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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaaagtctaaacttgtgtagctctgtttttctatccagaaattgtcaatctgcagatctgtttttgtttttgacttgataacgctgacttgataactcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAGTACGCATTCCAGATAATTGATGCTGGGTTATGGCTATGTAACTAGCTGT

Basic information

species Zea mays
transcript GRMZM2G006468_T04
intron # 10
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|211436290|gb|FL481825.1|FL481825
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|33100633|gb|CF060593.1|CF060593
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|14244855|gb|BG842793.2|BG842793
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|13177701|gb|BG349130.1|BG349130
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|14243138|gb|BG840841.2|BG840841
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|113655660|gb|DW809180.1|DW809180
EST:     CGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: CGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|28984501|gb|BQ539125.2|BQ539125
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAA                         AGATGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|16379972|gb|BI993236.1|BI993236
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGATCTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|60396153|gb|DN229022.1|DN229022
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|211186706|gb|FL252851.1|FL252851
EST:     GGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: GGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAA-CTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|13382144|gb|BG458819.1|BG458819
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|16925921|gb|BM078989.1|BM078989
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|13177698|gb|BG349129.1|BG349129
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|37426214|gb|CF650858.1|CF650858
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|18650378|gb|BM499197.1|BM499197
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAGCTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCT-AATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|33102029|gb|CF061989.1|CF061989
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCA
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGC-ATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCA
EST: gi|60358728|gb|DN225701.1|DN225701
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|13178340|gb|BG349598.1|BG349598
EST:     AAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|211505179|gb|FL436188.1|FL436188
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|211507463|gb|FL431647.1|FL431647
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|60353604|gb|DN220577.1|DN220577
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|71774336|gb|DR972214.1|DR972214
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|60353656|gb|DN220629.1|DN220629
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAAATGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|116813437|gb|EC855888.1|EC855888
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATCAAGATGATGCCCAGCTGAATTCCAA
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|76010925|gb|DT938095.1|DT938095
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|89755425|gb|DY685846.1|DY685846
EST:     AGGACAAACTGATGCGGCTGAGGTTTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|33100890|gb|CF060850.1|CF060850
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGTGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|13178561|gb|BG349819.1|BG349819
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|16377885|gb|BI992166.1|BI992166
EST:     AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTCTGGATGGAGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
EST: gi|60346391|gb|DN213364.1|DN213364
EST:     AGGACAAACTGATGCGGCTGAGGTTTAAGCGGAAGAACTGGGCCTGACAG                         CGTTGCATGTTTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG
genomic: AGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAG

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: 42 (upstream exon), 47 (downstream exon)
Score: 32

CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAGTACGCATTCCAGATAATTGATGCTGGGTTATGGCTATGTAACTAGCTGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 205

CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAGTACGCATTCCAGATAATTGATGCTGGGTTATGGCTATGTAACTAGCTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAGTACGCATTCCAGATAATTGATGCTGGGTTATGGCTATGTAACTAGCTGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 65

CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGGCCTGACAGgttaaagtct ... ctcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAGTACGCATTCCAGATAATTGATGCTGGGTTATGGCTATGTAACTAGCTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcagatctgtttttgtttttgacttgataacgctgacttgataactcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAGTACGCATTCCAGATAATTGATGCTGGGTTATGGCTATGTAACTAGCTGT
                                       tgataac  putative branch site (score: 65)
                                             ctcct  CT-rich tract
          tttttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaaagtctaaacttgtgtagctctgtttttctatccagaaattgtcaatctgcagatctgtttttgtttttgacttgataacgctgacttgataactcctaacagCGTTGCATGTCTGGATGGTGTAAATAAAGATGATGCCCAGCTGAATTCCAGTACGCATTCCAGATAATTGATGCTGGGTTATGGCTATGTAACTAGCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG