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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcaataataaaaaaaacctcgctctccaatttgctgcatatatatacacatgttcttccttttttggaactcgaccaagttacaaaattttcataatttttggatcttgcattatgctcttgcagctgggttcatgatcttgcattaaattttttttggttcagGGTAACAGCGCTGGAAGTGGTTCGGCTCCAAAGAAGGCTAGGGTTCAGACCTCTTCTTCAGCACAGTCTACCCTAAAG

Basic information

species Zea mays
transcript GRMZM2G083749_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083749_T05 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g13000.1 (Oryza sativa), 3'ss of exon 2
gtgagcaataataaaaaaaacctcgctctccaatttgctgcatatatatacacatgttcttccttttttggaactcgaccaagttacaaaattttcataatttttggatcttgcattatgctcttgcagctgggttcatgatcttgcattaaattttttttggttcagGGTAACAGCGCTGGAAGTGGTTCGGCTCCAAAGAAGGCTAGGGTTCAGACCTCTTCTTCAGCACAGTCTACCCTAAAG
                                            |||||| |  || || ||     ||||     ||| | | |  ||     |||| ||    || ||||||       | |||||  ||| ||  | |  |||  ||   | | |  || | ||| |||||||| | |  |  ||||| ||||  |||||||||||||||||  ||||||||||||| || ||||||||||||
--------------------------------------------tatatatagttgctcatc-----ttgg-----gacaaggatggaatggcctcatgat----ggttcttgc-------ttttgca-ttggcttgtttaatttg--ttgtttctctgctgctgcagTGTAACAGCACAGAGACAGGTTCAGCTCTTAAGAAGGCTAGGGTTCAAGCCTCTTCTTCAGCGCAATCTACCCTAAAG
















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|211051350|gb|FK945215.1|FK945215
EST:     TGCCGCCGGCACCGGATCTGAAGAATCATCACTCCGATAACTCTTCTGAG                         GGTAACAGCGCTGGAAGTGGTTCGGCTCCAAAGAAGGCTAGGGTTCAGACC
genomic: TGCCGCCGGCACCGGATCTGAAGAATCATCACTCCGATAACTCTTCTGAGgtgagcaata ... tttggttcagGGTAACAGCGCTGGAAGTGGTTCGGCTCCAAAGAAGGCTAGGGTTCAGACC
EST: gi|91874519|gb|EB404476.1|EB404476
EST:     TGCCGCCGGCACCGGATCTGAAGAATCATCACTCCGATAACTCTTCTGAG                         GGTAACAGCGCTGGAAGTGGTTCGGCTCCAAAGAAGGCTAGGGTTCAGACC
genomic: TGCCGCCGGCACCGGATCTGAAGAATCATCACTCCGATAACTCTTCTGAGgtgagcaata ... tttggttcagGGTAACAGCGCTGGAAGTGGTTCGGCTCCAAAGAAGGCTAGGGTTCAGACC
EST: gi|78115486|gb|DV533874.1|DV533874
EST:     TGCCGCCGGCACCGGATCTGAAGAATCATCCCTCCGATAACTCTTCTGAG                         GGTAACAGCGCTG
genomic: TGCCGCCGGCACCGGATCTGAAGAATCATCACTCCGATAACTCTTCTGAGgtgagcaata ... tttggttcagGGTAACAGCGCTG
EST: gi|50339291|gb|CO534417.1|CO534417
EST:     TGCCGCCGGCACCGGATCTGAAGAATCATCACTCCGATAACTCTTCTGAG                         GGTAACAGCGCTGGAAGTGGTTCGGCTCCAAAGAAGGCTAGGGTTCAGACC
genomic: TGCCGCCGGCACCGGATCTGAAGAATCATCACTCCGATAACTCTTCTGAGgtgagcaata ... tttggttcagGGTAACAGCGCTGGAAGTGGTTCGGCTCCAAAGAAGGCTAGGGTTCAGACC
EST: gi|94472188|gb|EB701146.1|EB701146
EST:     TGCCGCCGGCACCGGATCTGAAGAATCATCACTCCGATAACTCTTCTGAG                         GGTAACAGCGCTGGAAGTGGTTCGGCTCCAAAGAAGGCTAGGGTTCAGACC
genomic: TGCCGCCGGCACCGGATCTGAAGAATCATCACTCCGATAACTCTTCTGAGgtgagcaata ... tttggttcagGGTAACAGCGCTGGAAGTGGTTCGGCTCCAAAGAAGGCTAGGGTTCAGACC
EST: gi|148932563|gb|EC876392.2|EC876392
EST:     TGCCGCCGGCACCGGATCTGAAGAATCATCACTCCGATAACTCTTCTGAG                         GGTAACAGCGCTGGAAGTGGTTCGGCTC
genomic: TGCCGCCGGCACCGGATCTGAAGAATCATCACTCCGATAACTCTTCTGAGgtgagcaata ... tttggttcagGGTAACAGCGCTGGAAGTGGTTCGGCTC
EST: gi|148981124|gb|EE027442.2|EE027442
EST:     TGCCGCCGGCACCGGATCTGAAGAATCATCACTCCGATAACTCTTCTGAG                         GGTAACAGCGCTGGAAGTGGTTCGGCTCCAAAGAAGGCTAGGGTTCAGACC
genomic: TGCCGCCGGCACCGGATCTGAAGAATCATCACTCCGATAACTCTTCTGAGgtgagcaata ... tttggttcagGGTAACAGCGCTGGAAGTGGTTCGGCTCCAAAGAAGGCTAGGGTTCAGACC
EST: gi|149095094|gb|EE180702.2|EE180702
EST:     TGCCGCCGGCACCGGATCTGAAGAATCATCACTCCGATAACTCTTCTGAG                         GGTAACAGCGCTGGAAGTGGTTCGGCTCCAAAGAAGGCTAGGGTTCAGACC
genomic: TGCCGCCGGCACCGGATCTGAAGAATCATCACTCCGATAACTCTTCTGAGgtgagcaata ... tttggttcagGGTAACAGCGCTGGAAGTGGTTCGGCTCCAAAGAAGGCTAGGGTTCAGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattatgctcttgcagctgggttcatgatcttgcattaaattttttttggttcagGGTAACAGCGCTGGAAGTGGTTCGGCTCCAAAGAAGGCTAGGGTTCAGACCTCTTCTTCAGCACAGTCTACCCTAAAG
                                        tttttttt  CT-rich tract
                           atcttgcattaaattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcaataataaaaaaaacctcgctctccaatttgctgcatatatatacacatgttcttccttttttggaactcgaccaagttacaaaattttcataatttttggatcttgcattatgctcttgcagctgggttcatgatcttgcattaaattttttttggttcagGGTAACAGCGCTGGAAGTGGTTCGGCTCCAAAGAAGGCTAGGGTTCAGACCTCTTCTTCAGCACAGTCTACCCTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG