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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAGGAGGTTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattcagatttcactgtgcactatttttcgctgttctatagtttctttgtttgtcattgatacaagtgacattttcccag

Basic information

species Zea mays
transcript GRMZM2G014136_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014136_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os06g24704.1 (Oryza sativa), 5'ss of exon 11
CCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAGGAGGTTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattcagatttcactgtgcactatttttcgctgttctatagtttctttgtttgtcattgatacaagtgacattttcccag
| || ||||||| |||||| ||||||||||||| |  ||      ||||||||||  | |||| |||||||| |||| |||||| ||||||||||||||||||||  || | ||| ||||  || | || || ||     ||      ||| || | | | |  |    |||||||||  ||||
CTTGCTCTGCTTGAGGGAGCGAGATTTACTGAAACGATTCACCACGGAGGTTTCTAACTATCTGGCACAAGGAGAAAACAGAGAGAAGGCTTTGATGCTGgtaaa--tctgcttttactgcacatt-ttcttggcgagcttaa-----cttagtgtctaacttgt----gtgacatttatccag
















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|213191931|gb|FM185346.1|FM185346
EST:     TTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTG                         AGTTATCAAGTTGCTGAAGACTTGGC
genomic: TTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGC
EST: gi|32922953|gb|CF027765.1|CF027765
EST:     TTTCTCTCCATCTTGCCCAAGGTGAAAGCAGAGAAAAGGCTTTGATGCTG                         AGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
genomic: TTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
EST: gi|78122591|gb|DV540975.1|DV540975
EST:     TTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTG                         AGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTACGATC
genomic: TTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTACGATC
EST: gi|32922640|gb|CF027452.1|CF027452
EST:     TTTCTCTCCATCTTGCCCAAGGTGAAAGCAGAGAAAAGGCTTTGATGCTG                         AGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
genomic: TTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
EST: gi|32923445|gb|CF028257.1|CF028257
EST:     TTTCTCTCCATCTTGCCCAAGGTGAAAGCAGAGAAAAGGCTTTGATGCTG                         AGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
genomic: TTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
EST: gi|32921856|gb|CF026668.1|CF026668
EST:     TTTCTCTCCATCTTGCCCAAGGTGAAAGCAGAGAAAAGGCTTTGATGCTG                         AGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
genomic: TTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
EST: gi|32920309|gb|CF025121.1|CF025121
EST:     TTTCTCTCCATCTTGCCCAAGGTGAAAGCAGAGAAAAGGCTTTGATGCTG                         AGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
genomic: TTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
EST: gi|32922125|gb|CF026937.1|CF026937
EST:     TTTCTCTCCATCTTGCCCAAGGTGAAAGCAGAGAAAAGGCTTTGATGCTG                         AGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGT
genomic: TTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGT
EST: gi|32923051|gb|CF027863.1|CF027863
EST:     TTTCTCTCCATCTTGCCCAAGGTGAAAGCAGAGAAAAGGCTTTGATGCTG                         AGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
genomic: TTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
EST: gi|31356814|gb|CD441171.1|CD441171
EST:     TTTCTCTCCATCTTGCCCAAGGTGAAAGCAGAGAAAAGGCTTTGATGCTG                         AGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTACGATC
genomic: TTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTACGATC
EST: gi|78118416|gb|DV536802.1|DV536802
EST:     TTTCTCTCCTTCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGTTG                         AGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTACGATC
genomic: TTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTACGATC
EST: gi|24766737|gb|CA401884.1|CA401884
EST:     CAAGGTGAAAGCAGAGAAAAGGCTTTGATGCTG                         AGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTACGATC
genomic: CAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTACGATC
EST: gi|5739931|gb|AI947621.1|AI947621
EST:     AGGCGAAAGCAGAGAAAAGGCTTTGATGCTG                         AGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTACGATC
genomic: AGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTACGATC
EST: gi|32921929|gb|CF026741.1|CF026741
EST:     TTTCTCTCCATCTTGCCCAAGGTGAAAGCAGAGAAAAGGCTTTGATGCTG                         AGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
genomic: TTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
EST: gi|32922523|gb|CF027335.1|CF027335
EST:     TTTCTCTCCATCTTGCCCAAGGTGAAAGCAGAGAAAAGGCTTTGATGCTG                         AGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
genomic: TTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
EST: gi|32922152|gb|CF026964.1|CF026964
EST:     TTTCTCTCCATCTTGCCCAAGGTGAAAGCAGAGAAAAGGCTTTGATGCTG                         AGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
genomic: TTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
EST: gi|32923374|gb|CF028186.1|CF028186
EST:     TTTCTCTCCATCTTGCCCAAGGTGAAAGCAGAGAAAAGGCTTTGATGCTG                         AGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
genomic: TTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
EST: gi|32922298|gb|CF027110.1|CF027110
EST:     TTTCTCTCCATCTTGCCCAAGGTGAAAGCAGAGAAAAGGCTTTGATGCTG                         AGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
genomic: TTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
EST: gi|32922571|gb|CF027383.1|CF027383
EST:     TTTCTCTACATATTGCCCAAGGTGAAAGCAGAGAAAAGGCTTTGATGCTG                         AGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGT
genomic: TTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGT
EST: gi|32922304|gb|CF027116.1|CF027116
EST:     TTTCTCTCCATCTTGCCCAAGGTGAAAGCAGAGAAAAGGCTTTGATGCTG                         AGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA
genomic: TTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTA

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: 83

CCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAGGAGGTTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTACGATCCTCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 273

CCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAGGAGGTTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTACGATCCTCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 264

CCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAGGAGGTTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTACGATCCTCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 96

CCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAGGAGGTTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattca ... attttcccagAGTTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTACGATCCTCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAGGAGGTTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGATGCTGgtaaaattcagatttcactgtgcactatttttcgctgttctatagtttctttgtttgtcattgatacaagtgacattttcccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG