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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATAAGTGCCCCTCCAACCGAAAACCTGTCCTTCTCCGCGCACTCCACCCCACTCGCCGCCGCCGCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaatgttctgtggtctctccgtgcaggcgaacctttgcgcgtcgtctctctctgatagtctgttcgtcgcgcag

Basic information

species Zea mays
transcript GRMZM2G024354_T01
intron # 1
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|211049492|gb|FL332043.1|FL332043
EST:     GCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGG                         GGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: GCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|37420683|gb|CF648037.1|CF648037
EST:     GCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGG                         GGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: GCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|31612151|gb|CD568773.1|CD568773
EST:     GCCGCCGCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGG                         GGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: GCCGCCGCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|211015164|gb|FL318464.1|FL318464
EST:     CCACTCGCCGCCGCCGCTGCCACCGGCGCTTGCTGCCGCAGCCGCCATGG                         GGGCGTACAAGTACGTGTCGGAACKATGGAGGAGGAAGCAGTCGGACGTGA
genomic: CCACTCGCCGCCGCCGCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|93283374|gb|EB675638.1|EB675638
EST:     CACCGCCGCTTGCTGCCGCAGCCGCCATGG                         GGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: CACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|149074390|gb|EE162776.2|EE162776
EST:     CCGCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGG                         GGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: CCGCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|211309973|gb|FL324772.1|FL324772
EST:     GCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGG                         GGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: GCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|5499068|gb|AI854935.1|AI854935
EST:     GCCGCCTGCTGCCGCAGCCGCCATGG                         GGGCGTACAAGTATGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: GCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|29129791|gb|CB380495.1|CB380495
EST:     CGCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGG                         GGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: CGCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|22713904|gb|BU197434.1|BU197434
EST:     CGCCGCCTGCTGCCGCAGCCGCCATGG                         GGGCGTACAAGTATGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: CGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|211240153|gb|FL362208.1|FL362208
EST:     GCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGG                         GGGCGTACAAGTACGTGTCG
genomic: GCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCG
EST: gi|211010460|gb|FL351127.1|FL351127
EST:     CCACTCGCCGCCGCCGCTGCTACCGCTGCTTGCTGCCGCAGCCGCCATGG                         GGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: CCACTCGCCGCCGCCGCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|211329125|gb|FL346007.1|FL346007
EST:     CCGCCGCCGCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGG                         GGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: CCGCCGCCGCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|31355299|gb|CD439656.1|CD439656
EST:     ACTCGCCGCCGCCGCTGCCAACGCCGCCTGCTCCCGCAGCCGCCATGG                         GGGCGTACAAGTATGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: ACTCGCCGCCGCCGCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|5398768|gb|AI812233.1|AI812233
EST:     TGCTGCCGCAGCCGCCATGG                         GGGCGTACAAGTATGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: TGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|211542993|gb|FL309294.1|FL309294
EST:     GCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGG                         GGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: GCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|30031772|gb|CB833623.1|CB833623
EST:     GCCGCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGG                         GGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: GCCGCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|148990298|gb|EE031897.2|EE031897
EST:     CTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGG                         GGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: CTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|30031777|gb|CB833628.1|CB833628
EST:     CACCGCCGCTTGCTGCCGCAGCCGTCATGG                         GGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: CACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|211381491|gb|FL249895.1|FL249895
EST:     GCAGCCGCCATGG                         GGGCGTACAAGTATGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: GCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|60400339|gb|DN233146.1|DN233146
EST:     CTTGCTGCCGCAGCCGCCATGG                         GGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: CTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|20300116|gb|BQ163059.1|BQ163059
EST:     GCCAACGCCGCCTGCTGCCGCAGCCGCCATGG                         GGGCGTACAAGTATGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: GCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|211183118|gb|FL314049.1|FL314049
EST:     GCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGG                         GGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: GCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
EST: gi|211386164|gb|FL339785.1|FL339785
EST:     GCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGG                         GGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: GCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGA

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: 49 (upstream exon), 49 (downstream exon)
Score: 429

ATATAAGTGCCCCTCCAACCGAAAACCTGTCCTTCTCCGCGCACTCCACCCCACTCGCCGCCGCCGCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGATGCGCTTCGTGCAGCGCGTGCGCTGCTGGGAGTACAGGCAGCAGCCGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 280

ATATAAGTGCCCCTCCAACCGAAAACCTGTCCTTCTCCGCGCACTCCACCCCACTCGCCGCCGCCGCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGATGCGCTTCGTGCAGCGCGTGCGCTGCTGGGAGTACAGGCAGCAGCCGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 262

ATATAAGTGCCCCTCCAACCGAAAACCTGTCCTTCTCCGCGCACTCCACCCCACTCGCCGCCGCCGCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGATGCGCTTCGTGCAGCGCGTGCGCTGCTGGGAGTACAGGCAGCAGCCGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 268

ATATAAGTGCCCCTCCAACCGAAAACCTGTCCTTCTCCGCGCACTCCACCCCACTCGCCGCCGCCGCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaat ... cgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGATGCGCTTCGTGCAGCGCGTGCGCTGCTGGGAGTACAGGCAGCAGCCGTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATAAGTGCCCCTCCAACCGAAAACCTGTCCTTCTCCGCGCACTCCACCCCACTCGCCGCCGCCGCTGCCACCGCCGCTTGCTGCCGCAGCCGCCATGGgtgagcaaatgttctgtggtctctccgtgcaggcgaacctttgcgcgtcgtctctctctgatagtctgttcgtcgcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC