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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTAGACTCACTTGTGGAGAAGTTTGTTACACCTGAATCATCTCAGGGAGAGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacctaaaagcttcattaaatattgtagttccttggtttggttttgggaacataaagtagattgtaataccatttgattgctattaaggataaa...

Basic information

species Zea mays
transcript GRMZM2G178294_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178294_T04 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g11200.1 (Oryza sativa), 5'ss of exon 11
TTTAGACTCACTTGTGGAGAAGTTTGTTACACCTGAATCATCTCAGGGAGAGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacctaaaagcttcattaaatattgtagttccttggtttggttttgggaacataaagtagattgtaataccatttgattgctattaaggataaa-----------
|||||| ||||| || ||||||||| ||||| ||||| || |  | || || ||  ||||||||| |||||| || || |||||||||||||||||||||||||  | | | ||||||       | || | |||||  |  |   || |     | || ||||      |  |    |||  | |||    || || ||           
TTTAGATTCACTGGTCGAGAAGTTTCTTACAGCTGAACCAACCGAAGGGGAAGTCACAAGTCTAGCTGACAAGGAAGACATATCTTCCATATTTTTAGAGgtaa--ttcttcaaagct-------acatggcagttctctt-taaagtatcttccatattaagttacccatcttgaagtttt-tagctcaggagcattaaaactgcaaatt
















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|32930152|gb|CF034964.1|CF034964
EST:     AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAG                         TTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
genomic: AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
EST: gi|32933149|gb|CF037961.1|CF037961
EST:     AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAG                         TTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
genomic: AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
EST: gi|32935217|gb|CF040029.1|CF040029
EST:     AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAG                         TTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
genomic: AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
EST: gi|211488019|gb|FL401529.1|FL401529
EST:     AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAG                         TTTTTGAATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
genomic: AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
EST: gi|60399477|gb|DN232289.1|DN232289
EST:     AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAG                         TTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
genomic: AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
EST: gi|211296491|gb|FL380959.1|FL380959
EST:     AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAG                         TTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
genomic: AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
EST: gi|211371062|gb|FL377775.1|FL377775
EST:     AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAG                         TTTTTGAATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
genomic: AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
EST: gi|32933726|gb|CF038538.1|CF038538
EST:     AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAG                         TTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
genomic: AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
EST: gi|9731923|gb|BE510675.1|BE510675
EST:     AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAG                         TTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
genomic: AGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
EST: gi|74245848|gb|DT653762.1|DT653762
EST:     ATATTTTTAGAG                         TTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG
genomic: ATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGG

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), 49 (downstream exon)
Score: 329

TTTAGACTCACTTGTGGAGAAGTTTGTTACACCTGAATCATCTCAGGGAGAGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGGCATACAACTCTTTTTTCATGTAAGAGAAGCATTCTGCCATCAAAGAAAC


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 106

TTTAGACTCACTTGTGGAGAAGTTTGTTACACCTGAATCATCTCAGGGAGAGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGGCATACAACTCTTTTTTCATGTAAGAGAAGCATTCTGCCATCAAAGAAAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 176

TTTAGACTCACTTGTGGAGAAGTTTGTTACACCTGAATCATCTCAGGGAGAGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGGCATACAACTCTTTTTTCATGTAAGAGAAGCATTCTGCCATCAAAGAAAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 136

TTTAGACTCACTTGTGGAGAAGTTTGTTACACCTGAATCATCTCAGGGAGAGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacc ... ttgtctgcagTTTTTGGATCTCTTTGGGGATGCAAAGTCAATCAAGAAGGCTTTAACTCGGCATACAACTCTTTTTTCATGTAAGAGAAGCATTCTGCCATCAAAGAAAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTAGACTCACTTGTGGAGAAGTTTGTTACACCTGAATCATCTCAGGGAGAGGTGGCAAGTCTAGTTGACAAAGAGGAAATATCTTCCATATTTTTAGAGgtaaaatacctaaaagcttcattaaatattgtagttccttggtttggttttgggaacataaagtagattgtaataccatttgattgctattaaggataaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaggataa