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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGCAGTTGTGGAACTCAGGCAACACGgtaggcgtttttttttcttctttatgttgtgtttttatattaccctcactccataacaccatttgcaaaaaaaataaaaactccagtttgttctgtactg...

Basic information

species Zea mays
transcript GRMZM2G011893_T02
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|60352045|gb|DN219018.1|DN219018
EST:     GCGGCAGTTGTGGAACTCAGGCAACACG                         AATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
genomic: GCGGCAGTTGTGGAACTCAGGCAACACGgtaggcgttt ... tttgttccagAATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
EST: gi|78179760|gb|DV550133.1|DV550133
EST:     GCGGCAGTTGTGGAACTCAGGCAACACG                         AATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
genomic: GCGGCAGTTGTGGAACTCAGGCAACACGgtaggcgttt ... tttgttccagAATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
EST: gi|60393994|gb|DN226864.1|DN226864
EST:     GCGGCAGTTGTGGAACTCAGGCAACACG                         AATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
genomic: GCGGCAGTTGTGGAACTCAGGCAACACGgtaggcgttt ... tttgttccagAATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
EST: gi|211290372|gb|FL395524.1|FL395524
EST:     GCGGCAGTTGTGGAACTCAGGCAACACG                         AATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
genomic: GCGGCAGTTGTGGAACTCAGGCAACACGgtaggcgttt ... tttgttccagAATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
EST: gi|60348982|gb|DN215955.1|DN215955
EST:     GCGGCAGTTGTGGAACTCAGGCAACACG                         AATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
genomic: GCGGCAGTTGTGGAACTCAGGCAACACGgtaggcgttt ... tttgttccagAATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
EST: gi|8577165|gb|BE129802.1|BE129802
EST:     GCGGCAGTTGTGGAACTCAGGCAACACG                         AATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
genomic: GCGGCAGTTGTGGAACTCAGGCAACACGgtaggcgttt ... tttgttccagAATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
EST: gi|78122303|gb|DV540687.1|DV540687
EST:     GCGGCAGTTGTGGAACTCAGGCAACACG                         AATATTGACGTTTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
genomic: GCGGCAGTTGTGGAACTCAGGCAACACGgtaggcgttt ... tttgttccagAATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
EST: gi|60352117|gb|DN219090.1|DN219090
EST:     GCGGCAGTTGTGGAACTCAGGCAACACG                         AATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
genomic: GCGGCAGTTGTGGAACTCAGGCAACACGgtaggcgttt ... tttgttccagAATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
EST: gi|71428221|gb|DR809271.1|DR809271
EST:     GCGGCAGTTGTGGAACTCAGGCAACCCG                         AATATTGACGTTTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
genomic: GCGGCAGTTGTGGAACTCAGGCAACACGgtaggcgttt ... tttgttccagAATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
EST: gi|60350066|gb|DN217039.1|DN217039
EST:     GCGGCAGTTGTGGAACTCAGGCAACACG                         AATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
genomic: GCGGCAGTTGTGGAACTCAGGCAACACGgtaggcgttt ... tttgttccagAATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
EST: gi|12047218|gb|BF729357.1|BF729357
EST:     GCGGCAGTTGTGGAACTCAGGCAACACG                         AATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
genomic: GCGGCAGTTGTGGAACTCAGGCAACACGgtaggcgttt ... tttgttccagAATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
EST: gi|60357511|gb|DN224484.1|DN224484
EST:     GCGGCAGTTGTGGAACTCAGGCAACACG                         AATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
genomic: GCGGCAGTTGTGGAACTCAGGCAACACGgtaggcgttt ... tttgttccagAATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
EST: gi|211246375|gb|FL451973.1|FL451973
EST:     GCGGCAGTTGTGGAACTCAGGCAACACG                         AATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA
genomic: GCGGCAGTTGTGGAACTCAGGCAACACGgtaggcgttt ... tttgttccagAATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTA

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: 28 (upstream exon), 48 (downstream exon)
Score: 253

GCGGCAGTTGTGGAACTCAGGCAACACGgtaggcgttt ... tttgttccagAATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTG


Block sizes: 28 (upstream exon), 48 (downstream exon)
Score: 299

GCGGCAGTTGTGGAACTCAGGCAACACGgtaggcgttt ... tttgttccagAATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 524

GCGGCAGTTGTGGAACTCAGGCAACACGgtaggcgttt ... tttgttccagAATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTG


Block sizes: 28 (upstream exon), 48 (downstream exon)
Score: 230

GCGGCAGTTGTGGAACTCAGGCAACACGgtaggcgttt ... tttgttccagAATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGGCAGTTGTGGAACTCAGGCAACACGgtaggcgtttttttttcttctttatgttgtgtttttatattaccctcactccataacaccatttgcaaaaaaaataaaaactccagtttgttctgtactg

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