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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAAgtatctataatatactgttatatgtttcttctcacaacttgtagccaagttggtttgatgaatattttatttttatttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g32610.4
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32610.2 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G059671_T04 (Zea mays), 5'ss of exon 14
GTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAAgtat--ctataatatac-tgttat-atgtttcttctcacaacttg--tagccaagttggtttgatgaat-attttatttttatttgcag
|| || ||||| |||||||| || || | ||||||||| || ||||| ||||||||||| |||||||||||| |||| || |||||||||   | || |     ||| |||| || ||| |||  | ||||||  |||     | | || ||| ||||||| |  |||||| ||   |   |||
GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGCGTTGATCCGAAAGTGGCGGCAGTAATCGAGTCCTGCTGGGTCAGgtgtaatactaacatacgtgctattatgcattttctcattactcaaccatcgaacttgttttgatggaccattttaattgcttactcag
















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|87015028|gb|CI273426.1|CI273426
EST:     AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAA                         AGAACTCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
genomic: AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAAgtatctataa ... ttatttgcagAGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
EST: gi|88322006|gb|CI673156.1|CI673156
EST:     AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAA                         AGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
genomic: AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAAgtatctataa ... ttatttgcagAGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
EST: gi|88550234|gb|CI480191.1|CI480191
EST:     AGTAGCGTTGATCCAAAATTGGCGGCAATAATGGAATCCTGCTGGACCAA                         AGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGANACC
genomic: AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAAgtatctataa ... ttatttgcagAGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
EST: gi|38480856|gb|CF964945.1|CF964945
EST:     AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCGGGCTGGACAAA                         AGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
genomic: AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAAgtatctataa ... ttatttgcagAGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
EST: gi|86833192|gb|CI334787.1|CI334787
EST:     AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAA                         AGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
genomic: AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAAgtatctataa ... ttatttgcagAGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
EST: gi|58689699|gb|CK078386.1|CK078386
EST:     AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAA                         AGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
genomic: AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAAgtatctataa ... ttatttgcagAGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
EST: gi|88538562|gb|CI467604.1|CI467604
EST:     AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGGTGGACAAA                         AGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
genomic: AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAAgtatctataa ... ttatttgcagAGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
EST: gi|88511876|gb|CI439382.1|CI439382
EST:     GAATCCTGCTGGACAAA                         AGGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAAC
genomic: GAATCCTGCTGGACAAAgtatctataa ... ttatttgcagA-GAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAAC
EST: gi|29631490|gb|CB636499.1|CB636499
EST:     AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAA                         AGAACCCTGGCGACGCCCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
genomic: AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAAgtatctataa ... ttatttgcagAGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
EST: gi|88536264|gb|CI466004.1|CI466004
EST:     AGTAGCNTTGATCCAAAAGTGGCGGCAATGATGGAATCCTGCTGGACAAA                         AGAACCCTGGCGACGGCCGTCTTTTGCCANTATCATGGAATCCCTGAAACC
genomic: AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAAgtatctataa ... ttatttgcagAGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
EST: gi|88555780|gb|CI486061.1|CI486061
EST:     AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAA                         AGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
genomic: AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAAgtatctataa ... ttatttgcagAGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
EST: gi|88553314|gb|CI483416.1|CI483416
EST:     TGCTGGACAGA                         AGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
genomic: TGCTGGACAAAgtatctataa ... ttatttgcagAGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
EST: gi|88444780|gb|CI696208.1|CI696208
EST:     AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAA                         AGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
genomic: AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAAgtatctataa ... ttatttgcagAGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
EST: gi|29679116|gb|CB675391.1|CB675391
EST:     AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAA                         AGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC
genomic: AGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAAgtatctataa ... ttatttgcagAGAACCCTGGCGACGACCGTCTTTTGCCAGTATCATGGAATCCCTGAAACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTAGCAGCTGTTGGTTTTAATGGGCGAAGGCTTGAAATTCCAAGTAGCGTTGATCCAAAAGTGGCGGCAATAATGGAATCCTGCTGGACAAAgtatctataatatactgttatatgtttcttctcacaacttgtagccaagttggtttgatgaatattttatttttatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA