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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaacacattattgttacttttttcaaactgtttttcatcatttgtgatgtaactaatgttttctgattattatttttgtctagAATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGACGGTAAAACAG

Basic information

species Zea mays
transcript GRMZM5G840928_T03
intron # 5
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|78120737|gb|DV539121.1|DV539121
EST:     GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAA                         AATTGGTGATGTAAC
genomic: GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAAgtaagaacac ... ttttgtctagAATTGGTGATGTAAC
EST: gi|71763117|gb|DR961054.1|DR961054
EST:     GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAA                         AATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
genomic: GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAAgtaagaacac ... ttttgtctagAATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
EST: gi|76282803|gb|DV022371.1|DV022371
EST:     GACGTAGATGAGGAAAGTGCTTTTGAGCAGCTAATCGCACTTTGCCAAAA                         AATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
genomic: GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAAgtaagaacac ... ttttgtctagAATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
EST: gi|60400995|gb|DN233802.1|DN233802
EST:     GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAA                         AATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
genomic: GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAAgtaagaacac ... ttttgtctagAATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
EST: gi|211044162|gb|FL460073.1|FL460073
EST:     GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAA                         AATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
genomic: GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAAgtaagaacac ... ttttgtctagAATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
EST: gi|94474415|gb|EB703373.1|EB703373
EST:     GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAA                         AATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
genomic: GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAAgtaagaacac ... ttttgtctagAATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
EST: gi|71766336|gb|DR964273.1|DR964273
EST:     GACGTAGATGAGGAAAGTGCTTTTGAGCAGCTAATCGCACTTTGCCAAAA                         AATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
genomic: GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAAgtaagaacac ... ttttgtctagAATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
EST: gi|76011914|gb|DT939084.1|DT939084
EST:     GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAA                         AATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
genomic: GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAAgtaagaacac ... ttttgtctagAATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
EST: gi|76020591|gb|DT947761.1|DT947761
EST:     GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAA                         AATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
genomic: GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAAgtaagaacac ... ttttgtctagAATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
EST: gi|60345505|gb|DN212478.1|DN212478
EST:     GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAA                         AATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
genomic: GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAAgtaagaacac ... ttttgtctagAATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
EST: gi|78122651|gb|DV541035.1|DV541035
EST:     GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAA                         AATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
genomic: GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAAgtaagaacac ... ttttgtctagAATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
EST: gi|60400210|gb|DN233017.1|DN233017
EST:     GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAA                         AATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
genomic: GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAAgtaagaacac ... ttttgtctagAATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
EST: gi|78122650|gb|DV541034.1|DV541034
EST:     GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAA                         AATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA
genomic: GACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAAgtaagaacac ... ttttgtctagAATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGA

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: 47 (upstream exon), 47 (downstream exon)
Score: 183

CACCAAATGTCTATGAGTACAAGCGTCTTGTTCAGAAGGTTCTTAACTGTGACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAAgtaagaacac ... ttttgtctagAATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGACGGTAAAACAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 55

CACCAAATGTCTATGAGTACAAGCGTCTTGTTCAGAAGGTTCTTAACTGTGACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAAgtaagaacac ... ttttgtctagAATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGACGGTAAAACAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 76

CACCAAATGTCTATGAGTACAAGCGTCTTGTTCAGAAGGTTCTTAACTGTGACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAAgtaagaacac ... ttttgtctagAATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGACGGTAAAACAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 64

CACCAAATGTCTATGAGTACAAGCGTCTTGTTCAGAAGGTTCTTAACTGTGACGTAGATGAGGAAAGTGCTTCTGAGCAGCTAATCGCACTTTGCCAAAAgtaagaacac ... ttttgtctagAATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGACGGTAAAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttttcatcatttgtgatgtaactaatgttttctgattattatttttgtctagAATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGACGGTAAAACAG
                                            tttttgtct  CT-rich tract
                     taactaatgttttctg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaacacattattgttacttttttcaaactgtttttcatcatttgtgatgtaactaatgttttctgattattatttttgtctagAATTGGTGATGTAACAATAATGCAGAAAGGAAAAGCTGATGTCATCAGTGACGGTAAAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT