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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGACACCTATAAGCACCAACCCTAGCCCAAAACCCCGCTTCCACTTCACAGCCTCTCCGCCTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAGgtacgcctttgccctttgctcgccaccttcctacctcctggggtccccgtgccgtgcttgccgccggtggattggtttgctcgtatgatctgggttctcg...

Basic information

species Zea mays
transcript GRMZM2G145280_T01
intron # 1
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|211389707|gb|FL262574.1|FL262574
EST:     CCGCCTCCGCTCCTCGCGCCGCCG-CGCGTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: CCGCCTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
EST: gi|74237761|gb|DT645675.1|DT645675
EST:     CCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: CCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
EST: gi|8665447|gb|BE186263.1|BE186263
EST:     CGCCGCGTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: CGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
EST: gi|76292773|gb|DV032341.1|DV032341
EST:     CCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: CCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
EST: gi|149112712|gb|EE191403.2|EE191403
EST:     CCGCCTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: CCGCCTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
EST: gi|211281009|gb|FL194228.1|FL194228
EST:     GCCGCCGCGTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: GCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
EST: gi|211311383|gb|FL406198.1|FL406198
EST:     GCCTCTCCGCCTCCGCTCCT--CGCCGCCGCCGCGTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: GCCTCTCCGCCTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
EST: gi|211277402|gb|FL194200.1|FL194200
EST:     GCCTCCCCGCCTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: GCCTCTCCGCCTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
EST: gi|211129397|gb|FL066373.1|FL066373
EST:     CGCCTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: CGCCTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
EST: gi|29947149|gb|CB816506.1|CB816506
EST:     CTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: CTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
EST: gi|211271424|gb|FK945754.1|FK945754
EST:     GCCGCCGCGTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: GCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
EST: gi|211129398|gb|FL066374.1|FL066374
EST:     CTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: CTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
EST: gi|28873512|gb|CB329492.1|CB329492
EST:     CTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: CTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
EST: gi|211281010|gb|FL194229.1|FL194229
EST:     CCTCTCCGCCTCCGCTCCTCGCGCCGCCGCCGCGTTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAKGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: CCTCTCCGCCTCCGCTCCTCGCGCCGCCGCCGCG-TCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
EST: gi|211281012|gb|FL194231.1|FL194231
EST:     CTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: CTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
EST: gi|89761946|gb|DY689760.1|DY689760
EST:     CTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: CTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
EST: gi|71300935|gb|DR786496.1|DR786496
EST:     GCGTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: GCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
EST: gi|20208265|gb|BQ134354.1|BQ134354
EST:     TCTCCTCCTGTACAG                         GTAAGAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCC
genomic: TCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGT---AAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCC
EST: gi|30705140|gb|CD058672.1|CD058672
EST:     GCGTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: GCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
EST: gi|32913773|gb|CF018585.1|CF018585
EST:     GCCGCGTCTCCTCCTGTACAG                         GTAAGAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCC
genomic: GCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGT---AAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCC
EST: gi|78106398|gb|DV524816.1|DV524816
EST:     CGCCTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: CGCCTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
EST: gi|211281013|gb|FL194232.1|FL194232
EST:     TCCGCCTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCGCTGTACAG                         GTAAGGAGAGGAYGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCA
genomic: TCCGCCTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTC-CTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCA
EST: gi|211441593|gb|FK945760.1|FK945760
EST:     GCCGCCGCGTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAGGGCGAAATSGTGAAGCACAACAACGTCATCCCCAA
genomic: GCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
EST: gi|74234821|gb|DT642735.1|DT642735
EST:     CGCCGCCGCCGCGTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: CGCCGCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
EST: gi|37416945|gb|CF646124.1|CF646124
EST:     GCCTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAG                         GTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA
genomic: GCCTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAA

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: 662

CGACACCTATAAGCACCAACCCTAGCCCAAAACCCCGCTTCCACTTCACAGCCTCTCCGCCTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAACGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 733

CGACACCTATAAGCACCAACCCTAGCCCAAAACCCCGCTTCCACTTCACAGCCTCTCCGCCTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAACGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 675

CGACACCTATAAGCACCAACCCTAGCCCAAAACCCCGCTTCCACTTCACAGCCTCTCCGCCTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAACGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 387

CGACACCTATAAGCACCAACCCTAGCCCAAAACCCCGCTTCCACTTCACAGCCTCTCCGCCTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAGgtacgccttt ... tgatgtgcagGTAAGGAGAGGAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAACGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGACACCTATAAGCACCAACCCTAGCCCAAAACCCCGCTTCCACTTCACAGCCTCTCCGCCTCCGCTCCTCGCGCCGCCGCCGCGTCTCCTCCTGTACAGgtacgcctttgccctttgctcgccaccttcctacctcctggggtccccgtgccgtgcttgccgccggtggattggtttgctcgtatgatctgggttctcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC