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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGCGAGCCGGGACACCGTCGCCGCCGGCCGCCCGCTGTCCGACGCGCAGAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAGgtaactctgtcgcccctaattaacttcatttcgtacgatagctgtgtctgagaaatgtgtcggtaggtgtgtagagccatacctaaattttttttcgtcctccgccactggctgcgggtgctag

Basic information

species Zea mays
transcript GRMZM2G020418_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|33467366|gb|CF244415.1|CF244415
EST:     GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAG                         GGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
genomic: GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAGgtaactctgt ... cgggtgctagGGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
EST: gi|91876075|gb|EB406032.1|EB406032
EST:     GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAG                         GGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
genomic: GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAGgtaactctgt ... cgggtgctagGGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
EST: gi|76018426|gb|DT945596.1|DT945596
EST:     GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAG                         GGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
genomic: GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAGgtaactctgt ... cgggtgctagGGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
EST: gi|50332975|gb|CO528101.1|CO528101
EST:     GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAG                         GGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
genomic: GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAGgtaactctgt ... cgggtgctagGGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
EST: gi|76021688|gb|DT948858.1|DT948858
EST:     GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAG                         GGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
genomic: GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAGgtaactctgt ... cgggtgctagGGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
EST: gi|78077065|gb|DV505499.1|DV505499
EST:     GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAG                         GGTTTGGCTCGAGATGGGGAAGGCAAAGAGCA-GGGCCCTAAATTCGCGGC
genomic: GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAGgtaactctgt ... cgggtgctagGGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
EST: gi|74245267|gb|DT653181.1|DT653181
EST:     GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAG                         GGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
genomic: GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAGgtaactctgt ... cgggtgctagGGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
EST: gi|88752947|gb|DY537088.1|DY537088
EST:     GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAG                         GGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
genomic: GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAGgtaactctgt ... cgggtgctagGGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
EST: gi|50330327|gb|CO525453.1|CO525453
EST:     GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAG                         GGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
genomic: GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAGgtaactctgt ... cgggtgctagGGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
EST: gi|50326784|gb|CO521910.1|CO521910
EST:     GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAG                         GGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
genomic: GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAGgtaactctgt ... cgggtgctagGGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
EST: gi|211106067|gb|FL115242.1|FL115242
EST:     GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAG                         GGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
genomic: GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAGgtaactctgt ... cgggtgctagGGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
EST: gi|78087731|gb|DV516124.1|DV516124
EST:     GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAG                         GGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
genomic: GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAGgtaactctgt ... cgggtgctagGGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
EST: gi|93013576|gb|EB639096.1|EB639096
EST:     GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAG                         GGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
genomic: GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAGgtaactctgt ... cgggtgctagGGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
EST: gi|50326825|gb|CO521951.1|CO521951
EST:     GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAG                         GGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
genomic: GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAGgtaactctgt ... cgggtgctagGGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
EST: gi|148956652|gb|EC902508.2|EC902508
EST:     GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAG                         GGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC
genomic: GAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAGgtaactctgt ... cgggtgctagGGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGC

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: 46 (upstream exon), 49 (downstream exon)
Score: 47

GCCGCGAGCCGGGACACCGTCGCCGCCGGCCGCCCGCTGTCCGACGCGCAGAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAGgtaactctgt ... cgggtgctagGGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAA


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 34

GCCGCGAGCCGGGACACCGTCGCCGCCGGCCGCCCGCTGTCCGACGCGCAGAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAGgtaactctgt ... cgggtgctagGGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAA


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 31

GCCGCGAGCCGGGACACCGTCGCCGCCGGCCGCCCGCTGTCCGACGCGCAGAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAGgtaactctgt ... cgggtgctagGGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 25

GCCGCGAGCCGGGACACCGTCGCCGCCGGCCGCCCGCTGTCCGACGCGCAGAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAGgtaactctgt ... cgggtgctagGGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGCGAGCCGGGACACCGTCGCCGCCGGCCGCCCGCTGTCCGACGCGCAGAGCCTCGTGTCCAAGCGTGGCAAGTTCAAGCTCGGATTCTTCCGTCCAGgtaactctgtcgcccctaattaacttcatttcgtacgatagctgtgtctgagaaatgtgtcggtaggtgtgtagagccatacctaaattttttttcgtcctccgccactggctgcgggtgctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT