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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATAGAGAAAATTACAGGAGAAGGCCTGACATCTGTCTTCCAGGGCTCTCAGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttcatgtgcttattatttgtactcttgtagccatccaagttgtgctattccatgattgaccatctgacagaattcgagataaagtgttcatgag...

Basic information

species Zea mays
transcript GRMZM2G458549_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G458549_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g61710.1 (Oryza sativa), 5'ss of exon 9
AATAGAGAAAATTACAGGAGAAGGCCTGACATCTGTCTTCCAGGGCTCTCAGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttcatgtgcttattatttgtactcttgtagccatccaagttgtgcta--ttccatgattgaccatctgacagaattcgagataaagtgttcatgag
||||||||||||||||||  || ||||||||||| |||||||| ||||||| || || ||||||||| ||| ||| |||||||| | |||| |||||||||||  || | | || |    | |  |||||       || |     ||||  |  |    |  || |  || |      |||| |    |  |||   |  |
AATAGAGAAAATTACAGGTCAAAGCCTGACATCTATCTTCCAGAGCTCTCAAACTTCCTTGGATGTTCTAAGAGCAGCAAAGCATTTCAAGTTATTTCAGgtgatttccctttgatg--cagtcctactcagtagaacaactcttctgtggaaaatctgttttttaaagatattttgtcattctattatacatgtctctttg
















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|50337770|gb|CO532896.1|CO532896
EST:     GCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: GCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|60349907|gb|DN216880.1|DN216880
EST:     AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|67018909|gb|CO447658.1|CO447658
EST:     AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTCTTAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|149071532|gb|EE159923.2|EE159923
EST:     AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTTTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|76011230|gb|DT938400.1|DT938400
EST:     AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|78111011|gb|DV529408.1|DV529408
EST:     AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|60338971|gb|DN205944.1|DN205944
EST:     AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|110524608|gb|EE028792.1|EE028792
EST:     AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|32944106|gb|CF048925.1|CF048925
EST:     AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|88746509|gb|DY530650.1|DY530650
EST:     TCATGGGATGTTATAAAAGCGGAAAAGCACTACAAGCTTTTTCAG                         CGTGCGACCCATGTCTTTTTTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: TCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|32833835|gb|CD973513.1|CD973513
EST:     AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|87152649|gb|DY397438.1|DY397438
EST:     AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|37386348|gb|CF630360.1|CF630360
EST:     AGACGTCATTGGAAGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTCTGAAGCAAGGAGAGTTTATGCTTTCAGGGAT
genomic: AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|148960155|gb|EE153405.2|EE153405
EST:     AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|17921536|gb|BM259187.1|BM259187
EST:     AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|211541591|gb|FL022794.1|FL022794
EST:     AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|17921866|gb|BM259517.1|BM259517
EST:     AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|67016317|gb|CO445066.1|CO445066
EST:     AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|76912625|gb|DV164824.1|DV164824
EST:     CAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTATTTTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: CAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|32943061|gb|CF047880.1|CF047880
EST:     AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|211541592|gb|FL022795.1|FL022795
EST:     CGTCATTGGATGTCTAAATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: CGTCATTGGATGT-T--ATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|71318358|gb|DR795941.1|DR795941
EST:     AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|32835728|gb|CD975406.1|CD975406
EST:     AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|74231837|gb|DT639751.1|DT639751
EST:     GACGTCATTGGATGTTTATAAAAGGGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTTTATTTTGAAGCAAGGAGGGTTTATGTTTTCAGGGAT
genomic: GACGTCATTGGATG-TTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|50337771|gb|CO532897.1|CO532897
EST:     GCGGCAAAGCACTACAAGCTATTTCTG                         CGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: GCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|71773515|gb|DR971415.1|DR971415
EST:     AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTTTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: AGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
EST: gi|78085243|gb|DV513636.1|DV513636
EST:     GACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAG                         CGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT
genomic: GACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttca ... ttaatttcagCGTGCGACCCATGTCTACTCTGAAGCAAGGAGGGTTTATGCTTTCAGGGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATAGAGAAAATTACAGGAGAAGGCCTGACATCTGTCTTCCAGGGCTCTCAGACGTCATTGGATGTTATAAAAGCGGCAAAGCACTACAAGCTATTTCAGgtggatttcatgtgcttattatttgtactcttgtagccatccaagttgtgctattccatgattgaccatctgacagaattcgagataaagtgttcatgag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT