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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatatggcttcattatagagtttatccctgtttcatacttttattgttttctgtgacctaactaatatgttaatctgtttgttgtttggtgacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG

Basic information

species Zea mays
transcript GRMZM5G876003_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G876003_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g38060.2 (Oryza sativa), 3'ss of exon 1
-tatatggcttcattatagagtttatccctgtttcatacttttattgttttctgtgacctaactaatatgttaatctgtttgttgtttggtg-acatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG
 ||||||  |   |||   | |||| |     || || |||| | | |||| | |  |  | |||||  ||| || ||||| || | || ||  ||   |||||||||||||||||||||||||| ||||| ||||||||||| ||||| ||||||||||||||
ttatatgaatgttttacttattttaccttctgtttattctttgaattttttttct--ctgagctaattagttgatatgttttttttatgatgtgcactctagATGCGTGCAAGGTTATCTGGTGGTCATTTCAGAATGTTAAATGAGAAACTATACACTTGCAG
















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|76923220|gb|DV169382.1|DV169382
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
EST: gi|211194090|gb|FL377673.1|FL377673
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
EST: gi|76281989|gb|DV021557.1|DV021557
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
EST: gi|74240435|gb|DT648349.1|DT648349
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
EST: gi|31354696|gb|CD439053.1|CD439053
EST:     AGCCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
EST: gi|71435218|gb|DR816268.1|DR816268
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
EST: gi|71429033|gb|DR810083.1|DR810083
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
EST: gi|71434799|gb|DR815849.1|DR815849
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGGGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
EST: gi|37423471|gb|CF649463.1|CF649463
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
EST: gi|211163247|gb|FL415263.1|FL415263
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
EST: gi|78074350|gb|DV502784.1|DV502784
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
EST: gi|50329972|gb|CO525098.1|CO525098
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
EST: gi|211327567|gb|FL371066.1|FL371066
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
EST: gi|211025381|gb|FL421226.1|FL421226
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
EST: gi|76922748|gb|DV169154.1|DV169154
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
EST: gi|76917955|gb|DV167089.1|DV167089
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCACCACCTCGAGTCTACTGCACAAG                         ATGCGTGCAAGGTTACCTGGTGGCCCATTTTAAGAATGTTAA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCC-ATTTTA-GAATGTTAA
EST: gi|78108382|gb|DV526800.1|DV526800
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
EST: gi|74245743|gb|DT653657.1|DT653657
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
EST: gi|148948106|gb|EC893615.2|EC893615
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
EST: gi|149071083|gb|EE159484.2|EE159484
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
EST: gi|91055947|gb|EB166365.1|EB166365
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
EST: gi|149100899|gb|EE186995.2|EE186995
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
EST: gi|78080458|gb|DV508870.1|DV508870
EST:     AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAG                         ATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA
genomic: AGGCCGCTGCTATGCCGAAGAGAGGCAACACCTCGAGTCTACTGGACAAGgtaatctatc ... gacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttctgtgacctaactaatatgttaatctgtttgttgtttggtgacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG
             taactaatatgttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatatggcttcattatagagtttatccctgtttcatacttttattgttttctgtgacctaactaatatgttaatctgtttgttgtttggtgacatcttagATGCGTGCAAGGTTATCTGGTGGCCATTTTAGAATGTTAAACGAGAAGCTATACACTTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC