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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcgtttccagatttctgggtttttttttttttggatgcgattcgtgggttttcttgatgctaatgggggcgggctcgatcgatcgatccccgatgtagGTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCGCCGGTCGCCGAGGAAGACGGCGTCGCCGTCGTCAGGCGAGCGTTCGAGG

Basic information

species Oryza sativa
transcript LOC_Os10g28320.4
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g28320.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G813143_T02 (Zea mays), 3'ss of exon 1
-tttcgtttccagatttctgggtttttttttttttggatgcgattcgtgggttttcttgatgctaatgggggcgggctcgatcgatcgatccccgatgtagGTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCGCCGGTCGCCGAGGAAGACGGCGTCGCCGTCGTCAGGCGAGCGTTCGAGG
 | | |  |    | |      ||     |  |||   | | ||| |   | ||| ||| ||    |  |  ||     | | |  ||||     ||| ||||||||||||| || |||||||||||||||||||| || || ||||| || || ||  | ||  |||  ||  ||| | |  ||| ||  ||||| ||||
atattgcctgtgcactaggaaattcagaatcattttcctacaattggatcggttt-ttgttgtggttttgatcgattgggcttgtgcgatgtgaaatgcagGTGTCCAAGCTTGGCTTCGGGTGCATGGGCCTCACTGGAGTGTACAACGCCCCTGTTCCTGACCAAGCTGGGATCGACATAATCAAGCACGCGTTTGAGG
















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|29661845|gb|CB658120.1|CB658120
EST:     TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAG                         GTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
genomic: TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAGgtaagcaaac ... cccgatgtagGTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
EST: gi|33665546|gb|CF296513.1|CF296513
EST:     TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAG                         GTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
genomic: TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAGgtaagcaaac ... cccgatgtagGTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
EST: gi|88570556|gb|CI661929.1|CI661929
EST:     TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAG                         GTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
genomic: TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAGgtaagcaaac ... cccgatgtagGTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
EST: gi|88330876|gb|CI636888.1|CI636888
EST:     TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAG                         GTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
genomic: TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAGgtaagcaaac ... cccgatgtagGTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
EST: gi|88288363|gb|CI661568.1|CI661568
EST:     TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAG                         GTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
genomic: TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAGgtaagcaaac ... cccgatgtagGTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
EST: gi|88740122|gb|CI763630.1|CI763630
EST:     TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAG                         GTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
genomic: TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAGgtaagcaaac ... cccgatgtagGTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
EST: gi|88765993|gb|CI775083.1|CI775083
EST:     TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAG                         GTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
genomic: TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAGgtaagcaaac ... cccgatgtagGTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
EST: gi|88313763|gb|CI597394.1|CI597394
EST:     TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAG                         GTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
genomic: TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAGgtaagcaaac ... cccgatgtagGTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
EST: gi|88314009|gb|CI600011.1|CI600011
EST:     TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAG                         GTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
genomic: TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAGgtaagcaaac ... cccgatgtagGTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
EST: gi|86885716|gb|CI309843.1|CI309843
EST:     TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAG                         GTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
genomic: TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAGgtaagcaaac ... cccgatgtagGTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
EST: gi|88358029|gb|CI650765.1|CI650765
EST:     TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAG                         GTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
genomic: TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAGgtaagcaaac ... cccgatgtagGTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
EST: gi|88570554|gb|CI661927.1|CI661927
EST:     TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAG                         GTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
genomic: TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAGgtaagcaaac ... cccgatgtagGTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
EST: gi|88570743|gb|CI662116.1|CI662116
EST:     TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAG                         GTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
genomic: TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAGgtaagcaaac ... cccgatgtagGTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
EST: gi|88332260|gb|CI639287.1|CI639287
EST:     TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAG                         GTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
genomic: TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAGgtaagcaaac ... cccgatgtagGTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
EST: gi|29687719|gb|CB683994.1|CB683994
EST:     TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAG                         GTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
genomic: TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAGgtaagcaaac ... cccgatgtagGTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
EST: gi|88826098|gb|CI776663.1|CI776663
EST:     TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAG                         GTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG
genomic: TGGAGCACGTCCAGATCCCGAGAGTGAAGCTGGGAACCCAGGGCCTCGAGgtaagcaaac ... cccgatgtagGTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgggttttcttgatgctaatgggggcgggctcgatcgatcgatccccgatgtagGTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCGCCGGTCGCCGAGGAAGACGGCGTCGCCGTCGTCAGGCGAGCGTTCGAGG
              tgctaat  putative branch site (score: 2)
                                           tcccc  putative PPT
     ttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcgtttccagatttctgggtttttttttttttggatgcgattcgtgggttttcttgatgctaatgggggcgggctcgatcgatcgatccccgatgtagGTGTCCAAGCTCGGGTTCGGGTGCATGGGCCTCACCGGCGTCTACAATGCGCCGGTCGCCGAGGAAGACGGCGTCGCCGTCGTCAGGCGAGCGTTCGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA