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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgctcgatagtggaaatgtcggcaccctgttggttgcatttggctggaggctaaacagttgcgtgttctcatggtgcag

Basic information

species Zea mays
transcript GRMZM2G113873_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113873_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g25940.4 (Oryza sativa), 5'ss of exon 4
GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgct-cgatagtggaaatgtcggcaccctgttggttgcatttggctggag--gctaaacagttgcgtgttctcatggtgcag-------------------------------------------------
|||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||| |||||||||||||||||||| | |     ||    ||  |  |   | |    |  |  ||  |||    |||||   |  | | |    | || ||| |                                                 
GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACTGAGGCATTGGAGAAGAAGATGAGgtgatgtttcccctttgttgctggtgtaatattttcttcttgaaatgaatggttctgctaattggaagtgggaatgcttgatgctgtgttggttttagtggatgggattttgattgctctacttcgatgtttcag

upper sequence: GRMZM2G113873_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g25940.2 (Oryza sativa), 5'ss of exon 3
GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgct-cgatagtggaaatgtcggcaccctgttggttgcatttggctggag--gctaaacagttgcgtgttctcatggtgcag--------------
|||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||| |||||||||||||||||||| | |     ||    ||  |  |   | |    |  |  ||  |||    |||||   |  | | |    | || ||| |              
GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACTGAGGCATTGGAGAAGAAGATGAGgtgatgtttcccctttgttgctggtgtaatattttcttcttgaaatgaatggttctgctaattggaagtgggaatgcttgatgctgtgttggttttagtg
















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|149076129|gb|EE164714.2|EE164714
EST:     TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG                         CGCACTGGAGAAAGCAGAGTCCACAGTGTTCGTGGCATCGGGGATGTATGC
genomic: TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgctcg ... catggtgcagCGCACTGGAGAAAGCAGAGTCCACAGTGTTCGTGGCATCGGGGATGTATGC
EST: gi|148936104|gb|EC880167.2|EC880167
EST:     TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG                         CGCACTGGAGAAAGCAGAGTCCACAGTGTTCGTGGCATCGGGGATGTATGC
genomic: TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgctcg ... catggtgcagCGCACTGGAGAAAGCAGAGTCCACAGTGTTCGTGGCATCGGGGATGTATGC
EST: gi|149102766|gb|EE288113.2|EE288113
EST:     TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG                         CGCACTGGAGAAAGCAGAGTCCACAGTGTTCGTGGCATCGGGGATGTATGC
genomic: TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgctcg ... catggtgcagCGCACTGGAGAAAGCAGAGTCCACAGTGTTCGTGGCATCGGGGATGTATGC
EST: gi|78110794|gb|DV529192.1|DV529192
EST:     TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG                         CGCACTGGAGAAAGCAGAGTCCACAGTGTTCGTGGCATCGGGGATGTATGC
genomic: TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgctcg ... catggtgcagCGCACTGGAGAAAGCAGAGTCCACAGTGTTCGTGGCATCGGGGATGTATGC
EST: gi|78086437|gb|DV514830.1|DV514830
EST:     TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG                         CGCACTGGAGAAAGCAGAGTCCACAGTGTTCGTGGCATCGGGGATGTATGC
genomic: TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgctcg ... catggtgcagCGCACTGGAGAAAGCAGAGTCCACAGTGTTCGTGGCATCGGGGATGTATGC
EST: gi|76010979|gb|DT938149.1|DT938149
EST:     TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG                         CGCACTGGAGAAAGCAGAGTCCACAGTGTTCGTGGCATCGGGGATGTATGC
genomic: TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgctcg ... catggtgcagCGCACTGGAGAAAGCAGAGTCCACAGTGTTCGTGGCATCGGGGATGTATGC
EST: gi|9794536|gb|BE552844.1|BE552844
EST:     TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG                         CGCACTGGAGAAAGCAGAGTCCA
genomic: TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgctcg ... catggtgcagCGCACTGGAGAAAGCAGAGTCCA
EST: gi|149030074|gb|EE286293.2|EE286293
EST:     TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG                         CGCACTGGAGAAAGCAGAGTCCACAGTGTTCGTGGCATCGGGGATGTATGC
genomic: TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgctcg ... catggtgcagCGCACTGGAGAAAGCAGAGTCCACAGTGTTCGTGGCATCGGGGATGTATGC
EST: gi|29130696|gb|CB381400.1|CB381400
EST:     TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG                         CGCACTGGAGAAAGCAGAGTCCACAGTGTTCGTGGCATCGGGGATGTATGC
genomic: TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgctcg ... catggtgcagCGCACTGGAGAAAGCAGAGTCCACAGTGTTCGTGGCATCGGGGATGTATGC
EST: gi|93013670|gb|EB639190.1|EB639190
EST:     TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG                         CGCACTGGAGAAAGCAGAGTCCACAGTGTTCGTGGCATCGGGGATGTATGC
genomic: TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgctcg ... catggtgcagCGCACTGGAGAAAGCAGAGTCCACAGTGTTCGTGGCATCGGGGATGTATGC
EST: gi|101401317|gb|EB822336.1|EB822336
EST:     TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG                         CGCACTGGAGAAAGCAGAGTCCACAGTGTTCGTGGCATCGGGGATGTATGC
genomic: TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgctcg ... catggtgcagCGCACTGGAGAAAGCAGAGTCCACAGTGTTCGTGGCATCGGGGATGTATGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgctcgatagtggaaatgtcggcaccctgttggttgcatttggctggaggctaaacagttgcgtgttctcatggtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG