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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacaaagataaatgttacagttatgtgacaaaatattaaaaatattctctggtttcatatgctggtaattaattttatttatcctttttgcgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGATCCTACATTTCGAGAAGAGCTTCTTAACTTTACACAAAGGGGGCGTATTC

Basic information

species Zea mays
transcript GRMZM2G114513_T02
intron # 3
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|211095367|gb|FL067776.1|FL067776
EST:     ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
EST: gi|211097837|gb|FL067788.1|FL067788
EST:     ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
EST: gi|211079577|gb|FL056323.1|FL056323
EST:     ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
EST: gi|211097840|gb|FL067791.1|FL067791
EST:     ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
EST: gi|21760018|gb|BQ635559.1|BQ635559
EST:     ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
EST: gi|211095370|gb|FL067779.1|FL067779
EST:     ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
EST: gi|211095362|gb|FL067771.1|FL067771
EST:     ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTATATCCATAGACTTCTTCGTGAGGGTGA
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTA-ATCCATAGACTTCTTCGTGAGGGTGA
EST: gi|211050621|gb|FL256688.1|FL256688
EST:     ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
EST: gi|211053578|gb|FL256705.1|FL256705
EST:     ACTGTATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTAATCCATA
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATA
EST: gi|211050623|gb|FL256690.1|FL256690
EST:     ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
EST: gi|211092897|gb|FL067767.1|FL067767
EST:     ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
EST: gi|33099286|gb|CF059246.1|CF059246
EST:     ACTGCATCCACGCTCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
EST: gi|211097835|gb|FL067786.1|FL067786
EST:     ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
EST: gi|211095373|gb|FL067782.1|FL067782
EST:     ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
EST: gi|211095375|gb|FL067784.1|FL067784
EST:     ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
EST: gi|9254928|gb|BE345396.1|BE345396
EST:     ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GGTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
EST: gi|211097834|gb|FL067785.1|FL067785
EST:     ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
EST: gi|211095371|gb|FL067780.1|FL067780
EST:     ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
EST: gi|211092899|gb|FL067769.1|FL067769
EST:     ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
EST: gi|211053572|gb|FL256699.1|FL256699
EST:     ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
EST: gi|32823840|gb|CD963562.1|CD963562
EST:     ACTGCATCCACGCTCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
EST: gi|211095369|gb|FL067778.1|FL067778
EST:     ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
EST: gi|211095366|gb|FL067775.1|FL067775
EST:     ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT                         GTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT
genomic: ACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGAT

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: 175

AGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGATCCTACATTTCGAGAAGAGCTTCTTAACTTTACACAAAGGGGGCGTATTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 210

AGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGATCCTACATTTCGAGAAGAGCTTCTTAACTTTACACAAAGGGGGCGTATTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 227

AGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGATCCTACATTTCGAGAAGAGCTTCTTAACTTTACACAAAGGGGGCGTATTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 120

AGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATTgtaagttcta ... cgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGATCCTACATTTCGAGAAGAGCTTCTTAACTTTACACAAAGGGGGCGTATTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctggtttcatatgctggtaattaattttatttatcctttttgcgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGATCCTACATTTCGAGAAGAGCTTCTTAACTTTACACAAAGGGGGCGTATTC
                     aattaat  putative branch site (score: 120)
                                tttatcctttttgc  putative PPT
                 tggtaattaattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacaaagataaatgttacagttatgtgacaaaatattaaaaatattctctggtttcatatgctggtaattaattttatttatcctttttgcgacatgtagGTTGCTCTGAAAGCACTTGTAGTAATCCATAGACTTCTTCGTGAGGGTGATCCTACATTTCGAGAAGAGCTTCTTAACTTTACACAAAGGGGGCGTATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT