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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttccccatcttttcaacttgtgatgtacaatttggccccaggaaatttactaacgtaacgtgcttgtgatgtggcagGAGCTGAGGGTAATAACTTGATTCCAGCAAGAGAAGACGATTTATCGCCAAAGAAAAGAACGTGTTTGAATGAGAATAATTCTGAGAGAGCTTCAAGAGA

Basic information

species Zea mays
transcript GRMZM2G179024_T01
intron # 5
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|211068419|gb|FL394011.1|FL394011
EST:     TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAA                         GAGCTAAGGGTAATAACTTGATCCCAGCAAGCGAAGACGATTTATCGCCAA
genomic: TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAAgtaattttcc ... gatgtggcagGAGCTGAGGGTAATAACTTGATTCCAGCAAGAGAAGACGATTTATCGCCAA
EST: gi|211271454|gb|FL402761.1|FL402761
EST:     TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAA                         GAGCTAAGGGTAATAACTTGATCCCAGCAAGCGAAGACGATTTATCGCCAA
genomic: TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAAgtaattttcc ... gatgtggcagGAGCTGAGGGTAATAACTTGATTCCAGCAAGAGAAGACGATTTATCGCCAA
EST: gi|211464201|gb|FL411568.1|FL411568
EST:     TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAA                         GAGCTAAGGGTAATAACTTGATCCCAGCAAGCGAAGACGATTTATCGCCAA
genomic: TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAAgtaattttcc ... gatgtggcagGAGCTGAGGGTAATAACTTGATTCCAGCAAGAGAAGACGATTTATCGCCAA
EST: gi|211074649|gb|FL417767.1|FL417767
EST:     TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAA                         GAGCTAAGGGTAATAACTTGATCCCAGCAAGCGAAGACGATTTATCGCCAA
genomic: TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAAgtaattttcc ... gatgtggcagGAGCTGAGGGTAATAACTTGATTCCAGCAAGAGAAGACGATTTATCGCCAA
EST: gi|211283973|gb|FL373342.1|FL373342
EST:     TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAA                         GAGCTAAGGGTAATAACTTGATCCCAGCAAGCGAAGACGATTTATCGCCAA
genomic: TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAAgtaattttcc ... gatgtggcagGAGCTGAGGGTAATAACTTGATTCCAGCAAGAGAAGACGATTTATCGCCAA
EST: gi|211068119|gb|FL380670.1|FL380670
EST:     TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAA                         GAGCTAAGGGTAATAACTTGATCCCAGCAAGCGAAGACGATTTATCGCCAA
genomic: TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAAgtaattttcc ... gatgtggcagGAGCTGAGGGTAATAACTTGATTCCAGCAAGAGAAGACGATTTATCGCCAA
EST: gi|211009321|gb|FL418112.1|FL418112
EST:     TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAA                         GAGCTAAGGGTAATAACTTGATCCCAGCAAGCGAAGACGATTTATCGCCAA
genomic: TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAAgtaattttcc ... gatgtggcagGAGCTGAGGGTAATAACTTGATTCCAGCAAGAGAAGACGATTTATCGCCAA
EST: gi|211447902|gb|FL396731.1|FL396731
EST:     TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAA                         GAGCTAAGGGTAATAACTTGATCCCAGCAAGCGAAGACGATTTATCGCCAA
genomic: TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAAgtaattttcc ... gatgtggcagGAGCTGAGGGTAATAACTTGATTCCAGCAAGAGAAGACGATTTATCGCCAA
EST: gi|211311125|gb|FL384821.1|FL384821
EST:     TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAA                         GAGCTAAGGGTAATAACTTGATCCCAGCAAGCGAAGACGATTTATCGCCAA
genomic: TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAAgtaattttcc ... gatgtggcagGAGCTGAGGGTAATAACTTGATTCCAGCAAGAGAAGACGATTTATCGCCAA
EST: gi|211211823|gb|FL379549.1|FL379549
EST:     TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAA                         GAGCTAAGGGTAATAACTTGATCCCAGCAAGCGAAGACGATTTATCGCCAA
genomic: TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAAgtaattttcc ... gatgtggcagGAGCTGAGGGTAATAACTTGATTCCAGCAAGAGAAGACGATTTATCGCCAA
EST: gi|211160047|gb|FL415234.1|FL415234
EST:     TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAA                         GAGCTAAGGGTAATAACTTGATCCCAGCAAGCGAAGACGATTTATCGCCAA
genomic: TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAAgtaattttcc ... gatgtggcagGAGCTGAGGGTAATAACTTGATTCCAGCAAGAGAAGACGATTTATCGCCAA
EST: gi|211363255|gb|FL387048.1|FL387048
EST:     TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAA                         GAGCTAAGGGTAATAACTTGATCCCAGCAAGCGAAGACGATTTATCGCCAA
genomic: TATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAAgtaattttcc ... gatgtggcagGAGCTGAGGGTAATAACTTGATTCCAGCAAGAGAAGACGATTTATCGCCAA

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: 55

CAAACAGACAACATTTTGGAGTATAAGCAATCAACTCAAAGGCACTTGTCTATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAAgtaattttcc ... gatgtggcagGAGCTGAGGGTAATAACTTGATTCCAGCAAGAGAAGACGATTTATCGCCAAAGAAAAGAACGTGTTTGAATGAGAATAATTCTGAGAGAGCTTCAAGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 157

CAAACAGACAACATTTTGGAGTATAAGCAATCAACTCAAAGGCACTTGTCTATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAAgtaattttcc ... gatgtggcagGAGCTGAGGGTAATAACTTGATTCCAGCAAGAGAAGACGATTTATCGCCAAAGAAAAGAACGTGTTTGAATGAGAATAATTCTGAGAGAGCTTCAAGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

CAAACAGACAACATTTTGGAGTATAAGCAATCAACTCAAAGGCACTTGTCTATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAAgtaattttcc ... gatgtggcagGAGCTGAGGGTAATAACTTGATTCCAGCAAGAGAAGACGATTTATCGCCAAAGAAAAGAACGTGTTTGAATGAGAATAATTCTGAGAGAGCTTCAAGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

CAAACAGACAACATTTTGGAGTATAAGCAATCAACTCAAAGGCACTTGTCTATTCCTAGCCACAAGAATGTTGAGCTAAATGGACAGACCAAAATACAAAgtaattttcc ... gatgtggcagGAGCTGAGGGTAATAACTTGATTCCAGCAAGAGAAGACGATTTATCGCCAAAGAAAAGAACGTGTTTGAATGAGAATAATTCTGAGAGAGCTTCAAGAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtacaatttggccccaggaaatttactaacgtaacgtgcttgtgatgtggcagGAGCTGAGGGTAATAACTTGATTCCAGCAAGAGAAGACGATTTATCGCCAAAGAAAAGAACGTGTTTGAATGAGAATAATTCTGAGAGAGCTTCAAGAGA
                    aaatttactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattttccccatcttttcaacttgtgatgtacaatttggccccaggaaatttactaacgtaacgtgcttgtgatgtggcagGAGCTGAGGGTAATAACTTGATTCCAGCAAGAGAAGACGATTTATCGCCAAAGAAAAGAACGTGTTTGAATGAGAATAATTCTGAGAGAGCTTCAAGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA