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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acctattacaatggtcatggtcttgaacttttgatcaatgttgccctctcttttacaaggttctgtctaatgtgaaaaagagtctgatttgtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCACATTACTCAATTCGTCATTGGTCAGCATTGAGTGGTGTCGATACTGAAC

Basic information

species Zea mays
transcript GRMZM2G048045_T01
intron # 4
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|21432290|gb|BQ547780.1|BQ547780
EST:     AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAG                         CTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
genomic: AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
EST: gi|88756008|gb|DY540149.1|DY540149
EST:     AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAG                         CTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
genomic: AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
EST: gi|78103766|gb|DV522194.1|DV522194
EST:     AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAG                         CTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
genomic: AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
EST: gi|211456722|gb|FL410364.1|FL410364
EST:     AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAG                         CTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
genomic: AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
EST: gi|211509379|gb|FL412049.1|FL412049
EST:     AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAG                         CTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
genomic: AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
EST: gi|33101585|gb|CF061545.1|CF061545
EST:     AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAG                         CTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
genomic: AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
EST: gi|148942098|gb|EC887100.2|EC887100
EST:     AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAG                         CTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
genomic: AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
EST: gi|211109347|gb|FL402577.1|FL402577
EST:     AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAG                         CTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
genomic: AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
EST: gi|211447310|gb|FL370711.1|FL370711
EST:     AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAG                         CTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTA
genomic: AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTA
EST: gi|71332422|gb|DR803167.1|DR803167
EST:     AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAG                         CTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
genomic: AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
EST: gi|211169918|gb|FL423118.1|FL423118
EST:     AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAG                         CTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
genomic: AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
EST: gi|13126325|gb|BG316895.1|BG316895
EST:     AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAG                         CTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
genomic: AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
EST: gi|7137774|gb|AW499263.1|AW499263
EST:     GTCAACTATTCTACATTTTCAG                         CTTCGAAATTTGGTATGGTCTACGTCCAAGCATGACATCTACCTAGTATCA
genomic: GTCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
EST: gi|211536231|gb|FL396284.1|FL396284
EST:     GTTCAGACGAAATACTCCGATCGATTAAGTCAACTATTCTACATTT-CAG                         CTTCGAAAATTTGGGNATGGGCTACGTCCAAGCATGACATCTACCTAGTA-
genomic: GTTCAGACGAAATACTC-GATCGATTAAGTCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTCGAAA-TTTGGT-ATGGGCTACGTCCAAGCATGACATCTACCTAGTAT
EST: gi|9952999|gb|BE639582.1|BE639582
EST:     AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAG                         CTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACA
genomic: AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACA
EST: gi|71320210|gb|DR796860.1|DR796860
EST:     AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAG                         CTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA
genomic: AGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCA

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: 218

GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCACATTACTCAATTCGTCATTGGTCAGCATTGAGTGGTGTCGATACTGAAC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 203

GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCACATTACTCAATTCGTCATTGGTCAGCATTGAGTGGTGTCGATACTGAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 192

GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCACATTACTCAATTCGTCATTGGTCAGCATTGAGTGGTGTCGATACTGAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 239

GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCACATTACTCAATTCGTCATTGGTCAGCATTGAGTGGTGTCGATACTGAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctcttttacaaggttctgtctaatgtgaaaaagagtctgatttgtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCACATTACTCAATTCGTCATTGGTCAGCATTGAGTGGTGTCGATACTGAAC
     ttttacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acctattacaatggtcatggtcttgaacttttgatcaatgttgccctctcttttacaaggttctgtctaatgtgaaaaagagtctgatttgtgcctgcagCTTCGAAATTTGGTATGGGCTACGTCCAAGCATGACATCTACCTAGTATCACATTACTCAATTCGTCATTGGTCAGCATTGAGTGGTGTCGATACTGAAC

- - - - - - - -catggtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattt