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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgttcggtagtggaaatgtcgacacattgtaggttgcatttggttggaggctaaacagttgcatattctcatggtgcag

Basic information

species Zea mays
transcript GRMZM2G075153_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075153_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g25940.4 (Oryza sativa), 5'ss of exon 4
GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgt----------tcggtagtggaaa----tgtcgacacattgtaggttgcatttggttggaggctaaacagttgcatattctcatggtgcag--------------------------------------
|||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||| |||||||||||||||||||||          | | | ||| ||     | |      | || | | | |   |  ||||| |    |  | |  ||  | |  ||||                                          
GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACTGAGGCATTGGAGAAGAAGATGAGgtgatgtttcccctttgttgctggtgtaatattttcttcttgaaatgaatggttctgctaattggaagtgggaatgcttgatgctgtgttggttttagtggatgggattttgattgctctacttcgatgtttcag

upper sequence: GRMZM2G075153_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g25940.2 (Oryza sativa), 5'ss of exon 3
GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgttc----------ggtagtggaaa----tgtcgacacattgtaggttgcatttggttggaggctaaacagttgcatattctcatggtgcag---
|||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||| ||||||||||||||||||||||           | | ||| ||     | |      | || | | | |   |  ||||| |    |  | |  ||  | |  ||||       
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|211234235|gb|FL407898.1|FL407898
EST:     TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG                         CGCACTGGAGAAAGCAGAGTCCACCGTGTTTGTGGCGTCAGGGATGTATGC
genomic: TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgttcg ... catggtgcagCGCACTGGAGAAAGCAGAGTCCACCGTGTTTGTGGCGTCAGGGATGTATGC
EST: gi|30705385|gb|CD058765.1|CD058765
EST:     TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG                         CGCACTGGAGAAAGCAGAGTCCACCGTGTTTGTGGCGTCAGGGATGTATGC
genomic: TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgttcg ... catggtgcagCGCACTGGAGAAAGCAGAGTCCACCGTGTTTGTGGCGTCAGGGATGTATGC
EST: gi|30705650|gb|CD058859.1|CD058859
EST:     TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG                         CGCACTGGAGAAAGCAGAGTCCACCGTGTTTGTGGCGTCAGGGATGTATGC
genomic: TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgttcg ... catggtgcagCGCACTGGAGAAAGCAGAGTCCACCGTGTTTGTGGCGTCAGGGATGTATGC
EST: gi|29946125|gb|CB815991.1|CB815991
EST:     TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG                         CGCACTGGAGAAAGCAGAGTCCACCGTGTTTGTGGCGTCAGGGATGTATGC
genomic: TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgttcg ... catggtgcagCGCACTGGAGAAAGCAGAGTCCACCGTGTTTGTGGCGTCAGGGATGTATGC
EST: gi|149074757|gb|EE163186.2|EE163186
EST:     TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG                         CGCACTGGAGAAAGCAGAGTCCACCGTGTTTGTGGCGTCAGGGATGTATGC
genomic: TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgttcg ... catggtgcagCGCACTGGAGAAAGCAGAGTCCACCGTGTTTGTGGCGTCAGGGATGTATGC
EST: gi|149108488|gb|EE189677.2|EE189677
EST:     TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG                         CGCACTGGAGAAAGCAGAGTCCACCGTGTTTGTGGCGTCAGGGATGTATGC
genomic: TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgttcg ... catggtgcagCGCACTGGAGAAAGCAGAGTCCACCGTGTTTGTGGCGTCAGGGATGTATGC
EST: gi|148948278|gb|EC893795.2|EC893795
EST:     TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG                         CGCACTGGAGAAAGCAGAGTCCACCGTGTTTGTGGCGTCAGGGATGTATGC
genomic: TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgttcg ... catggtgcagCGCACTGGAGAAAGCAGAGTCCACCGTGTTTGTGGCGTCAGGGATGTATGC
EST: gi|38229609|gb|CF919922.1|CF919922
EST:     TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG                         CGCACTGGAGAAAGCAGAGTCCACCGTGTTTGTGGCGTCAGGGATGTATGC
genomic: TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgttcg ... catggtgcagCGCACTGGAGAAAGCAGAGTCCACCGTGTTTGTGGCGTCAGGGATGTATGC
EST: gi|211066604|gb|FL423906.1|FL423906
EST:     TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG                         CGCACTGGAGAAAGCAGAGTCCACCGTGTTTGTGGCGTCAGGGATGTATGC
genomic: TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgttcg ... catggtgcagCGCACTGGAGAAAGCAGAGTCCACCGTGTTTGTGGCGTCAGGGATGTATGC
EST: gi|91873684|gb|EB403641.1|EB403641
EST:     TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG                         CGCACTGGAGAAAGCAGAGTCCACCGTGTTTGTGGCGTCAGGGATGTATGC
genomic: TATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgttcg ... catggtgcagCGCACTGGAGAAAGCAGAGTCCACCGTGTTTGTGGCGTCAGGGATGTATGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAGgtgatgttcggtagtggaaatgtcgacacattgtaggttgcatttggttggaggctaaacagttgcatattctcatggtgcag

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