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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcctttctctttcatttcattcacagatgccataatcttcccttttctaaagatgtttgaggcttatacggttgttttaatttggtagGAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGATGAACTTTAAACGGTTCCGGCGTGGACAAAGAAAATTTCACCAGGAAGCA

Basic information

species Zea mays
transcript GRMZM2G052875_T02
intron # 15
splice site 3'
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|60350253|gb|DN217226.1|DN217226
EST:     ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAG                         GAGCTGCAAAACAAACTGGATGCCATGTTTTCGAAGCAGCCCGGGCATGAT
genomic: ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAGgtcctttctc ... aatttggtagGAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
EST: gi|211376353|gb|FL146646.1|FL146646
EST:     ATGTGGCTGTATTGTCGACGCCCGCACTCTGCGTTGAGGAGAAGCTGAAG                         GAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
genomic: ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAGgtcctttctc ... aatttggtagGAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
EST: gi|18964528|gb|BM661058.1|BM661058
EST:     ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAG                         GAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
genomic: ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAGgtcctttctc ... aatttggtagGAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
EST: gi|18964529|gb|BM661059.1|BM661059
EST:     ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAG                         GAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
genomic: ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAGgtcctttctc ... aatttggtagGAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
EST: gi|33092076|gb|CF052070.1|CF052070
EST:     ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAG                         GAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
genomic: ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAGgtcctttctc ... aatttggtagGAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
EST: gi|211376351|gb|FL146644.1|FL146644
EST:     ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAG                         GAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
genomic: ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAGgtcctttctc ... aatttggtagGAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
EST: gi|87151897|gb|DY396686.1|DY396686
EST:     ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAG                         GAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
genomic: ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAGgtcctttctc ... aatttggtagGAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
EST: gi|211084967|gb|FL399106.1|FL399106
EST:     ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAG                         GAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
genomic: ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAGgtcctttctc ... aatttggtagGAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
EST: gi|110950038|gb|EE170195.1|EE170195
EST:     ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAG                         GAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
genomic: ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAGgtcctttctc ... aatttggtagGAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
EST: gi|211376352|gb|FL146645.1|FL146645
EST:     ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAG                         GAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
genomic: ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAGgtcctttctc ... aatttggtagGAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
EST: gi|67026048|gb|CO454797.1|CO454797
EST:     ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAG                         GAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
genomic: ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAGgtcctttctc ... aatttggtagGAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
EST: gi|32855947|gb|CD995628.1|CD995628
EST:     ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAG                         GAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
genomic: ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAGgtcctttctc ... aatttggtagGAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
EST: gi|30306637|gb|CD001310.1|CD001310
EST:     ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAG                         GAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT
genomic: ATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAGgtcctttctc ... aatttggtagGAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGAT

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), 47 (downstream exon)
Score: 142

GTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAGgtcctttctc ... aatttggtagGAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGATGAACTTTAAACGGTTCCGGCGTGGACAAAGAAAATTTCACCAGGAAGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 137

GTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAGgtcctttctc ... aatttggtagGAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGATGAACTTTAAACGGTTCCGGCGTGGACAAAGAAAATTTCACCAGGAAGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 198

GTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAGgtcctttctc ... aatttggtagGAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGATGAACTTTAAACGGTTCCGGCGTGGACAAAGAAAATTTCACCAGGAAGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 182

GTATGTTGCTGTATTGTCGACGCCCGCACTCTGCGTCGAGGAGAAGCTGAAGgtcctttctc ... aatttggtagGAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGATGAACTTTAAACGGTTCCGGCGTGGACAAAGAAAATTTCACCAGGAAGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcttcccttttctaaagatgtttgaggcttatacggttgttttaatttggtagGAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGATGAACTTTAAACGGTTCCGGCGTGGACAAAGAAAATTTCACCAGGAAGCA
                                      ttgttttaattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcctttctctttcatttcattcacagatgccataatcttcccttttctaaagatgtttgaggcttatacggttgttttaatttggtagGAGCTGCAAAACAAACTGGATGCCATGTCTTCGAAGCAGCCCGGGCATGATGAACTTTAAACGGTTCCGGCGTGGACAAAGAAAATTTCACCAGGAAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA