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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatctgcgctccagttggctttttatttggaactgcagtaggtcttatctacatgtcattcaagcataatactgatgcaaataagtgtttgatgtgtagGAGGGAGGGGTGGCCATTCGTTTGCAGCGAGCGGACTGCCACCTACACTTAGGAAAGATTTTGGGAGAATCTTTTAGTCCTGAATCCGGAGGAATGCCGA

Basic information

species Zea mays
transcript GRMZM2G092959_T01
intron # 6
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|60339170|gb|DN206143.1|DN206143
EST:     TAGGCTGACAGAACCTCCACCAACTACAATGGGTGACGGAATGCTCTGGG                         GAGGGAGGGGTGGCCATTCGTTTGCAGCGAGCGGACTGCCACCTACACTTA
genomic: TAGGCTGACAGAACCTCCACCAACTACAATGGGTGACGGAATGCTCTGGGgtaattttca ... tgatgtgtagGAGGGAGGGGTGGCCATTCGTTTGCAGCGAGCGGACTGCCACCTACACTTA
EST: gi|211287615|gb|FL250250.1|FL250250
EST:     TAGGCTGACAGAACCTCCACCAACTACAATGGGTGACGGAATGCTCTGGG                         GAGGGAGGGGTGGCCATTCGTTTGCNGNGAGCGGACTGCCACCTACACTTA
genomic: TAGGCTGACAGAACCTCCACCAACTACAATGGGTGACGGAATGCTCTGGGgtaattttca ... tgatgtgtagGAGGGAGGGGTGGCCATTCGTTTGCAGCGAGCGGACTGCCACCTACACTTA
EST: gi|60358925|gb|DN225898.1|DN225898
EST:     TAGGCTGACAGAACCTCCACCAACTACAATGGGTGACGGAATGCTCTGGG                         GAGGGAGGGGTGGCCATTCGTTTGCAGCGAGCGGACTGCCACCTACACTTA
genomic: TAGGCTGACAGAACCTCCACCAACTACAATGGGTGACGGAATGCTCTGGGgtaattttca ... tgatgtgtagGAGGGAGGGGTGGCCATTCGTTTGCAGCGAGCGGACTGCCACCTACACTTA
EST: gi|32848083|gb|CD987764.1|CD987764
EST:     TAGGCTGACAGAACCTCCACCAACTACAATGGGTGACGGAATGCTCTGGG                         GAGGGAGGGGTGGCCATTCGTTTGCAGCGAGCGGACTGCCACCTACACTTA
genomic: TAGGCTGACAGAACCTCCACCAACTACAATGGGTGACGGAATGCTCTGGGgtaattttca ... tgatgtgtagGAGGGAGGGGTGGCCATTCGTTTGCAGCGAGCGGACTGCCACCTACACTTA
EST: gi|37399356|gb|CF637005.1|CF637005
EST:     TAGGCTGACAGAACCTCCACCAACTACAATGGGTGACGGAATGCTCTGGG                         GAGGGAGGGGTGGCCATTCGTTTGCAGCGAGCGGACTGCCACCTACACTTA
genomic: TAGGCTGACAGAACCTCCACCAACTACAATGGGTGACGGAATGCTCTGGGgtaattttca ... tgatgtgtagGAGGGAGGGGTGGCCATTCGTTTGCAGCGAGCGGACTGCCACCTACACTTA
EST: gi|60354878|gb|DN221851.1|DN221851
EST:     TAGGCTGACAGAACCTCCACCAACTACAATGGGTGACGGAATGCTCTGGG                         GAGGGAGGGGTGGCCATTCGTTTGCAGCGAGCGGACTGCCACCTACACTTA
genomic: TAGGCTGACAGAACCTCCACCAACTACAATGGGTGACGGAATGCTCTGGGgtaattttca ... tgatgtgtagGAGGGAGGGGTGGCCATTCGTTTGCAGCGAGCGGACTGCCACCTACACTTA

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: 317

ATCCGACCGATGAGGGCTCATCACAATGGTCAGCCTGTCTGGTCTAATTATAGGCTGACAGAACCTCCACCAACTACAATGGGTGACGGAATGCTCTGGGgtaattttca ... tgatgtgtagGAGGGAGGGGTGGCCATTCGTTTGCAGCGAGCGGACTGCCACCTACACTTAGGAAAGATTTTGGGAGAATCTTTTAGTCCTGAATCCGGAGGAATGCCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 322

ATCCGACCGATGAGGGCTCATCACAATGGTCAGCCTGTCTGGTCTAATTATAGGCTGACAGAACCTCCACCAACTACAATGGGTGACGGAATGCTCTGGGgtaattttca ... tgatgtgtagGAGGGAGGGGTGGCCATTCGTTTGCAGCGAGCGGACTGCCACCTACACTTAGGAAAGATTTTGGGAGAATCTTTTAGTCCTGAATCCGGAGGAATGCCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 272

ATCCGACCGATGAGGGCTCATCACAATGGTCAGCCTGTCTGGTCTAATTATAGGCTGACAGAACCTCCACCAACTACAATGGGTGACGGAATGCTCTGGGgtaattttca ... tgatgtgtagGAGGGAGGGGTGGCCATTCGTTTGCAGCGAGCGGACTGCCACCTACACTTAGGAAAGATTTTGGGAGAATCTTTTAGTCCTGAATCCGGAGGAATGCCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 361

ATCCGACCGATGAGGGCTCATCACAATGGTCAGCCTGTCTGGTCTAATTATAGGCTGACAGAACCTCCACCAACTACAATGGGTGACGGAATGCTCTGGGgtaattttca ... tgatgtgtagGAGGGAGGGGTGGCCATTCGTTTGCAGCGAGCGGACTGCCACCTACACTTAGGAAAGATTTTGGGAGAATCTTTTAGTCCTGAATCCGGAGGAATGCCGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatctacatgtcattcaagcataatactgatgcaaataagtgtttgatgtgtagGAGGGAGGGGTGGCCATTCGTTTGCAGCGAGCGGACTGCCACCTACACTTAGGAAAGATTTTGGGAGAATCTTTTAGTCCTGAATCCGGAGGAATGCCGA
                     ataatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatctgcgctccagttggctttttatttggaactgcagtaggtcttatctacatgtcattcaagcataatactgatgcaaataagtgtttgatgtgtagGAGGGAGGGGTGGCCATTCGTTTGCAGCGAGCGGACTGCCACCTACACTTAGGAAAGATTTTGGGAGAATCTTTTAGTCCTGAATCCGGAGGAATGCCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - gctccag
- - - - - - - - - - - - - - - - actgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatgc