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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTGgtaatgatacatctctactatattagagcatcagttttttcagttccactatcgttgtgctccccccacatttaaataataaaaatgttaaaattatgca...

Basic information

species Zea mays
transcript GRMZM2G053531_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053531_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os08g26870.3 (Oryza sativa), 5'ss of exon 9
ACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTGgtaatgatacatctctactatattagagcatcagttttttcagttccactatcgttgtgctccccccacatttaaataataaaaatgttaaaattatgca-
||||||||| ||||||||||| |||||||||||||||||| || |  |||||||||||||||||||| | |||||||||||||| ||||||||||||  ||      |  | |  |      | || ||  ||  | |  || |  || |  |  |     |  |  || |    | | |       | | | 
ACCTGATGGGCAGCCATGTGTCGAGGCTCAAGAGTTTGGATTGATCCGGAACATGCTCATTGCAGCTGTTGAAGAGAGATACAAAGATGCTGgtaattttattatcgtgttgtggtgttat-taagattcatcgatgcacctttttttttttttgcggggaagattcatcagtgcattctgtctgacaaggac
















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|74035418|gb|DT535906.1|DT535906
EST:     GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
genomic: GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTGgtaatgatac ... acttgaacagCATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
EST: gi|6695554|gb|AW288662.1|AW288662
EST:     GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATNCAAGGATGCTG                         CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
genomic: GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTGgtaatgatac ... acttgaacagCATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
EST: gi|84969850|gb|DW468264.1|DW468264
EST:     GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
genomic: GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTGgtaatgatac ... acttgaacagCATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
EST: gi|60358119|gb|DN225092.1|DN225092
EST:     GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
genomic: GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTGgtaatgatac ... acttgaacagCATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
EST: gi|78109883|gb|DV528299.1|DV528299
EST:     GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
genomic: GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTGgtaatgatac ... acttgaacagCATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
EST: gi|12968885|gb|BG265726.1|BG265726
EST:     GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGA
genomic: GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTGgtaatgatac ... acttgaacagCATCATGGAAGGA
EST: gi|60341680|gb|DN208653.1|DN208653
EST:     GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
genomic: GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTGgtaatgatac ... acttgaacagCATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
EST: gi|88754483|gb|DY538624.1|DY538624
EST:     GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATTCGGCTCAGGTTTAAGCGGGAGAACTGGG
genomic: GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTGgtaatgatac ... acttgaacagCATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
EST: gi|113702906|gb|EE680410.1|EE680410
EST:     GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
genomic: GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTGgtaatgatac ... acttgaacagCATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
EST: gi|60394174|gb|DN227044.1|DN227044
EST:     GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
genomic: GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTGgtaatgatac ... acttgaacagCATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
EST: gi|116822203|gb|EC865582.1|EC865582
EST:     GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
genomic: GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTGgtaatgatac ... acttgaacagCATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
EST: gi|32846823|gb|CD986504.1|CD986504
EST:     GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
genomic: GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTGgtaatgatac ... acttgaacagCATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
EST: gi|6828185|gb|AW331828.1|AW331828
EST:     GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
genomic: GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTGgtaatgatac ... acttgaacagCATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
EST: gi|60359057|gb|DN226030.1|DN226030
EST:     GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
genomic: GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTGgtaatgatac ... acttgaacagCATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
EST: gi|78021679|gb|DV490066.1|DV490066
EST:     GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG
genomic: GGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTGgtaatgatac ... acttgaacagCATCATGGAAGGACAAACTGATTCGGCTCAGGTCTAAGCGGGAGAACTGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTGgtaatgatacatctctactatattagagcatcagttttttcagttccactatcgttgtgctccccccacatttaaataataaaaatgttaaaattatgca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG