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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGCAGAACGGTCTTTTTATCAACTCCTGTTTCGCACATTGCCAAAGTGAGAGACAGGACACATGGTACGCAGGGGATTCTCCTCGTCTCGGTAACAAGgtacgcaaactctgcggtgatgccatgaaaaacattctcgcttcgaaagatttcctgactgtctgaactctgagctcctacatgtaaaaccagtagtctcatcagacccatcccatgtactttttttcttggatatgcag

Basic information

species Oryza sativa
transcript LOC_Os07g44070.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g44070.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G160569_T03 (Zea mays), 5'ss of exon 7
AAGGCAGAACGGTCTTTTTATCAACTCCTGTTTCGCACATTGCCAAAGTGAGAGACAGGACACATGGTACGCAGGGGATTCTCCTCGTCTCGGTAACAAGgtacgcaaactctgcggtgatgccatgaa--aaacattc----tcgcttcgaaagatttcctgactgtctgaactctgagctcctacatgtaaaaccagtagtctcatcagacccatcccatgtactttttttcttggatatgcag
|||||| || ||||| || |||||||| ||||| || |||||||| || ||||||||||| || ||||||||     | || || ||||| |||||||||||||||    |        | || |  ||  ||| || |    ||| ||  |   |     |   || |  |  |   ||    |   | |   || || | |||  ||     | | |  | |||                    
AAGGCAAAATGGTCTGTTCATCAACTCATGTTTTGCTCATTGCCAGAGCGAGAGACAGGATACTTGGTACGCGAACAACTCGCCACGTCTTGGTAACAAGgtacgcgtgttagaaacaaacgcaaacaacgaaatatccggcctcggttacacgaagcattttgttggcgaagtt---agtcgatctgtctctgacgagcattct--tcgacatcttacggtttacag------------------
















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|88224344|gb|CI224193.1|CI224193
EST:     AGGACACATGGTACGCAGGGGATTCTCCTCGTCTCGGTAACAAG                         AGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG
genomic: AGGACACATGGTACGCAGGGGATTCTCCTCGTCTCGGTAACAAGgtacgcaaac ... ggatatgcagAGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG
EST: gi|88847013|gb|CI001285.1|CI001285
EST:     AGAGACAGGACACACGGTACGCAGGGGATTCTCCTCGTCTCGGTAACAAG                         AGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG
genomic: AGAGACAGGACACATGGTACGCAGGGGATTCTCCTCGTCTCGGTAACAAGgtacgcaaac ... ggatatgcagAGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG
EST: gi|88246350|gb|CI246199.1|CI246199
EST:     AGAGACAGGACACATGGTACGCAGGGGATTCTCCTCGTCTCGGTAACAAG                         AGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG
genomic: AGAGACAGGACACATGGTACGCAGGGGATTCTCCTCGTCTCGGTAACAAGgtacgcaaac ... ggatatgcagAGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG
EST: gi|86498098|gb|CI140731.1|CI140731
EST:     AGAGACAGGACACATGGTACGCAGGGGATTCTCCTCGTCTCGGTAACAAG                         AGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG
genomic: AGAGACAGGACACATGGTACGCAGGGGATTCTCCTCGTCTCGGTAACAAGgtacgcaaac ... ggatatgcagAGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG
EST: gi|88837502|gb|CI078862.1|CI078862
EST:     GGGATTCTCCTCGTCTCGGTAACAAG                         AGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG
genomic: GGGATTCTCCTCGTCTCGGTAACAAGgtacgcaaac ... ggatatgcagAGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG
EST: gi|88849021|gb|CI087543.1|CI087543
EST:     AGAGACAGGACACATGGTACGCAGGGGATTCTCCTCGTCTCGGTAACAAG                         AGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG
genomic: AGAGACAGGACACATGGTACGCAGGGGATTCTCCTCGTCTCGGTAACAAGgtacgcaaac ... ggatatgcagAGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG
EST: gi|88226291|gb|CI226207.1|CI226207
EST:     AGAGACAGGACACATGGTACGCAGGGGATTCTCCTCGTCTCGGTAACAAG                         AGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG
genomic: AGAGACAGGACACATGGTACGCAGGGGATTCTCCTCGTCTCGGTAACAAGgtacgcaaac ... ggatatgcagAGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG
EST: gi|86500530|gb|CI143163.1|CI143163
EST:     AGAGACAGGACACATGGTACGCAGGGGATTCTCCTCGTCTCGGTAACAAG                         AGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG
genomic: AGAGACAGGACACATGGTACGCAGGGGATTCTCCTCGTCTCGGTAACAAGgtacgcaaac ... ggatatgcagAGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG
EST: gi|86436207|gb|CI117929.1|CI117929
EST:     CTCGGTAACAAG                         AGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG
genomic: CTCGGTAACAAGgtacgcaaac ... ggatatgcagAGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG
EST: gi|29685047|gb|CB681322.1|CB681322
EST:     AGAGACAGGACACATGGTACGCAGGGGATTCTCCTCGTCTCGGTAACAAG                         AGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG
genomic: AGAGACAGGACACATGGTACGCAGGGGATTCTCCTCGTCTCGGTAACAAGgtacgcaaac ... ggatatgcagAGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG
EST: gi|88834050|gb|CI077531.1|CI077531
EST:     AGAGACAGGACACATGGTACGCAGGGGATTCTCCTCGTCTCGGTAACAAG                         AGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG
genomic: AGAGACAGGACACATGGTACGCAGGGGATTCTCCTCGTCTCGGTAACAAGgtacgcaaac ... ggatatgcagAGAATTGCTGAAGCAGTAGGCGACTGGTTTTTCGATAGGGCAGACGCGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGGCAGAACGGTCTTTTTATCAACTCCTGTTTCGCACATTGCCAAAGTGAGAGACAGGACACATGGTACGCAGGGGATTCTCCTCGTCTCGGTAACAAGgtacgcaaactctgcggtgatgccatgaaaaacattctcgcttcgaaagatttcctgactgtctgaactctgagctcctacatgtaaaaccagtagtctcatcagacccatcccatgtactttttttcttggatatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC