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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGCAGCTTACCTCTTCAGCAACGACGGGCAGCTCAAGCAGCAGTTCGAGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCACgtatatatatacgcatggctgctgacatttgtcttgctgagtctgctaccatagctgatgcatggctgactgctttgctttctgaactgtgtgcag

Basic information

species Zea mays
transcript GRMZM2G103546_T01
intron # 9
splice site 5'
intron type U2

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|211402085|gb|FL455832.1|FL455832
EST:     ATCATGTTCAACGACACCGGCATCCAC                         CTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGARCGGCATGGGC
genomic: ATCATGTTCAACGACACCGGCATCCACgtatatatat ... ctgtgtgcagCTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGC
EST: gi|50334541|gb|CO529667.1|CO529667
EST:     AGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCCC                         CTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGC
genomic: AGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCACgtatatatat ... ctgtgtgcagCTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGC
EST: gi|148972862|gb|EE023861.2|EE023861
EST:     AGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCAC                         CTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGC
genomic: AGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCACgtatatatat ... ctgtgtgcagCTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGC
EST: gi|148935989|gb|EC880041.2|EC880041
EST:     AGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCCC                         CTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGC
genomic: AGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCACgtatatatat ... ctgtgtgcagCTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGC
EST: gi|211402086|gb|FL455833.1|FL455833
EST:     AGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCAC                         CTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGC
genomic: AGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCACgtatatatat ... ctgtgtgcagCTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGC
EST: gi|78110408|gb|DV528820.1|DV528820
EST:     AGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCAC                         CTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGC
genomic: AGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCACgtatatatat ... ctgtgtgcagCTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGC
EST: gi|94476507|gb|EB705465.1|EB705465
EST:     AGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCAC                         CTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGC
genomic: AGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCACgtatatatat ... ctgtgtgcagCTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGC
EST: gi|110951590|gb|EE171642.1|EE171642
EST:     AGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCCC                         CTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGC
genomic: AGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCACgtatatatat ... ctgtgtgcagCTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGC
EST: gi|71439164|gb|DR820214.1|DR820214
EST:     AGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCAC                         CTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGC
genomic: AGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCACgtatatatat ... ctgtgtgcagCTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGC
EST: gi|89760410|gb|DY688829.1|DY688829
EST:     AGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCAC                         CTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGC
genomic: AGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCACgtatatatat ... ctgtgtgcagCTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGC
EST: gi|50325620|gb|CO520746.1|CO520746
EST:     AGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCAC                         CTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGC
genomic: AGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCACgtatatatat ... ctgtgtgcagCTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 34 (downstream exon)
Score: 21

GCTGGCAGCTTACCTCTTCAGCAACGACGGGCAGCTCAAGCAGCAGTTCGAGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCACgtatatatat ... ctgtgtgcagCTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGCGCCTACCACGGCGCCTTCAGCTTCGACGCCTTCTCCCACAGGAAGGCCG


Block sizes: 20 (upstream exon), 31 (downstream exon)
Score: 3

GCTGGCAGCTTACCTCTTCAGCAACGACGGGCAGCTCAAGCAGCAGTTCGAGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCACgtatatatat ... ctgtgtgcagCTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGCGCCTACCACGGCGCCTTCAGCTTCGACGCCTTCTCCCACAGGAAGGCCG


Block sizes: 30 (upstream exon), 20 (downstream exon)
Score: 1

GCTGGCAGCTTACCTCTTCAGCAACGACGGGCAGCTCAAGCAGCAGTTCGAGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCACgtatatatat ... ctgtgtgcagCTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGCGCCTACCACGGCGCCTTCAGCTTCGACGCCTTCTCCCACAGGAAGGCCG


Block sizes: 40 (upstream exon), 39 (downstream exon)
Score: 51

GCTGGCAGCTTACCTCTTCAGCAACGACGGGCAGCTCAAGCAGCAGTTCGAGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCACgtatatatat ... ctgtgtgcagCTGACAAACCCGAACCTGCCGTTCGGAGGAGTCGGGGAGAGCGGCATGGGCGCCTACCACGGCGCCTTCAGCTTCGACGCCTTCTCCCACAGGAAGGCCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGCAGCTTACCTCTTCAGCAACGACGGGCAGCTCAAGCAGCAGTTCGAGAGGACCGTCTCGGCGGGAGGGATCATGTTCAACGACACCGGCATCCACgtatatatatacgcatggctgctgacatttgtcttgctgagtctgctaccatagctgatgcatggctgactgctttgctttctgaactgtgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA