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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcactattaaactggccaatctttttcacaacataaacgacaaagtaagaaaatccttcatgtctgttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG

Basic information

species Zea mays
transcript GRMZM2G098569_T01
intron # 9
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|76293424|gb|DV032992.1|DV032992
EST:     TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTT                         GAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTTgtaagcacta ... gttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|9953883|gb|BE640466.1|BE640466
EST:     TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCCTTCTGTTT                         GAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTTgtaagcacta ... gttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|76293423|gb|DV032991.1|DV032991
EST:     TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTT                         GAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTTgtaagcacta ... gttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|78117581|gb|DV535968.1|DV535968
EST:     TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTT                         GAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTTgtaagcacta ... gttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|149100778|gb|EE186872.2|EE186872
EST:     TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTT                         GAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTTgtaagcacta ... gttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|9028732|gb|BE238772.1|BE238772
EST:     TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCCTTCTGTTT                         GAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTTgtaagcacta ... gttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|60339232|gb|DN206205.1|DN206205
EST:     TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTT                         GAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTTgtaagcacta ... gttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|60359240|gb|DN226213.1|DN226213
EST:     TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTT                         GAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTTgtaagcacta ... gttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|60355012|gb|DN221985.1|DN221985
EST:     TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTT                         GAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTTgtaagcacta ... gttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|148951737|gb|EC897492.2|EC897492
EST:     TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTT                         GAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTTgtaagcacta ... gttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|60341646|gb|DN208619.1|DN208619
EST:     TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTT                         GAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTTgtaagcacta ... gttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|148964885|gb|EE015747.2|EE015747
EST:     TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTT                         GAAAATTACGGAAAGTTTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTTgtaagcacta ... gttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|71310909|gb|DR791757.1|DR791757
EST:     TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTT                         GAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTTgtaagcacta ... gttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|101397216|gb|EB820532.1|EB820532
EST:     TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTT                         GAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTTgtaagcacta ... gttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|6501120|gb|AW202493.1|AW202493
EST:     GAGCATTCTGTTT                         GAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: GAGCATTCTGTTTgtaagcacta ... gttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|60353036|gb|DN220009.1|DN220009
EST:     TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTT                         GAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTTgtaagcacta ... gttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG

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: 174

ATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTTgtaagcacta ... gttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 627

ATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTTgtaagcacta ... gttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 567

ATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTTgtaagcacta ... gttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 258

ATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTTgtaagcacta ... gttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttttcacaacataaacgacaaagtaagaaaatccttcatgtctgttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG
                                          tctgttc  CT-rich tract
                         taagaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcactattaaactggccaatctttttcacaacataaacgacaaagtaagaaaatccttcatgtctgttcaaacagGAAAATTACGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT