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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGTATCCAAGCTGTTTAATGTGCCGCTACTTAATGTCACAACATCCTTTGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAAgtaagcaaatcaagattcccatttgttttctgaaagctctgttgtttgcattacactgattagtgtttagttctcacctag

Basic information

species Zea mays
transcript GRMZM5G890665_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G890665_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g01580.2 (Oryza sativa), 5'ss of exon 2
TTGGTATCCAAGCTGTTTAATGTGCCGCTACTTAATGTCACAACATCCTTTGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACA-CTGGAGGTGAAAgtaagcaaatcaagattcccatttgttttctgaaagctc----tgttgtttgcattacactgattagtgtttagttctcacctag
 |||||||||||||| | ||||| ||  | || || ||||| |||||||||||||| ||||||||||||  ||||| | |||  |||| ||       ||||||| |||        ||  ||||| ||| | ||| ||     | |||||||||    ||||||||||||||||||||||| |||
-TGGTATCCAAGCTGCTCAATGTCCCATTGCTCAACGTCACCACATCCTTTGTTGCCGAGCAGCAGGCAGTGGATGCCGATTATAACAGCTCCGTAAAAAAgtaaccaatctgcacatcttatttgctttttaaaatctttccttcttgtttgcacactactgattagtgtttagttctcacatag

upper sequence: GRMZM5G890665_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g01580.1 (Oryza sativa), 5'ss of exon 2
TTGGTATCCAAGCTGTTTAATGTGCCGCTACTTAATGTCACAACATCCTTTGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACA-CTGGAGGTGAAAgtaagcaaatcaagattcccatttgttttctgaaagctctg----ttgtttgcattacactgattagtgtttagttctcacctag
 |||||||||||||| | ||||| ||  | || || ||||| |||||||||||||| ||||||||||||  ||||| | |||  |||| ||       ||||||| |||        ||  ||||| ||| | ||| || |     |||||||||    ||||||||||||||||           
-TGGTATCCAAGCTGCTCAATGTCCCATTGCTCAACGTCACCACATCCTTTGTTGCCGAGCAGCAGGCAGTGGATGCCGATTATAACAGCTCCGTAAAAAAgtaaccaatctgcacatcttatttgctttttaaaatctttccttcttgtttgcacactactgattagtgtttag-----------

upper sequence: GRMZM5G890665_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA07G19210.1 (Glycine max), 5'ss of exon 4
TTGGTATCCAAGCTGTTTAATGTGCCGCTACTTAATGTCACAACATCCTTTGTTGCTGAGCAGCAGGCA---------AAGGATGGCAATTCGAACACTGGAGGTGAAA-
               || ||||| ||  |||||||||| || |||||||||||||| ||| ||||||||         ||||| |   | || |      | | |||||   ||| |    ||||       ||     |||| | | | | |||   ||||| | |||  |  |    | ||   || |||  |                                             
------------GCATTCAATGTTCCTTTACTTAATGTTACTACATCCTTTGTTGCGGAGGAGCAGGCACTGATTAGGAAGGAGGAAGAGTCCATTCTGAGTGATGAAAATGgtatgtttttcaactaaggtatcacagtttcagtaggatgtgtacatttgcttgacatggtcacagattttcctttttcagatgtatatacaaataatttttatctcatgtgggtcatgatttctcag

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|211025188|gb|FL300504.1|FL300504
EST:     TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGGGAAA                         GAGATGAATTTTTGACGCCACTAGAGAAGGCAAGGCAACCTAAAGA-GGTT
genomic: TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAAgtaagcaaat ... tctcacctagGAGATGAATTTTTGACGCCACTAGAGAAGGCAAGGCAACC-AAAGAAGGTT
EST: gi|211025184|gb|FL300500.1|FL300500
EST:     TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGGGAAA                         GAGATGAATTTTTGACGCCACTAGAGAANGGCAGGGCAACCAAAGAAGGTT
genomic: TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAAgtaagcaaat ... tctcacctagGAGATGAATTTTTGACGCCACTAGAGAA-GGCAAGGCAACCAAAGAAGGTT
EST: gi|148939832|gb|EC884537.2|EC884537
EST:     TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAA                         GAGATGAATTTTTGACGCCACTAGAGAAGGCAAGGCAACCAAAGAAGGTTC
genomic: TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAAgtaagcaaat ... tctcacctagGAGATGAATTTTTGACGCCACTAGAGAAGGCAAGGCAACCAAAGAAGGTTC
EST: gi|149072460|gb|EE160737.2|EE160737
EST:     TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAA                         T
genomic: TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAAgtaagcaaat ... tctcacctag-
EST: gi|149072460|gb|EE160737.2|EE160737
EST:     TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAA                         T
genomic: TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAAgtaagcaaat ... tctcacctag-
EST: gi|149072460|gb|EE160737.2|EE160737
EST:     TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAA                         T
genomic: TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAAgtaagcaaat ... tctcacctag-
EST: gi|149072460|gb|EE160737.2|EE160737
EST:     TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAA                         T
genomic: TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAAgtaagcaaat ... tctcacctag-
EST: gi|149072460|gb|EE160737.2|EE160737
EST:     TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAA                         T
genomic: TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAAgtaagcaaat ... tctcacctag-
EST: gi|149072460|gb|EE160737.2|EE160737
EST:     TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAA                         T
genomic: TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAAgtaagcaaat ... tctcacctag-
EST: gi|149072460|gb|EE160737.2|EE160737
EST:     TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAA                         T
genomic: TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAAgtaagcaaat ... tctcacctag-
EST: gi|149072460|gb|EE160737.2|EE160737
EST:     TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAA                         T
genomic: TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAAgtaagcaaat ... tctcacctag-
EST: gi|149072460|gb|EE160737.2|EE160737
EST:     TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAA                         T
genomic: TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAAgtaagcaaat ... tctcacctag-
EST: gi|149072460|gb|EE160737.2|EE160737
EST:     TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAA                         T
genomic: TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAAgtaagcaaat ... tctcacctag-
EST: gi|149072460|gb|EE160737.2|EE160737
EST:     TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAA                         T
genomic: TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAAgtaagcaaat ... tctcacctag-
EST: gi|211025185|gb|FL300501.1|FL300501
EST:     TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAA                         GAGATGAATTTTTGACGCCACTAGAGAAGGCAAGGCAACCAAAGAAGGTTC
genomic: TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAAgtaagcaaat ... tctcacctagGAGATGAATTTTTGACGCCACTAGAGAAGGCAAGGCAACCAAAGAAGGTTC
EST: gi|211025182|gb|FL300498.1|FL300498
EST:     TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGGGAAA                         GAGATGAATTTTTGACGCCACTAGAGAAGGCAAGGCAACCAAAGAAGGTTC
genomic: TGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAAgtaagcaaat ... tctcacctagGAGATGAATTTTTGACGCCACTAGAGAAGGCAAGGCAACCAAAGAAGGTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGTATCCAAGCTGTTTAATGTGCCGCTACTTAATGTCACAACATCCTTTGTTGCTGAGCAGCAGGCAAAGGATGGCAATTCGAACACTGGAGGTGAAAgtaagcaaatcaagattcccatttgttttctgaaagctctgttgtttgcattacactgattagtgtttagttctcacctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG