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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACCGCAGTCTCTGAAGAAGCTGAGCCTCCGGTCGCTCAAGCGGTCCCTGGACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgcttagctgttaactctgttctttcctcgggtggttcaaaatcctatcagggattctaactgcgtattctcttgatcttgctgcggcggcggtggtgcag

Basic information

species Zea mays
transcript GRMZM2G017089_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017089_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g21990.1 (Oryza sativa), 5'ss of exon 2
AACCGCAGTCTCTGAAGAAGCTGAGCCTCCGGTCGCTCAAGCGGTCCCTGGACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgcttagctgttaactctgttctttcctcgggtggttcaaaatcctatcagggattctaactgcgtattctcttgatcttgctgcggcggcggtggtgcag-----
| |||||||| ||||||||||||||||||  |||||||||||| || |  ||||||||||| ||  | ||| ||||||||||||| |||||  | |||||||||   |     |||     |||||  |   | |||        | || |||| | | | |  |  ||      | ||      ||| |  ||  |  |||| | |      
AGCCGCAGTCGCTGAAGAAGCTGAGCCTCAAGTCGCTCAAGCGCTCGCACGACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctgcgcgctcccctctctgcccc--catcgttcaccctagaaccctaacggcgctgtttgctaaactgtttcccccctttggtttggttgttgtggcggacggcag
















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|76013838|gb|DT941008.1|DT941008
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
EST: gi|211485186|gb|FL175528.1|FL175528
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACAGTGCGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
EST: gi|211479427|gb|FL175510.1|FL175510
EST:     ACCTCTTCGCCCCGGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTA
genomic: ACCTCTTCGCCCCGG-CGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTA
EST: gi|211485184|gb|FL175526.1|FL175526
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
EST: gi|76013076|gb|DT940246.1|DT940246
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
EST: gi|31440974|gb|CD510405.1|CD510405
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCA
EST: gi|78123946|gb|DV542330.1|DV542330
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCAGACGCAGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
EST: gi|78085590|gb|DV513983.1|DV513983
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
EST: gi|211104567|gb|FL375458.1|FL375458
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
EST: gi|211482306|gb|FL175513.1|FL175513
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
EST: gi|31909081|gb|CD650740.1|CD650740
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGCACGGTGCGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
EST: gi|78089068|gb|DV517459.1|DV517459
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
EST: gi|211482314|gb|FL175521.1|FL175521
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACNGTGCGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
EST: gi|211482317|gb|FL175524.1|FL175524
EST:     AC-TCTTCGCCCCGGCGCACGCCCTCCTCTTTCACGCC-GACGCCGAGAG                         CAAGCGGATTC
genomic: ACCTCTTCGCCCCGGCGCACGCCCTCCTCTT-CACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTC
EST: gi|148951460|gb|EC897185.2|EC897185
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
EST: gi|88755751|gb|DY539892.1|DY539892
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGTGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
EST: gi|211479425|gb|FL175508.1|FL175508
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
EST: gi|94478034|gb|EB706992.1|EB706992
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
EST: gi|148943611|gb|EC888674.2|EC888674
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
EST: gi|149079798|gb|EE168796.2|EE168796
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
EST: gi|148950913|gb|EC896543.2|EC896543
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
EST: gi|71436555|gb|DR817605.1|DR817605
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
EST: gi|211482312|gb|FL175519.1|FL175519
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
EST: gi|148962621|gb|EE013511.2|EE013511
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
EST: gi|76019935|gb|DT947105.1|DT947105
EST:     GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAG                         CAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA
genomic: GACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgc ... ggtggtgcagCAAGCGGATTCGTACTGGGTGCAAGGTGAGTGCGGAGTACGGTGCGGTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACCGCAGTCTCTGAAGAAGCTGAGCCTCCGGTCGCTCAAGCGGTCCCTGGACCTCTTCGCCCCGGCGCACGCCCTCCTCTTCACGCCCGACGCCGAGAGgtaacctcgcttagctgttaactctgttctttcctcgggtggttcaaaatcctatcagggattctaactgcgtattctcttgatcttgctgcggcggcggtggtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC