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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttatgttcagctacatttatcgtcacatttttttagaaaacataaacctagacaaaacctgcatcgctgcttgattagtgtgatttattcccccacagGTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCCCAGAAGTGCTGGGCTGCTGGCAGCAAAAGAGACAAACAAGCAACTCTTT

Basic information

species Zea mays
transcript GRMZM2G021742_T02
intron # 4
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|93011955|gb|EB637475.1|EB637475
EST:     ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCC
genomic: ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tcccccacagGTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCC
EST: gi|148969290|gb|EE020060.2|EE020060
EST:     ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCC
genomic: ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tcccccacagGTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCC
EST: gi|78117952|gb|DV536339.1|DV536339
EST:     ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCC
genomic: ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tcccccacagGTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCC
EST: gi|78118268|gb|DV536655.1|DV536655
EST:     ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCC
genomic: ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tcccccacagGTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCC
EST: gi|60353183|gb|DN220156.1|DN220156
EST:     ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCC
genomic: ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tcccccacagGTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCC
EST: gi|50326108|gb|CO521234.1|CO521234
EST:     ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCC
genomic: ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tcccccacagGTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCC
EST: gi|60340700|gb|DN207673.1|DN207673
EST:     ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCC
genomic: ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tcccccacagGTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCC
EST: gi|76292483|gb|DV032051.1|DV032051
EST:     ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCC
genomic: ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tcccccacagGTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCC
EST: gi|71319736|gb|DR796618.1|DR796618
EST:     ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCC
genomic: ATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tcccccacagGTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCC

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), 47 (downstream exon)
Score: 126

ACTGGATAATACTGTAACTAAGCAGCCAGATTACAGGCTGTATGTGATCCATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tcccccacagGTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCCCAGAAGTGCTGGGCTGCTGGCAGCAAAAGAGACAAACAAGCAACTCTTT


Block sizes: 38 (upstream exon), 47 (downstream exon)
Score: 47

ACTGGATAATACTGTAACTAAGCAGCCAGATTACAGGCTGTATGTGATCCATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tcccccacagGTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCCCAGAAGTGCTGGGCTGCTGGCAGCAAAAGAGACAAACAAGCAACTCTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 35

ACTGGATAATACTGTAACTAAGCAGCCAGATTACAGGCTGTATGTGATCCATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tcccccacagGTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCCCAGAAGTGCTGGGCTGCTGGCAGCAAAAGAGACAAACAAGCAACTCTTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 33

ACTGGATAATACTGTAACTAAGCAGCCAGATTACAGGCTGTATGTGATCCATAAATTGAAGCATTTGCGTTTGCTGGATTTCAAGAAAGTGAAACAACAGgtgagcaata ... tcccccacagGTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCCCAGAAGTGCTGGGCTGCTGGCAGCAAAAGAGACAAACAAGCAACTCTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacctagacaaaacctgcatcgctgcttgattagtgtgatttattcccccacagGTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCCCAGAAGTGCTGGGCTGCTGGCAGCAAAAGAGACAAACAAGCAACTCTTT
                         gcttgat  putative branch site (score: 33)
                                        tttattccccc  putative PPT
                                     tgatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttatgttcagctacatttatcgtcacatttttttagaaaacataaacctagacaaaacctgcatcgctgcttgattagtgtgatttattcccccacagGTTTGTTCATTTCCTTTGGAATGGCTCCAAAATATGTTTTGGGATGGACCCCAGAAGTGCTGGGCTGCTGGCAGCAAAAGAGACAAACAAGCAACTCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- ttatgtt
- - - - -cagctac
- - - - - - - - - - - - - - - - - - - -aaacata
- - - - - - - - - - - - - - - - - - - - - - - - - -agacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgatt