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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggatatcatgctgagccattaaaaagcgaagtaaaaaaaatatcatctttctgttcagagctgaatgcggcttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAGCTTGCTGCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAA

Basic information

species Zea mays
transcript GRMZM2G021864_T01
intron # 18
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|33091337|gb|CF051331.1|CF051331
EST:     GCGTGAAGAGCTTCGACAACGAGATACACGACTGAAGCAGACG                         ATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
EST: gi|211215778|gb|FL437224.1|FL437224
EST:     GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG                         ATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAMAAAAGAAGTGCGGTCAG
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
EST: gi|32804257|gb|CD956493.1|CD956493
EST:     GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG                         ATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
EST: gi|78022987|gb|DV491374.1|DV491374
EST:     GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG                         ATTGGAGACCTGGAGCTTGAGCTGGAGG
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGG
EST: gi|32909144|gb|CF013956.1|CF013956
EST:     GCGTGAAGAGCTTCGGCAACGAGATACCCAACTGAAGCAGACG                         ATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
EST: gi|32931903|gb|CF036715.1|CF036715
EST:     GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG                         ATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
EST: gi|211458170|gb|FL127582.1|FL127582
EST:     GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG                         ATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
EST: gi|89248917|gb|DY620703.1|DY620703
EST:     GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG                         ATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
EST: gi|89758497|gb|DY687658.1|DY687658
EST:     GCGTGA-GAGCTTCGACAACGAGATACACAACTGAGGCAGACG                         ATTGGAGACCTGGAGCTT
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTT
EST: gi|5608024|gb|AI901691.1|AI901691
EST:     GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG                         ATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
EST: gi|6194461|gb|AW146565.1|AW146565
EST:     GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG                         ATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
EST: gi|32934210|gb|CF039022.1|CF039022
EST:     GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG                         ATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
EST: gi|78106767|gb|DV525185.1|DV525185
EST:     GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG                         ATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
EST: gi|116827696|gb|EC871624.1|EC871624
EST:     GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG                         ATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
EST: gi|32930527|gb|CF035339.1|CF035339
EST:     GCGTGAAGAGCTTCGACACCGAGATACCCAACTGAAGCAGACG                         ATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
EST: gi|5915604|gb|AW053245.1|AW053245
EST:     GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG                         ATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
EST: gi|32932800|gb|CF037612.1|CF037612
EST:     GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG                         ATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
EST: gi|5713643|gb|AI943635.1|AI943635
EST:     GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG                         ATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
EST: gi|32932808|gb|CF037620.1|CF037620
EST:     GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG                         ATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
EST: gi|91054831|gb|EB165249.1|EB165249
EST:     GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG                         ATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
EST: gi|13381810|gb|BG458485.1|BG458485
EST:     GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG                         ATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
EST: gi|12968788|gb|BG265825.1|BG265825
EST:     GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG                         ATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG
genomic: GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAG

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: 43 (upstream exon), 48 (downstream exon)
Score: 178

GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAGCTTGCTGCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 98

GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAGCTTGCTGCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 128

GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAGCTTGCTGCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 82

GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGgtatggatat ... ttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAGCTTGCTGCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaagtaaaaaaaatatcatctttctgttcagagctgaatgcggcttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAGCTTGCTGCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAA
                                            cttctttgt  CT-rich tract
     taaaaaaaatatcatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggatatcatgctgagccattaaaaagcgaagtaaaaaaaatatcatctttctgttcagagctgaatgcggcttctttgtagATTGGAGACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAGCTTGCTGCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC