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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCGGCCGTGGCGGGGACCGGGTCGTCCCTCTCCTCGCGCCGCAGTCGCAGCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgtttcgtctcgtcgtggggctttctgattcacgtgtgatgcctacgaagcggtgaggtattgtgtgtttttggttggtcttcttttggtgtgcgcag

Basic information

species Zea mays
transcript GRMZM2G180863_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|211174636|gb|FL281686.1|FL281686
EST:     GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCG                         AGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
genomic: GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
EST: gi|8367462|gb|BE050407.1|BE050407
EST:     GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCG                         AGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
genomic: GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
EST: gi|78088529|gb|DV516922.1|DV516922
EST:     GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCG                         AGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
genomic: GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
EST: gi|149112871|gb|EE191452.2|EE191452
EST:     GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCG                         AGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
genomic: GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
EST: gi|211172968|gb|FL281680.1|FL281680
EST:     GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCG                         AGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
genomic: GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
EST: gi|91051992|gb|EB162410.1|EB162410
EST:     GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCG                         AGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
genomic: GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
EST: gi|50339735|gb|CO534861.1|CO534861
EST:     GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCG                         AGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
genomic: GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
EST: gi|149006976|gb|EE040195.2|EE040195
EST:     GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCG                         AGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
genomic: GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
EST: gi|50325135|gb|CO520261.1|CO520261
EST:     GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCG                         AGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
genomic: GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
EST: gi|71770134|gb|DR968071.1|DR968071
EST:     GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCG                         AGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
genomic: GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
EST: gi|74243332|gb|DT651246.1|DT651246
EST:     GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCG                         AGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
genomic: GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
EST: gi|149000114|gb|EE037239.2|EE037239
EST:     GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCG                         AGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
genomic: GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
EST: gi|211172970|gb|FL281682.1|FL281682
EST:     GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCG                         AGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
genomic: GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
EST: gi|71766416|gb|DR964353.1|DR964353
EST:     GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCG                         AGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
genomic: GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
EST: gi|149079724|gb|EE168725.2|EE168725
EST:     GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCG                         AGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
genomic: GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
EST: gi|91053049|gb|EB163467.1|EB163467
EST:     GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCG                         AGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
genomic: GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
EST: gi|148973790|gb|EE024926.2|EE024926
EST:     GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCG                         AGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
genomic: GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
EST: gi|148947744|gb|EC893227.2|EC893227
EST:     GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCG                         AGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
genomic: GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
EST: gi|211172960|gb|FL281672.1|FL281672
EST:     GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCG                         AGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
genomic: GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
EST: gi|91874828|gb|EB404785.1|EB404785
EST:     GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCG                         AGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG
genomic: GCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGG

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), 48 (downstream exon)
Score: 21

CGCGGCCGTGGCGGGGACCGGGTCGTCCCTCTCCTCGCGCCGCAGTCGCAGCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGGATGAGCGGCGCCGAGTCCAGGACCGCGTGGGCGCCAAAGGTGCCCGCAC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 27

CGCGGCCGTGGCGGGGACCGGGTCGTCCCTCTCCTCGCGCCGCAGTCGCAGCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGGATGAGCGGCGCCGAGTCCAGGACCGCGTGGGCGCCAAAGGTGCCCGCAC


Block sizes: 45 (upstream exon), 33 (downstream exon)
Score: 12

CGCGGCCGTGGCGGGGACCGGGTCGTCCCTCTCCTCGCGCCGCAGTCGCAGCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGGATGAGCGGCGCCGAGTCCAGGACCGCGTGGGCGCCAAAGGTGCCCGCAC


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 11

CGCGGCCGTGGCGGGGACCGGGTCGTCCCTCTCCTCGCGCCGCAGTCGCAGCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgttt ... gtgtgcgcagAGATGCGTGCTCGGGAGCGAGCAGCTGCGGGTGGCGCATGAAGGGAAGCGGATGAGCGGCGCCGAGTCCAGGACCGCGTGGGCGCCAAAGGTGCCCGCAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCGGCCGTGGCGGGGACCGGGTCGTCCCTCTCCTCGCGCCGCAGTCGCAGCGTTGTCTCCTCGTCCTTCCGCGCAGCTGCCTCGCGCTTCCGCTCGCCGgtgagcgtttcgtctcgtcgtggggctttctgattcacgtgtgatgcctacgaagcggtgaggtattgtgtgtttttggttggtcttcttttggtgtgcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC