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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgctgcattggcaactacgctggcccatggtgagcttcttttatcagcagctgacgcagtgacgcctgactggcggtaaaatctgtatctggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGACTAAACATGCTTCCTCGCTGCGCTCAAGTGGGAGAACAAGAAATCAGCCT

Basic information

species Zea mays
transcript GRMZM2G055607_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|71431673|gb|DR812723.1|DR812723
EST:     AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAG                         GATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
genomic: AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAGgtaacgacca ... ggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
EST: gi|211383959|gb|FL013551.1|FL013551
EST:     AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAG                         GATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
genomic: AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAGgtaacgacca ... ggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
EST: gi|31441050|gb|CD510481.1|CD510481
EST:     AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAG                         GATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
genomic: AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAGgtaacgacca ... ggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
EST: gi|76911991|gb|DV164525.1|DV164525
EST:     AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGTCTCCAGCTGACGAAGCAG                         GATGCACTGTGACGCGCTGGTCCATCGTGAGCTTCTGATGCCAATTAGGAC
genomic: AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAGgtaacgacca ... ggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
EST: gi|71448567|gb|DR829617.1|DR829617
EST:     AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAG                         GATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
genomic: AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAGgtaacgacca ... ggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
EST: gi|211383960|gb|FL013552.1|FL013552
EST:     AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAG                         GATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
genomic: AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAGgtaacgacca ... ggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
EST: gi|88755485|gb|DY539626.1|DY539626
EST:     AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAG                         GATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
genomic: AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAGgtaacgacca ... ggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
EST: gi|50329390|gb|CO524516.1|CO524516
EST:     AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAG                         GATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
genomic: AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAGgtaacgacca ... ggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
EST: gi|71437590|gb|DR818640.1|DR818640
EST:     AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAG                         GATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
genomic: AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAGgtaacgacca ... ggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
EST: gi|211132575|gb|FL461421.1|FL461421
EST:     AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAG                         GATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
genomic: AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAGgtaacgacca ... ggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
EST: gi|28987385|gb|CB351608.1|CB351608
EST:     AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAG                         GATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
genomic: AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAGgtaacgacca ... ggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
EST: gi|211383961|gb|FL013553.1|FL013553
EST:     AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAG                         GATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
genomic: AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAGgtaacgacca ... ggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
EST: gi|71305861|gb|DR789056.1|DR789056
EST:     AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAG                         GATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
genomic: AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAGgtaacgacca ... ggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
EST: gi|91871874|gb|EB401831.1|EB401831
EST:     AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAG                         GATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
genomic: AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAGgtaacgacca ... ggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
EST: gi|211383958|gb|FL013550.1|FL013550
EST:     AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAG                         GATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
genomic: AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAGgtaacgacca ... ggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
EST: gi|50330184|gb|CO525310.1|CO525310
EST:     AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAG                         GATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC
genomic: AGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAGgtaacgacca ... ggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGAC

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), 43 (downstream exon)
Score: 54

TGTTTGTGACTTGTGAGTGAGAGCGGGATCCGACATCCGAGGAGAGGTCGAGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAGgtaacgacca ... ggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGACTAAACATGCTTCCTCGCTGCGCTCAAGTGGGAGAACAAGAAATCAGCCT


Block sizes: 47 (upstream exon), 35 (downstream exon)
Score: 25

TGTTTGTGACTTGTGAGTGAGAGCGGGATCCGACATCCGAGGAGAGGTCGAGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAGgtaacgacca ... ggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGACTAAACATGCTTCCTCGCTGCGCTCAAGTGGGAGAACAAGAAATCAGCCT


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 32

TGTTTGTGACTTGTGAGTGAGAGCGGGATCCGACATCCGAGGAGAGGTCGAGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAGgtaacgacca ... ggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGACTAAACATGCTTCCTCGCTGCGCTCAAGTGGGAGAACAAGAAATCAGCCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 77

TGTTTGTGACTTGTGAGTGAGAGCGGGATCCGACATCCGAGGAGAGGTCGAGGCCGGGCAAAGTCGAAGTCCGCGCTCCGGCCTCCAGCTGACGAAGCAGgtaacgacca ... ggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGACTAAACATGCTTCCTCGCTGCGCTCAAGTGGGAGAACAAGAAATCAGCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcagctgacgcagtgacgcctgactggcggtaaaatctgtatctggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGACTAAACATGCTTCCTCGCTGCGCTCAAGTGGGAGAACAAGAAATCAGCCT
                  gcctgac  putative branch site (score: 77)
                               taaaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgctgcattggcaactacgctggcccatggtgagcttcttttatcagcagctgacgcagtgacgcctgactggcggtaaaatctgtatctggtttaccagGATGCACTGTGACGCGCTGGCCCATGGTGAGCTTCTGATGCCAATTAGGACTAAACATGCTTCCTCGCTGCGCTCAAGTGGGAGAACAAGAAATCAGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA