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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCTTGCAGATGGGTCTTTCTCCGAATAAAGAACGAGGCATAGGTTTGCTTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAGgttcgttctgtttcatttattactattcctgttatatttcaattttttttatcagtagaattattttttacttgcaactaatgtctagtgataatgaagt...

Basic information

species Zea mays
transcript GRMZM2G039359_T07
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039359_T07 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g40200.1 (Oryza sativa), 5'ss of exon 2
TTCCTTGCAGATGGGTCTTTCTCCGAATAAAGAACGAGGCATAGGTTTGCTTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAGgttcgttctgtttcatttattactattcctgttatatttcaattttttttatcagtagaattattttttacttgcaactaatgtctagtgataatgaagt----
||| ||| |||||||||||||  | ||||||||| ||||||| || |||||||||||||| ||||||||||| ||||||||    |||||| |||| |||||| ||| |   ||||||||||   |  || ||||  ||  |  | | |  | |   ||||| || ||     |  | ||| || | |  ||  |    |    
TTCTTTGGAGATGGGTCTTTCCTCAAATAAAGAAAGAGGCATTGGCTTGCTTTGGGGTCCAGATATCACTCAACAGTTTCTATATACAAATAATTTAAAGgtttgttgtcactcatttatta---tctcttttatcattagaactatctggtgaactgaatttttgttgttaagttattaa-gtattgctatgcttttatggtc
















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|32926902|gb|CF031714.1|CF031714
EST:     TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAG                         CTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
genomic: TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAGgttcgttctg ... caacaaaaagCTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
EST: gi|32925093|gb|CF029905.1|CF029905
EST:     TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAG                         CTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
genomic: TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAGgttcgttctg ... caacaaaaagCTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
EST: gi|32935243|gb|CF040055.1|CF040055
EST:     TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAG                         CTAATCATCAGGTCACATGAAGGTCCAGACGCGGGAGACAAGCGACACGAT
genomic: TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAGgttcgttctg ... caacaaaaagCTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
EST: gi|32926929|gb|CF031741.1|CF031741
EST:     TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAG                         CTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
genomic: TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAGgttcgttctg ... caacaaaaagCTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
EST: gi|32925852|gb|CF030664.1|CF030664
EST:     TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAG                         CTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
genomic: TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAGgttcgttctg ... caacaaaaagCTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
EST: gi|32926314|gb|CF031126.1|CF031126
EST:     TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAG                         CTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACG
genomic: TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAGgttcgttctg ... caacaaaaagCTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACG
EST: gi|32926892|gb|CF031704.1|CF031704
EST:     TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAG                         CTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
genomic: TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAGgttcgttctg ... caacaaaaagCTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
EST: gi|32926827|gb|CF031639.1|CF031639
EST:     TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAG                         CTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
genomic: TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAGgttcgttctg ... caacaaaaagCTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
EST: gi|32935224|gb|CF040036.1|CF040036
EST:     TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAG                         CTAATCATCAGGTCACATGAAGGTCCAGACGCGGGAGACAAGCGACACGAT
genomic: TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAGgttcgttctg ... caacaaaaagCTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
EST: gi|32925644|gb|CF030456.1|CF030456
EST:     TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAG                         CTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
genomic: TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAGgttcgttctg ... caacaaaaagCTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
EST: gi|32926141|gb|CF030953.1|CF030953
EST:     TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAG                         CTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
genomic: TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAGgttcgttctg ... caacaaaaagCTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
EST: gi|211498889|gb|FL031325.1|FL031325
EST:     TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAG                         CTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
genomic: TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAGgttcgttctg ... caacaaaaagCTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
EST: gi|32926647|gb|CF031459.1|CF031459
EST:     TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAG                         CTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
genomic: TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAGgttcgttctg ... caacaaaaagCTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
EST: gi|26455936|gb|CA827519.1|CA827519
EST:     TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAG                         CTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
genomic: TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAGgttcgttctg ... caacaaaaagCTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
EST: gi|19822442|gb|BQ048466.1|BQ048466
EST:     TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAG                         CTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT
genomic: TTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAGgttcgttctg ... caacaaaaagCTAATCATCAGGTCACATGAAGGTCCAGACGCGAGAGACAAGCGACACGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCTTGCAGATGGGTCTTTCTCCGAATAAAGAACGAGGCATAGGTTTGCTTTGGGGTCCTGATATCACTCAGCAGTTTCTGAGGACAAATCATTTGAAGgttcgttctgtttcatttattactattcctgttatatttcaattttttttatcagtagaattattttttacttgcaactaatgtctagtgataatgaagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG