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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGCTGCATGGTTATTAAACAAGAAGAAAGCGGATGGATGGAGACGTTTAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAGgtggctcctgttctccgctcttatttttattgaacctttattcaaaataatgcattgcatgctttaaggaattaagctcaccccttataattactaaaat...

Basic information

species Oryza sativa
transcript LOC_Os07g26610.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g26610.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G173674_T01 (Zea mays), 5'ss of exon 2
----------ATTTGCTGCATGGTTATTAAACAAGAAGAAAGCGGATG-GATGGAGACGTT-TAAGAATTTCTGTTGGACATGAT----TCTCGAATTTCTGCACATAAATTGCAGgtggctcctgttctccgctcttatttttattgaacctttattcaaaataatgcattgcatgctttaaggaattaagctcaccccttataattactaaaat----
           ||   |   ||    || || | |       |    | | ||  |  |||   || |||   | ||  | ||      || || |      |||  ||  |  || ||   | | | |  |     ||||  |   ||| |   ||        | |  |   |  || |   | |      |||    ||        |||| |    
ATCTAAGAAAGTTGAATTTCTGAAGCTTCAAAATGGCAGTGACATTCGTGGTGTTGCTGTTGCTAGGATTGAAGGTGAGCCTGTCAACCTCACGGAAGATgtcactaaagctatagctgcagcttttgccgcatggctattaatcaagaaaccagatgacttgagacgtttaagaatctctgttggacatgattcatgaatttctgcacataaattgcag

upper sequence: LOC_Os07g26610.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G069676_T03 (Zea mays), 5'ss of exon 4
---ATTTGCTGCATGGTTATTAAACAAGAAGAAAGCGGATGGATGGAGACGTTTAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAGgtggctcctgttctccgctcttatttttattgaacctttattcaaaata---atgcattgcatgctttaaggaattaagctcacc-ccttataattactaaaat
    |||||||||||| | |||||||||   ||| | ||||| | ||||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||||| ||||||| |  | || |   || ||| | | | |   | ||||    |   |||  |  | || |  | |  |  |||    | | |    ||||    
AGCTTTTGCTGCATGGCTGTTAAACAAG---AAACCAGATGGCTTGAGACGTTTAAGAATCTCTGTTGGACATGATTCACGAATTTCTGCACATAAATTGCAGgtggatcctgttttttgttcat---ttaattaatcttatgaaccaaatttgcacatattttaatcctttattattggatatcaaaatcctgtttcaactagtg-
















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|88431706|gb|CI576897.1|CI576897
EST:     TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAG                         GATGCAGTTACTCTTGGAATTACCACTGCAGGGCATGATGTTTTACAATTT
genomic: TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAGgtggctcctg ... taattgtcagGATGCAGTTACTCTTGGAATTACCACTGCAGGGCATGATGTTTTACAATTT
EST: gi|88356963|gb|CI620851.1|CI620851
EST:     TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAG                         GATGCAGTTACTCTTGGAATTACCACT
genomic: TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAGgtggctcctg ... taattgtcagGATGCAGTTACTCTTGGAATTACCACT
EST: gi|88365076|gb|CI616495.1|CI616495
EST:     TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAG                         GATGCAGTTACTCTTGGAATTACCACTGCAG
genomic: TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAGgtggctcctg ... taattgtcagGATGCAGTTACTCTTGGAATTACCACTGCAG
EST: gi|88298983|gb|CI567986.1|CI567986
EST:     TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAG                         GATGCAGTTACTCTTGGAATTACCACTGCAGGGCATGATGTTTTACAATTT
genomic: TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAGgtggctcctg ... taattgtcagGATGCAGTTACTCTTGGAATTACCACTGCAGGGCATGATGTTTTACAATTT
EST: gi|88392307|gb|CI612781.1|CI612781
EST:     TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAG                         GATGCAGTTACTCTTGGAATTACCACTGGAGGGCATGATGTTTTACAATTT
genomic: TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAGgtggctcctg ... taattgtcagGATGCAGTTACTCTTGGAATTACCACTGCAGGGCATGATGTTTTACAATTT
EST: gi|88364874|gb|CI614492.1|CI614492
EST:     TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAG                         GATGCAGTTACTCTTGGAATTACCACTGCAGGGCATGATGTTTTACAATTT
genomic: TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAGgtggctcctg ... taattgtcagGATGCAGTTACTCTTGGAATTACCACTGCAGGGCATGATGTTTTACAATTT
EST: gi|88399621|gb|CI583355.1|CI583355
EST:     TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAG                         GATGCAGTTACTCTTGGAATTACCACTGCAGGGCATGA
genomic: TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAGgtggctcctg ... taattgtcagGATGCAGTTACTCTTGGAATTACCACTGCAGGGCATGA
EST: gi|88736243|gb|CI759751.1|CI759751
EST:     TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAG                         GATGCAGTTACTCTTGGAATTA
genomic: TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAGgtggctcctg ... taattgtcagGATGCAGTTACTCTTGGAATTA
EST: gi|33793170|gb|CF322466.1|CF322466
EST:     TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAG                         GATGCAGTTACTCTTGGAATTACCACTGCAGGGCATGATGTTTTACAATTT
genomic: TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAGgtggctcctg ... taattgtcagGATGCAGTTACTCTTGGAATTACCACTGCAGGGCATGATGTTTTACAATTT
EST: gi|88362534|gb|CI623874.1|CI623874
EST:     TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAG                         GATGCAGTTACTCTTGGAATTACCACTGCAGGGCATGATG
genomic: TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAGgtggctcctg ... taattgtcagGATGCAGTTACTCTTGGAATTACCACTGCAGGGCATGATG
EST: gi|88298548|gb|CI563543.1|CI563543
EST:     TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAG                         GATGCAGTTACTCTTGGAATTACCACTGCAGGGCATGATGTTTTACAATTT
genomic: TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAGgtggctcctg ... taattgtcagGATGCAGTTACTCTTGGAATTACCACTGCAGGGCATGATGTTTTACAATTT
EST: gi|29660678|gb|CB656953.1|CB656953
EST:     TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAG                         GATGCAGTTACTCTTGGAATTACCACTGCAGGGCATGATGTTTTACAATTT
genomic: TAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAGgtggctcctg ... taattgtcagGATGCAGTTACTCTTGGAATTACCACTGCAGGGCATGATGTTTTACAATTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTGCTGCATGGTTATTAAACAAGAAGAAAGCGGATGGATGGAGACGTTTAAGAATTTCTGTTGGACATGATTCTCGAATTTCTGCACATAAATTGCAGgtggctcctgttctccgctcttatttttattgaacctttattcaaaataatgcattgcatgctttaaggaattaagctcaccccttataattactaaaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcaccc