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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaacatatatgtacataagtggcagtaatccacactctacagtctttgctttccctagcaagaatcaagcatgcaatgtgacatctatcttgtaaacattcag

Basic information

species Zea mays
transcript GRMZM2G077233_T04
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077233_T04 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g18630.2 (Oryza sativa), 5'ss of exon 10
TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaacatatatgtacataagtggcagtaa-tccacactctacagtctttgctttccctagcaagaatcaagcatgcaatgtgacatctatcttgtaaacattcag---------
||| ||||||||||||||||   ||| |||||| | |||||||| ||||| ||||| || ||||| || ||||| || || || ||||||||| |  |  | |  |||    |||  || | |  ||||   | |   ||  ||        |  |     | |      |  | |   | | |||||||   ||||  |         
TACGTAGTGAAGCTGGAGCAGCAAGGTCAAACTGTTTGCATCAGCGGGTTCATGGCGTTCGACGTGCCACCTCCACGCGGCCCACTCTGgtacacaaattacac-tgtcatcaagaagcgggagctccatgttgttaggttctttgaccgtttgacgt---ttagcttctcgttatctgacccatcttgttg-cattgcgtttttgcag
















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|32839637|gb|CD979318.1|CD979318
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTAC-ACACTGTTTTTGA
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGA
EST: gi|67023174|gb|CO451923.1|CO451923
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCNG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|32858947|gb|CD998628.1|CD998628
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|60352365|gb|DN219338.1|DN219338
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|211384116|gb|FL248479.1|FL248479
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|5361060|gb|AI795675.1|AI795675
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|60349588|gb|DN216561.1|DN216561
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|8577168|gb|BE129805.1|BE129805
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|78021457|gb|DV489844.1|DV489844
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|113633153|gb|DW791221.1|DW791221
EST:     TTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: TTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG
EST: gi|31250410|gb|CD219434.1|CD219434
EST:     ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTG                         GATACTTGGTGATGTTTCTATGGGTGCCTACCACACTGTTTTTGACTTCGG
genomic: ATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaa ... aaacattcagGATACTTGGTGATGTTTTTATGGGTGCCTACCACACTGTTTTTGACTTCGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACATAGTGAAGCTGGAGCAAGCAGGACAAACTATCTGCATCAGTGGGTTTATGGCATTTGACGTACCGCCTCCTCGTGGTCCTCTCTGgtacgctgaacatatatgtacataagtggcagtaatccacactctacagtctttgctttccctagcaagaatcaagcatgcaatgtgacatctatcttgtaaacattcag

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