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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaatcctatttaggcagcagcctcttagattgatttgcactccttcctataagtagtaaagctactatcatatagtattggtggtgttgaaaa...

Basic information

species Zea mays
transcript GRMZM2G558539_T02
intron # 10
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|60339589|gb|DN206562.1|DN206562
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|60358480|gb|DN225453.1|DN225453
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|86471474|gb|DY237844.1|DY237844
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|5936814|gb|AW060082.1|AW060082
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|60354187|gb|DN221160.1|DN221160
EST:     AAGGCTCCAAAATGATTACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|76925222|gb|DV170325.1|DV170325
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|78179234|gb|DV549607.1|DV549607
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|60398906|gb|DN231722.1|DN231722
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|71300395|gb|DR786266.1|DR786266
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|60340147|gb|DN207120.1|DN207120
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|86474502|gb|DY240872.1|DY240872
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|71772068|gb|DR970005.1|DR970005
EST:     CGTTTTGGAGGCCAAAAGTTTTTACAG                         GGATGGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: CGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|8577220|gb|BE129857.1|BE129857
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|32932367|gb|CF037179.1|CF037179
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|211347566|gb|FL462326.1|FL462326
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|32832466|gb|CD972144.1|CD972144
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|60354933|gb|DN221906.1|DN221906
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|12047195|gb|BF729334.1|BF729334
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|110944775|gb|EE164932.1|EE164932
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTTTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACCCCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|71329626|gb|DR801542.1|DR801542
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|32833562|gb|CD973240.1|CD973240
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|211119819|gb|FL462976.1|FL462976
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|93011741|gb|EB637261.1|EB637261
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|93282521|gb|EB674785.1|EB674785
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|71321373|gb|DR797399.1|DR797399
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|71332095|gb|DR802954.1|DR802954
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
EST: gi|32833782|gb|CD973460.1|CD973460
EST:     AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAG                         GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT
genomic: AAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGAT

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: 48 (upstream exon), 49 (downstream exon)
Score: 452

GAAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 604

GAAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 522

GAAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 632

GAAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaa ... ttcatttcagGGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGGCTCCAAAATGACGACAAAACGTTTTGGAGGCCAAAAGTTCTTACAGgttagttaaatcctatttaggcagcagcctcttagattgatttgcactccttcctataagtagtaaagctactatcatatagtattggtggtgttgaaaa

- - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccttcc