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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taagattgatctgttgcatgcaagttgtaccttttcctttgttcaccttatttagagattaggtagtgcatctgtcactcatgtttggtttctctgctagGATGATGGAATACCTGAGGAGATGGAAGGCACCGTCGATGGATTGTCTGAAAAGGTCTCCAGGATGCACTCCTAAGGCAGGACTGTCCATGGCGACAGCA

Basic information

species Zea mays
transcript GRMZM5G828503_T01
intron # 1
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|4647185|gb|AI622260.1|AI622260
EST:     TAAGCGCTTCCAAGTGCGTCGTTGTCAGAAATAAACACCCAGAGCCAGAG                         GATGATGGAATACCTGAGGAGATGGAAGGCACCGTCGATGGATTGTCTGAA
genomic: TAAGCGCTTCCAAGTGCGTCGTTGTCAGAAATAAACACCCAGAGCCAGAGgtaatgctga ... tctctgctagGATGATGGAATACCTGAGGAGATGGAAGGCACCGTCGATGGATTGTCTGAA
EST: gi|6466745|gb|AW191405.1|AW191405
EST:     TAAGCGCTTCCAAGTGCGTCGTTGTCAGAAATAAACACCCAGAGCCAGAG                         GATGATGGAATACCTGAGGAGATGGAAGGCACCGTCGATGGATTGTCTGAA
genomic: TAAGCGCTTCCAAGTGCGTCGTTGTCAGAAATAAACACCCAGAGCCAGAGgtaatgctga ... tctctgctagGATGATGGAATACCTGAGGAGATGGAAGGCACCGTCGATGGATTGTCTGAA
EST: gi|5791393|gb|AI978185.1|AI978185
EST:     TAAGCGCTTCCAAGTGCGTCGTTGTCAGAAATAACCCCCCAGAGCCAGAG                         GATGATGGAATCCCTGAGGAGATGGAAGGCGCCGTCGATGGATTGTCTGAA
genomic: TAAGCGCTTCCAAGTGCGTCGTTGTCAGAAATAAACACCCAGAGCCAGAGgtaatgctga ... tctctgctagGATGATGGAATACCTGAGGAGATGGAAGGCACCGTCGATGGATTGTCTGAA
EST: gi|211031564|gb|FL471484.1|FL471484
EST:     TAAGCGCTTCCAAGTGCGTCGTTGTCAGAAATAAACACCCAGAGCCAGAG                         GATGATGGAATACCTGAGGAGATGGAAGGCACCGTCGATGGATTGTCTGAA
genomic: TAAGCGCTTCCAAGTGCGTCGTTGTCAGAAATAAACACCCAGAGCCAGAGgtaatgctga ... tctctgctagGATGATGGAATACCTGAGGAGATGGAAGGCACCGTCGATGGATTGTCTGAA
EST: gi|211391991|gb|FL471384.1|FL471384
EST:     TAAGCGCTTCCAAGTGCGTCGTTGTCAGAAATAAACACCCAGAGCCAGAG                         GATGATGGAATACCTGAGGAGATGGAAGGCACCGTCGATGGATTGTYTGAA
genomic: TAAGCGCTTCCAAGTGCGTCGTTGTCAGAAATAAACACCCAGAGCCAGAGgtaatgctga ... tctctgctagGATGATGGAATACCTGAGGAGATGGAAGGCACCGTCGATGGATTGTCTGAA
EST: gi|211280414|gb|FL033876.1|FL033876
EST:     AGCGCTTCCAAGTGCGTCGTTGTCAGAAATAAACACCCAGAGCCAGAG                         GATGATGGAATACCTGAGGAGATGGAAGGCACCGTCGATGGATTGTCTGAA
genomic: AGCGCTTCCAAGTGCGTCGTTGTCAGAAATAAACACCCAGAGCCAGAGgtaatgctga ... tctctgctagGATGATGGAATACCTGAGGAGATGGAAGGCACCGTCGATGGATTGTCTGAA
EST: gi|6827693|gb|AW331336.1|AW331336
EST:     TAAGCGCTTCCAAGTGCGTCGTTGTCAGAAATAAACACCCAGAGCCAGAG                         GATGATGGAATACCTGAGGAGATGGAAGGCACCGTCGATGGATTGTCTGAA
genomic: TAAGCGCTTCCAAGTGCGTCGTTGTCAGAAATAAACACCCAGAGCCAGAGgtaatgctga ... tctctgctagGATGATGGAATACCTGAGGAGATGGAAGGCACCGTCGATGGATTGTCTGAA

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), 49 (downstream exon)
Score: 173

TGTGAAACCCACAAGCTTAAGCTCTCGGAGCTACCTGAAGAGTGCAAGCATAAGCGCTTCCAAGTGCGTCGTTGTCAGAAATAAACACCCAGAGCCAGAGgtaatgctga ... tctctgctagGATGATGGAATACCTGAGGAGATGGAAGGCACCGTCGATGGATTGTCTGAAAAGGTCTCCAGGATGCACTCCTAAGGCAGGACTGTCCATGGCGACAGCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 163

TGTGAAACCCACAAGCTTAAGCTCTCGGAGCTACCTGAAGAGTGCAAGCATAAGCGCTTCCAAGTGCGTCGTTGTCAGAAATAAACACCCAGAGCCAGAGgtaatgctga ... tctctgctagGATGATGGAATACCTGAGGAGATGGAAGGCACCGTCGATGGATTGTCTGAAAAGGTCTCCAGGATGCACTCCTAAGGCAGGACTGTCCATGGCGACAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 225

TGTGAAACCCACAAGCTTAAGCTCTCGGAGCTACCTGAAGAGTGCAAGCATAAGCGCTTCCAAGTGCGTCGTTGTCAGAAATAAACACCCAGAGCCAGAGgtaatgctga ... tctctgctagGATGATGGAATACCTGAGGAGATGGAAGGCACCGTCGATGGATTGTCTGAAAAGGTCTCCAGGATGCACTCCTAAGGCAGGACTGTCCATGGCGACAGCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 120

TGTGAAACCCACAAGCTTAAGCTCTCGGAGCTACCTGAAGAGTGCAAGCATAAGCGCTTCCAAGTGCGTCGTTGTCAGAAATAAACACCCAGAGCCAGAGgtaatgctga ... tctctgctagGATGATGGAATACCTGAGGAGATGGAAGGCACCGTCGATGGATTGTCTGAAAAGGTCTCCAGGATGCACTCCTAAGGCAGGACTGTCCATGGCGACAGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttatttagagattaggtagtgcatctgtcactcatgtttggtttctctgctagGATGATGGAATACCTGAGGAGATGGAAGGCACCGTCGATGGATTGTCTGAAAAGGTCTCCAGGATGCACTCCTAAGGCAGGACTGTCCATGGCGACAGCA
                                           tttctctgct  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taagattgatctgttgcatgcaagttgtaccttttcctttgttcaccttatttagagattaggtagtgcatctgtcactcatgtttggtttctctgctagGATGATGGAATACCTGAGGAGATGGAAGGCACCGTCGATGGATTGTCTGAAAAGGTCTCCAGGATGCACTCCTAAGGCAGGACTGTCCATGGCGACAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - ctgttgc
- - - - - - - - -atgcaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgttt