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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttagctctccacggcattgccccctcgtttcattccttacctgtcatacaaaatgtattgtgctgtagtatgtatgcactcatttccagtttcttgcagCTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAATTCCAAAGGATGCGCGTAACTCTCACCATAGGTGTCATTGGCCTCTGTGT

Basic information

species Zea mays
transcript GRMZM2G164916_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164916_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g01450.1 (Oryza sativa), 3'ss of exon 1
---------------------------------------------------------------------------------tttagct---ctccacggcattgccc--cctcgtttcattcctta-cctgtcatacaaaatgtattgtgctgtagtatgtatgcactcatttccagtttcttgcagCTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAATTCCAAAGGATGCGCGTAACTCTCACCATAGGTGTCATTGGCCTCTGTGT
                                                                                   |||||   || |  ||  | |      ||| | || | | | | ||| || ||  | |  || |  |    ||| ||| || |  |    |  ||  ||||||| | ||||||| ||||| |||  ||||||||| |||    | || ||||  |||||||||||||| |||||  | ||||||||||| ||||||||||||||
gtgagcatccacatcctctttctgattcatgtttctggtgagcaccaggagtacttacatctggaatttgcttgcgttaaccctagcttctcttctaggtctggaagaagctcttctcctccttaaacctctcttaatacaactagta-gtaacagtttgt-tggatccgccccttgt--cttgcagGTGTAATGGCAAAAGAGCAGAGTGGATCCCCTAAGCCCAGGCAGCCAGTGTTCCAAAGGATGCGAGTAACGTTAACCATAGGTGTTATTGGCCTCTGTGT
















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|211278360|gb|FL132343.1|FL132343
EST:     TGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTG                         CTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAAT
genomic: TGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTGgttagttatg ... tttcttgcagCTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAAT
EST: gi|211278361|gb|FL132344.1|FL132344
EST:     TGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTG                         CTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAAT
genomic: TGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTGgttagttatg ... tttcttgcagCTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAAT
EST: gi|211278362|gb|FL132345.1|FL132345
EST:     TGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTG                         CTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAAT
genomic: TGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTGgttagttatg ... tttcttgcagCTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAAT
EST: gi|211404678|gb|FL116464.1|FL116464
EST:     TGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTG                         CTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAAT
genomic: TGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTGgttagttatg ... tttcttgcagCTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAAT
EST: gi|211432715|gb|FL449161.1|FL449161
EST:     TGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTG                         CTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAAT
genomic: TGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTGgttagttatg ... tttcttgcagCTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAAT
EST: gi|9952394|gb|BE638977.1|BE638977
EST:     TGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTG                         CTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAAT
genomic: TGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTGgttagttatg ... tttcttgcagCTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAAT
EST: gi|71775257|gb|DR973135.1|DR973135
EST:     TGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTG                         CTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAAT
genomic: TGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTGgttagttatg ... tttcttgcagCTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAAT
EST: gi|76018661|gb|DT945831.1|DT945831
EST:     TGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTG                         CTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAAT
genomic: TGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTGgttagttatg ... tttcttgcagCTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAAT
EST: gi|211280152|gb|FL132346.1|FL132346
EST:     TGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTG                         CTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAAT
genomic: TGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTGgttagttatg ... tttcttgcagCTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catacaaaatgtattgtgctgtagtatgtatgcactcatttccagtttcttgcagCTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAATTCCAAAGGATGCGCGTAACTCTCACCATAGGTGTCATTGGCCTCTGTGT
                                             tttcttgc  CT-rich tract
     aaaatgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttagctctccacggcattgccccctcgtttcattccttacctgtcatacaaaatgtattgtgctgtagtatgtatgcactcatttccagtttcttgcagCTCTAATGGCTAAAGAACAGGATGGATCCCCCAAGGTGCGCCACCCAGAATTCCAAAGGATGCGCGTAACTCTCACCATAGGTGTCATTGGCCTCTGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - -ccacggc
- - - - - - - - - - - - - - - -cattcct
- - - - - - - - - - - - - - - - - - - - - - -catacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgtattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatgc