCG
EST: gi|32948504|gb|BP185076.1|BP185076
EST:     AGAGGAGGCCAAAGGAGCTGCTTTGGCCAGTGATGCATTCTTCCCATTCG                         CTTGGAACGACGCCGTGGAGGAGGCGTGCCAGAACGGCATCGGCGTGATCG
genomic: AGAGGAGGCCAAAGGAGCTGCTTTGGCCAGTGATGCATTCTTCCCATTCGgtaagaacaa ... gcaacgacagCTTGGAACGACGCCGTGGAGGAGGCGTGCCAGAACGGCATCGGCGTGATCG
EST: gi|89194604|gb|CI117041.1|CI117041
EST:     AGAGGAGGCCAAAGGAGCTGCTTTGGCCAGTGATGCATTCTTCCCATTCG                         CTTGGAACGACGCCGTGGAGGAGGCGTGCCAGAACGGCATCGGCGTGATCG
genomic: AGAGGAGGCCAAAGGAGCTGCTTTGGCCAGTGATGCATTCTTCCCATTCGgtaagaacaa ... gcaacgacagCTTGGAACGACGCCGTGGAGGAGGCGTGCCAGAACGGCATCGGCGTGATCG
EST: gi|18386202|gb|BM419401.1|BM419401
EST:     AGAGGAGGCCAAAGGAGCTGCTTTGGCCAGTGATGCATTCTTCCCATTCG                         CTTGGAACGACGCCGTGGATGAGGCGTGCCAGAACGGCATCGGCGTGATCG
genomic: AGAGGAGGCCAAAGGAGCTGCTTTGGCCAGTGATGCATTCTTCCCATTCGgtaagaacaa ... gcaacgacagCTTGGAACGACGCCGTGGAGGAGGCGTGCCAGAACGGCATCGGCGTGATCG
EST: gi|55409415|gb|CV721791.1|CV721791
EST:     AGAGGAGGCCAAAGGAGCTGCTTTGGCCAGTGATGCATTCTTCCCATTCG                         CTTGGAACGACGCCGTGGA
genomic: AGAGGAGGCCAAAGGAGCTGCTTTGGCCAGTGATGCATTCTTCCCATTCGgtaagaacaa ... gcaacgacagCTTGGAACGACGCCGTGGA
EST: gi|18386348|gb|BM419546.1|BM419546
EST:     AGAGGAGGCCAAAGGAGCTGCTTTGGCCAGTGATGCATTCTTCCCATTCG                         CTTGGAACGACGCCGTGGATGAGGCGTGCCAGAACGGCATCGGCGTGATCG
genomic: AGAGGAGGCCAAAGGAGCTGCTTTGGCCAGTGATGCATTCTTCCCATTCGgtaagaacaa ... gcaacgacagCTTGGAACGACGCCGTGGAGGAGGCGTGCCAGAACGGCATCGGCGTGATCG
EST: gi|86493028|gb|CI135661.1|CI135661
EST:     AGAGGAGGCCAAAGGAGCTGCTTTGGCCAGTGATGCATTCTTCCCATTCG                         CTTGGAACGACGCCGTGGAGGAGGCGTGCCAGAACGGCATCGGCGTGATCG
genomic: AGAGGAGGCCAAAGGAGCTGCTTTGGCCAGTGATGCATTCTTCCCATTCGgtaagaacaa ... gcaacgacagCTTGGAACGACGCCGTGGAGGAGGCGTGCCAGAACGGCATCGGCGTGATCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaagaatcacatttttcgtgttcgttgatgccttccttacaatgcaacgacagCTTGGAACGACGCCGTGGAGGAGGCGTGCCAGAACGGCATCGGCGTGATCGCGGAGCCGAGCGGCAGCATGAGGGACGGCGACGCCGTCGACTGCTGCAA
                                   tccttac  putative branch site (score: 2)
          acattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtcacacacactacaagaacagctttgcaatgttgtcacattttgtaagaatcacatttttcgtgttcgttgatgccttccttacaatgcaacgacagCTTGGAACGACGCCGTGGAGGAGGCGTGCCAGAACGGCATCGGCGTGATCGCGGAGCCGAGCGGCAGCATGAGGGACGGCGACGCCGTCGACTGCTGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC