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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGACTCCCCTTCTCCTTCGACCTCCGCCGCTCGCCGCCGTTTCCCGTCCGCGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcctcctagtcccgcacctctttggtgcactgcacccgtgtctcctcctcgcagctgaccacgacacgacctcctcctcaacttgtatcgtcg...

Basic information

species Zea mays
transcript GRMZM2G080722_T02
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|6587608|gb|AW244926.1|AW244926
EST:     GTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCACCCTCGTGAGGGGACTTATGAGA
genomic: GTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211138214|gb|FL122277.1|FL122277
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCCTACTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCATGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211393122|gb|FK956090.1|FK956090
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTATCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211395750|gb|FK956107.1|FK956107
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTATCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211395748|gb|FK956105.1|FK956105
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCCTACTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCATGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211393118|gb|FK956086.1|FK956086
EST:     CGGCGGGGCCTCCTCCCCTCCCACTCCTACTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCATGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211393127|gb|FK956095.1|FK956095
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTATCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|32908833|gb|CF013646.1|CF013646
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|116818678|gb|EC861726.1|EC861726
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211395745|gb|FK956102.1|FK956102
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCCTACTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCATGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211393125|gb|FK956093.1|FK956093
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCCTACTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCATGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211393120|gb|FK956088.1|FK956088
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTATCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211395747|gb|FK956104.1|FK956104
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCCTACTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCATGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211137287|gb|FL122274.1|FL122274
EST:     CGGCGGCGCCTCCTCSCCTCCCACTCCTACTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCATGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211138215|gb|FL122278.1|FL122278
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCCTACTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCATGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211395746|gb|FK956103.1|FK956103
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTATCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211393121|gb|FK956089.1|FK956089
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCCTACTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCATGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211395743|gb|FK956100.1|FK956100
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCCTACTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCATGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211393123|gb|FK956091.1|FK956091
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCCTACTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCATGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211138212|gb|FL122275.1|FL122275
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCCTACTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCATGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211395741|gb|FK956098.1|FK956098
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTATCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211215605|gb|FL316840.1|FL316840
EST:     CGGCGGCGCTTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTATCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211138213|gb|FL122276.1|FL122276
EST:     CGGCGGCGCCTCCTCCCNNCCCACTCCTACTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCATGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211395742|gb|FK956099.1|FK956099
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTATCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211138217|gb|FL122280.1|FL122280
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCCTACTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCATGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211395740|gb|FK956097.1|FK956097
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTATCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211138218|gb|FL122281.1|FL122281
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCCTACTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCATGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211395752|gb|FK956109.1|FK956109
EST:     CGGCGGSSCCTCCTCCCCTCCCACTCCTACTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCATGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211395751|gb|FK956108.1|FK956108
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCCTACTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCATGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|32908771|gb|CF013584.1|CF013584
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|32908664|gb|CF013477.1|CF013477
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211138219|gb|FL122282.1|FL122282
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCCTACTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCATGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|149051827|gb|EE155954.2|EE155954
EST:     CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA
EST: gi|211138216|gb|FL122279.1|FL122279
EST:     CGGCGGCGCCTSCTCCCCTCCCACTCCTACTCGTTGTCGATCTCGTCTCG                         GGTACCATGGCAAGATCACTCTCCACSGCCCTCATGAGGGRACTTATGAGA
genomic: CGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGA

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), 48 (downstream exon)
Score: 77

CGACTCCCCTTCTCCTTCGACCTCCGCCGCTCGCCGCCGTTTCCCGTCCGCGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 55

CGACTCCCCTTCTCCTTCGACCTCCGCCGCTCGCCGCCGTTTCCCGTCCGCGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT


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

CGACTCCCCTTCTCCTTCGACCTCCGCCGCTCGCCGCCGTTTCCCGTCCGCGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 98

CGACTCCCCTTCTCCTTCGACCTCCGCCGCTCGCCGCCGTTTCCCGTCCGCGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcc ... tccgctgcagGGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGACTCCCCTTCTCCTTCGACCTCCGCCGCTCGCCGCCGTTTCCCGTCCGCGGCGGCGCCTCCTCCCCTCCCACTCTTCCTCGTTGTCGATCTCGTCTCGgttagtttcctcctagtcccgcacctctttggtgcactgcacccgtgtctcctcctcgcagctgaccacgacacgacctcctcctcaacttgtatcgtcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcctcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcctcc