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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttctctttagtcccattgaaattcatagatttaactgacgatctgatgggtttttctttgaccccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG

Basic information

species Zea mays
transcript GRMZM2G329306_T01
intron # 6
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|71329028|gb|DR801213.1|DR801213
EST:     TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG                         CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
genomic: TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATGgtttgttctc ... accccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
EST: gi|211484888|gb|FL049377.1|FL049377
EST:     CCGTGGAGAGCTTTAAACAGGCATTGGAGYTGGAGCCAAATGATG                         CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
genomic: CCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATGgtttgttctc ... accccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
EST: gi|32930877|gb|CF035689.1|CF035689
EST:     TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG                         CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
genomic: TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATGgtttgttctc ... accccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
EST: gi|113703884|gb|EE681388.1|EE681388
EST:     TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG                         CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
genomic: TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATGgtttgttctc ... accccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
EST: gi|211517927|gb|FL479799.1|FL479799
EST:     TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG                         CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
genomic: TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATGgtttgttctc ... accccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
EST: gi|149051834|gb|EE155961.2|EE155961
EST:     TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG                         CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
genomic: TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATGgtttgttctc ... accccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
EST: gi|78124365|gb|DV542749.1|DV542749
EST:     TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG                         CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
genomic: TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATGgtttgttctc ... accccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
EST: gi|71443878|gb|DR824928.1|DR824928
EST:     TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG                         CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
genomic: TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATGgtttgttctc ... accccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
EST: gi|60350322|gb|DN217295.1|DN217295
EST:     TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG                         CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
genomic: TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATGgtttgttctc ... accccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
EST: gi|32930670|gb|CF035482.1|CF035482
EST:     TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG                         CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
genomic: TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATGgtttgttctc ... accccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
EST: gi|88756259|gb|DY540400.1|DY540400
EST:     TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG                         CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
genomic: TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATGgtttgttctc ... accccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
EST: gi|76017867|gb|DT945037.1|DT945037
EST:     TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG                         CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
genomic: TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATGgtttgttctc ... accccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
EST: gi|88756258|gb|DY540399.1|DY540399
EST:     TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG                         CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
genomic: TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATGgtttgttctc ... accccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
EST: gi|32930642|gb|CF035454.1|CF035454
EST:     TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG                         CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
genomic: TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATGgtttgttctc ... accccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
EST: gi|149012518|gb|EE042586.2|EE042586
EST:     TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG                         CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
genomic: TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATGgtttgttctc ... accccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
EST: gi|211145441|gb|FL467393.1|FL467393
EST:     TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG                         CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
genomic: TGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATGgtttgttctc ... accccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG

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: 94

GCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATGgtttgttctc ... accccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 135

GCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATGgtttgttctc ... accccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

GCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATGgtttgttctc ... accccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 232

GCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATGgtttgttctc ... accccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaaattcatagatttaactgacgatctgatgggtttttctttgaccccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG
                                   tttttctttgacccc  CT-rich tract
     attcatagatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttctctttagtcccattgaaattcatagatttaactgacgatctgatgggtttttctttgaccccattagCTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG