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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACAAAAGCTGAGCCACCTATTTATTACATGCCAACTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAGgtatatcatagtgtcctactcaagaattttataacttgtgcatacacatgttcttgctcctgttctatgaacgttgtttgtgggtgaatcaaacttgtgagaaacactacag

Basic information

species Zea mays
transcript GRMZM2G102475_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102475_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g49520.2 (Oryza sativa), 5'ss of exon 9
---------------GACAAAAGCTGAGCCACCTATTTATTACATGCCAACTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAGgtatatcatagtgtcctactcaaga-attttataacttgtgcatacacatgttcttgctcctgttctatgaacgttgtttgtgggtgaatcaaacttgtgagaaacactacag
||||| || || ||||| ||||| ||||||||| |||||||||| ||||||||||| || |||| |||| |||||||||||||||||| | | | |||| ||| | || || | | ||| || ||| | | || ||| | || | || | |||
ATTGTTGTTTGTCAGGACAACTGCGGAACCACCAATTTACTACATGCCAGCTAAACCAATAATTGATGATCCGGCTATTGCTGAGGAGAACAAGGAAAAGgtattttct---gccctatataagtcaaagtaaaaacgctaagtttacaaatttttgaag--gatgaattgcgaccctttatacacacctccatct-acatgcaac-------

upper sequence: GRMZM2G102475_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g49520.1 (Oryza sativa), 5'ss of exon 9
GACAAAAGCTGAGCCACCTATTTATTACATGCCAACTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAGgtatatcatagtgtcctactcaaga-attttataacttgtgcatacacatgttcttgctcctgttctatgaacgttgtttgtgggtgaatcaaacttgtgagaaacactacag
||||| || || ||||| ||||| ||||||||| |||||||||| ||||||||||| || |||| |||| |||||||||||||||||| | | | |||| ||| | || || | | ||| || ||| | | || ||| | || | || | |||
GACAACTGCGGAACCACCAATTTACTACATGCCAGCTAAACCAATAATTGATGATCCGGCTATTGCTGAGGAGAACAAGGAAAAGgtattttct---gccctatataagtcaaagtaaaaacgctaagtttacaaatttttgaag--gatgaattgcgaccctttatacacacctccatct-acatgcaac-------
















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|60340299|gb|DN207272.1|DN207272
EST:     CTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAG                         GTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCAGTTTCAA
genomic: CTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAGgtatatcata ... aacactacagGTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCGGTTTCAA
EST: gi|87156896|gb|DY401685.1|DY401685
EST:     CTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAG                         GTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCAGTTTCAA
genomic: CTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAGgtatatcata ... aacactacagGTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCGGTTTCAA
EST: gi|149045934|gb|EE047932.2|EE047932
EST:     CTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAG                         GTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCGGTTTCAA
genomic: CTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAGgtatatcata ... aacactacagGTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCGGTTTCAA
EST: gi|60349148|gb|DN216121.1|DN216121
EST:     TGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAG                         GTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCGGTTTCAA
genomic: TGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAGgtatatcata ... aacactacagGTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCGGTTTCAA
EST: gi|67013106|gb|CO441855.1|CO441855
EST:     CTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAG                         GTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCAGTTTCAA
genomic: CTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAGgtatatcata ... aacactacagGTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCGGTTTCAA
EST: gi|60357834|gb|DN224807.1|DN224807
EST:     CTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAG                         GTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCAGTTTCAA
genomic: CTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAGgtatatcata ... aacactacagGTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCGGTTTCAA
EST: gi|22133799|gb|BQ833909.1|BQ833909
EST:     CTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAG                         GTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCAGTTTCAA
genomic: CTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAGgtatatcata ... aacactacagGTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCGGTTTCAA
EST: gi|26558420|gb|CA830655.1|CA830655
EST:     CTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAG                         GTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCAGTTTCAA
genomic: CTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAGgtatatcata ... aacactacagGTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCGGTTTCAA
EST: gi|60356392|gb|DN223365.1|DN223365
EST:     CTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAG                         GTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCGGTTTCAA
genomic: CTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAGgtatatcata ... aacactacagGTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCGGTTTCAA
EST: gi|31349518|gb|CD433875.1|CD433875
EST:     CTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAG                         GTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCAGTTTCAA
genomic: CTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAGgtatatcata ... aacactacagGTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCGGTTTCAA
EST: gi|60349348|gb|DN216321.1|DN216321
EST:     CTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAG                         GTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCAGTTTCAA
genomic: CTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAGgtatatcata ... aacactacagGTATTCGAAGAATGGAAATCTATGCGCAGGGCTGAGCTGACTCGGTTTCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACAAAAGCTGAGCCACCTATTTATTACATGCCAACTAAACCAATTATTGATGATCCAGCCATTGTTGAGCAGAACAAGGAAAAGgtatatcatagtgtcctactcaagaattttataacttgtgcatacacatgttcttgctcctgttctatgaacgttgtttgtgggtgaatcaaacttgtgagaaacactacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA