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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACACCCTGTCCCTTGCTCTAGTTGACACAGCAAGGCCAGGGACTACAGATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGGgtaaggaagctgtgtgctatgtttaatgctgtcatttttgtctgcccaagcgaccctttgtttttatccttatcagtaacttcttttcagcatgaaccatatgttttgctaagtaaatgtcatttgcacaagcag

Basic information

species Oryza sativa
transcript LOC_Os01g39310.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39310.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM5G873287_T01 (Zea mays), 5'ss of exon 1
GAACACCCTGTCCCTTGCTCTAGTTGACACAGCAAGGCCAGGGACTACAGATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGGgtaaggaagctgtgtgctatgtttaatgctgtcatttttgtctgcccaagcgaccctttgtttttatccttatcagtaacttcttttcagcatgaaccatatgttttgctaagtaaatgtcatttgcacaagcag
|||||| || ||| ||||||| ||||||||  |||  || |||||||| |||||||| ||||||| |  ||||||||||||||| || ||||||||||||||||  ||||||| |  ||  | | |     | || ||| |||||  |||| || |      ||| | |||| ||    |||  ||| ||||  ||  |||||||||||| || | ||| ||||  ||  |||||
GAACACTCTTTCCGTTGCTCTTGTTGACACCTCAAAACCTGGGACTACTGATAGGAGTATCCAATTGACCGATCCACTTGCCTCCAGTTCATGGGAAAGGgtaacaaagctgtattttacatgtcaaat--ttatgtttctctgctgaagcaacaccccagattt-tacttagca----ctttctttaagcacaaa--atatgttttgctgaggagatggcatt--catgagcag

upper sequence: LOC_Os01g39310.1 (Oryza sativa), 5'ss of exon 19
lower sequence: AC196426.3_FGT007 (Zea mays), 5'ss of exon 18
GAACACCCTGTCCCTTGCTCTAGTTGACACAGCAAGGCCAGGGACTACAGATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGGgtaaggaagctgtgtgctatgtttaatgctgtcatttttgtctgcccaagcgaccctttgtttttatccttatcagtaacttcttttcagcatgaaccatatgttttgctaagtaaatgtcatttgcacaagcag
|||||| || ||||||||||| ||||||||  |||| |  ||||||||||||||||| ||||||| || ||||||||| ||||| |||||||||||||||||||  ||||||| |  ||  | | |     | || ||  |||||  |||| || |   |||||||  |||| ||    |||  | | ||||  || || |||| ||||| || | ||| ||||  ||  |||||
GAACACTCTTTCCCTTGCTCTTGTTGACACTTCAAGACATGGGACTACAGATAGGAGTATCCAATTGTCCGATCCACTAGCCTCCAGCTCATGGGAAAGGgtaacaaagctgtattttacatgtcaaat--ttatgttcctctgctgaagcaacacccagttttta--cttagca----ctttctataagcacaaaacacatgtcttgctgaggagatgccatt--catgagcag
















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|29641074|gb|CB646081.1|CB646081
EST:     ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGG                         GTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
genomic: ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGGgtaaggaagc ... gcacaagcagGTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
EST: gi|58593976|gb|CF992284.1|CF992284
EST:     CTCATGGGAAAGG                         GTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
genomic: CTCATGGGAAAGGgtaaggaagc ... gcacaagcagGTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
EST: gi|88340407|gb|CI659613.1|CI659613
EST:     ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGG                         GTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
genomic: ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGGgtaaggaagc ... gcacaagcagGTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
EST: gi|157650537|gb|EX450171.1|EX450171
EST:     ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGG                         GTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
genomic: ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGGgtaaggaagc ... gcacaagcagGTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
EST: gi|38474188|gb|CF958320.1|CF958320
EST:     ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGG                         GTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
genomic: ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGGgtaaggaagc ... gcacaagcagGTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
EST: gi|58690187|gb|CK078874.1|CK078874
EST:     ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGG                         GTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
genomic: ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGGgtaaggaagc ... gcacaagcagGTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
EST: gi|58661468|gb|CK050148.1|CK050148
EST:     ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGG                         GTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
genomic: ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGGgtaaggaagc ... gcacaagcagGTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACACCCTGTCCCTTGCTCTAGTTGACACAGCAAGGCCAGGGACTACAGATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGGgtaaggaagctgtgtgctatgtttaatgctgtcatttttgtctgcccaagcgaccctttgtttttatccttatcagtaacttcttttcagcatgaaccatatgttttgctaagtaaatgtcatttgcacaagcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA