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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACTGGTCGGTGACGCATGTCGACTGGTCCGAAGGGAAGTGGCATCCCAAAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcggagcttttttttcaggcgcgaacaatccattaccttgtggcatttatttgactaacggtttcgcaaacggccacccag

Basic information

species Zea mays
transcript GRMZM2G099255_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099255_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os06g48700.1 (Oryza sativa), 5'ss of exon 9
GAACTGGTCGGTGACGCATGTCGACTGGTCCGAAGGGAAGTGGCATCCCAAAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcggagcttttttttcaggcgc--gaacaatccattaccttgtggcatttatttgactaacggttt-cgcaaacggccacccag------------------------------------
 || ||||| ||||| ||||| || ||||| ||||| || |||||||| ||||  ||||||||||  ||||||||||| || ||||| ||| | ||  |||| ||||| |   |  || | || ||    |||      |    | |||   ||||  || |    |  ||| ||||||   |  |                                        
AAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCTTTGAACTGCTTAAGAATATTTCGgtgagctctggtatacttgtacatgcaaaagaaggggaaacatacatgttttatttccttaatggccaattttcgcaaaaatctgcattcttgggatttgtctaattaataatgaaatttttgcag

upper sequence: GRMZM2G099255_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv04s0008g02630.t01 (Vitis vinifera), 5'ss of exon 9
GAACTGGTCGGTGACGCATGTCGACTGGTCCGAAGGGAAGTGGCATCCCAAAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcggagcttttttttcaggcgcgaacaatccattaccttgtggcatttatttgactaacggtttcgcaaacggccacccag-------
 |||||||| ||||| ||||| || ||||| ||||| ||||||||||| ||||  ||||||| |   |||   || | ||| || || | | | ||  | ||| | ||   |  || |  |      |          ||      |  |||  | ||    |   ||     | |  |               
AAACTGGTCTGTGACACATGTAGATTGGTCAGAAGGAAAGTGGCATCCAAAAGCATACAGGGGTCAAGACGTCAGTTACGAGCTCCTTAGGAATATTACAgtacgatccttgtcttatccttctattcagttttatttttcaagaatcacatgcaattctgcattagtccttgacattgttgttactatggcag
















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|113702130|gb|EE679634.1|EE679634
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|78105512|gb|DV523930.1|DV523930
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|78090001|gb|DV518375.1|DV518375
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|78024858|gb|DV493245.1|DV493245
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|211326914|gb|FL457046.1|FL457046
EST:     AAGTCTACACGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|76018436|gb|DT945606.1|DT945606
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|101398462|gb|EB821104.1|EB821104
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|86474172|gb|DY240542.1|DY240542
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|89252603|gb|DY624389.1|DY624389
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|78093093|gb|DV521467.1|DV521467
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|211295436|gb|FL439725.1|FL439725
EST:     AAGTCTACAGGGCTGCGGACMCAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|211482405|gb|FK951270.1|FK951270
EST:     AAGTCTATAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|86471048|gb|DY237418.1|DY237418
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|71774867|gb|DR972745.1|DR972745
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|101399747|gb|EB821720.1|EB821720
EST:     AAGTCTACAGGGCGGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|78077573|gb|DV506007.1|DV506007
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|101388829|gb|EB816396.1|EB816396
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|148961000|gb|EE011700.2|EE011700
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|37388428|gb|CF631423.1|CF631423
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|71767366|gb|DR965303.1|DR965303
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|149106921|gb|EE188822.2|EE188822
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|211485273|gb|FK951273.1|FK951273
EST:     AAGTCTATAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|71442672|gb|DR823722.1|DR823722
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|37394285|gb|CF634415.1|CF634415
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|14717652|gb|BI245302.1|BI245302
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|86469460|gb|DY235830.1|DY235830
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|149082889|gb|EE172120.2|EE172120
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|24768422|gb|CA403551.1|CA403551
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|50337694|gb|CO532820.1|CO532820
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|76912822|gb|DV164897.1|DV164897
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
EST: gi|148963210|gb|EE014187.2|EE014187
EST:     AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCG                         TCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG
genomic: AAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcgg ... ggccacccagTCCATCGACGAGAGCGTCCACGTTAGCAGCAACGCGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACTGGTCGGTGACGCATGTCGACTGGTCCGAAGGGAAGTGGCATCCCAAAGTCTACAGGGCTGCGGACACAAGCTTCGATCTGCTCAAGGACATCGCGgtaagctcggagcttttttttcaggcgcgaacaatccattaccttgtggcatttatttgactaacggtttcgcaaacggccacccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT