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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAAGGATCCTTGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGgtggtcaaggttgtttatcatatactgtaagtgtttgcaagaagaattagtctttgcgagatgggattgatttgcttgcttttgtag

Basic information

species Zea mays
transcript GRMZM2G107731_T02
intron # 4
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|71436912|gb|DR817962.1|DR817962
EST:     TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAG                         GTGGTCAAGGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAG
genomic: TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGgtggtcaagg ... gcttttgtagG-GG--A-G-----CGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAG
EST: gi|78116277|gb|DV534664.1|DV534664
EST:     TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAG                         GTGGTCAAGGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAG
genomic: TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGgtggtcaagg ... gcttttgtagG-GG--A-G-----CGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAG
EST: gi|149081200|gb|EE170309.2|EE170309
EST:     TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAG                         GGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
genomic: TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGgtggtcaagg ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
EST: gi|91874738|gb|EB404695.1|EB404695
EST:     TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAG                         GGGAGCGGTGAGCCCAAACGCAAGGTCATCAAGCATAGCAAGCTTGAAAAG
genomic: TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGgtggtcaagg ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
EST: gi|149027108|gb|EE046399.2|EE046399
EST:     TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAG                         GTGGTCAAGGGGAGCGGTGAGCAAAAACGCAAGGTCATCAAGCATAGCAAG
genomic: TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGgtggtcaagg ... gcttttgtagG-GG--A-G-----CGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAG
EST: gi|148994670|gb|EE034191.2|EE034191
EST:     TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAG                         GTGGTCAAGGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAG
genomic: TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGgtggtcaagg ... gcttttgtagG-GG--A-G-----CGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAG
EST: gi|148937207|gb|EC881388.2|EC881388
EST:     TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAG                         GTGGTCAAGGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAG
genomic: TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGgtggtcaagg ... gcttttgtagG-GG--A-G-----CGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAG
EST: gi|148961119|gb|EE011825.2|EE011825
EST:     TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAG                         GTGGTCAAGGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAG
genomic: TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGgtggtcaagg ... gcttttgtagG-GG--A-G-----CGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAG
EST: gi|149103903|gb|EE289318.2|EE289318
EST:     TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAG                         GTGGTCAAGGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAG
genomic: TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGgtggtcaagg ... gcttttgtagG-GG--A-G-----CGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAG
EST: gi|50326867|gb|CO521993.1|CO521993
EST:     TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAG                         GGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
genomic: TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGgtggtcaagg ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
EST: gi|71774542|gb|DR972420.1|DR972420
EST:     TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAG                         GGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
genomic: TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGgtggtcaagg ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
EST: gi|149071351|gb|EE159746.2|EE159746
EST:     TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAG                         GGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
genomic: TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGgtggtcaagg ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
EST: gi|31354731|gb|CD439088.1|CD439088
EST:     TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAG                         GGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
genomic: TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGgtggtcaagg ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
EST: gi|60358220|gb|DN225193.1|DN225193
EST:     TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGGTGGTCAAG                 
genomic: TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATC--AA-------AAGgtggtcaagg ... gc
EST: gi|91055771|gb|EB166189.1|EB166189
EST:     TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAG                         GGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG
genomic: TGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGgtggtcaagg ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAG

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), 48 (downstream exon)
Score: 40

GTGAAGGATCCTTGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGgtggtcaagg ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAGGACAAAGAGTTATTTCAACTAGCCCAGCAATACCACAAAGTGGTTGCAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 56

GTGAAGGATCCTTGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGgtggtcaagg ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAGGACAAAGAGTTATTTCAACTAGCCCAGCAATACCACAAAGTGGTTGCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 56

GTGAAGGATCCTTGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGgtggtcaagg ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAGGACAAAGAGTTATTTCAACTAGCCCAGCAATACCACAAAGTGGTTGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 41

GTGAAGGATCCTTGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGgtggtcaagg ... gcttttgtagGGGAGCGGTGAGCCAAAACGCAAGGTCATCAAGCATAGCAAGCTTGAGAAGGACAAAGAGTTATTTCAACTAGCCCAGCAATACCACAAAGTGGTTGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAAGGATCCTTGAAGGAAAATCGTGCATCAGAGCAAGTGGGCGCTCCAAGTGATCAAAAGgtggtcaaggttgtttatcatatactgtaagtgtttgcaagaagaattagtctttgcgagatgggattgatttgcttgcttttgtag

- - - - - - - AAGGAA
- - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - -  AGCAAG