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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAGgtaaatatcagcgtattaccgttgggcaaccaacaattactatatgtcgatggtattttacgagatctaataattgaacaaagttcaaacttaaaaacat...

Basic information

species Zea mays
transcript GRMZM2G161087_T01
intron # 17
splice site 5'
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|32934996|gb|CF039808.1|CF039808
EST:     CAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAG                         ATTATCAAAGATGGAAGAATCGATGTCCCAAGAGCTAGTGGTTGAGCGTGA
genomic: CAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAGgtaaatatca ... cttttctcagATTATCAAAGATGGAAGAATCGATGTCGCAAGAGCTAGTGGTTGAGTGTGA
EST: gi|87155360|gb|DY400149.1|DY400149
EST:     CAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAG                         ATTATCAAAGATGGAAGAATCGATGTCCCAAGAGCTAGTGGTTGAGCGTGA
genomic: CAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAGgtaaatatca ... cttttctcagATTATCAAAGATGGAAGAATCGATGTCGCAAGAGCTAGTGGTTGAGTGTGA
EST: gi|32931261|gb|CF036073.1|CF036073
EST:     CAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAG                         ATTATCAAAGATGGAAGAATCGATGTCCCAAGAGCTAGTGGTTGAGCGTGA
genomic: CAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAGgtaaatatca ... cttttctcagATTATCAAAGATGGAAGAATCGATGTCGCAAGAGCTAGTGGTTGAGTGTGA
EST: gi|32933316|gb|CF038128.1|CF038128
EST:     CAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAG                         ATTATCAAAGATGGAAGAATCGATGTCCCAAGAGCTAGTGGTTGAGCGTGA
genomic: CAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAGgtaaatatca ... cttttctcagATTATCAAAGATGGAAGAATCGATGTCGCAAGAGCTAGTGGTTGAGTGTGA
EST: gi|22546559|gb|BU098870.1|BU098870
EST:     CAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAG                         ATTATCAAAGATGGAAGAATCGATGTCCCAAGAGCTAGTGGTTGAGCGTGA
genomic: CAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAGgtaaatatca ... cttttctcagATTATCAAAGATGGAAGAATCGATGTCGCAAGAGCTAGTGGTTGAGTGTGA
EST: gi|26559353|gb|CA831588.1|CA831588
EST:     CAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAG                         ATTATCAAAGATGGAAGAATCGATGTCCCAAGAGCTAGTGGTTGAGCGTGA
genomic: CAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAGgtaaatatca ... cttttctcagATTATCAAAGATGGAAGAATCGATGTCGCAAGAGCTAGTGGTTGAGTGTGA
EST: gi|32934128|gb|CF038940.1|CF038940
EST:     CAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAG                         ATTATCAAAGATGGAAGAATCGATGTCCCAAGAGCTAGTGGTTGAGCGTGA
genomic: CAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAGgtaaatatca ... cttttctcagATTATCAAAGATGGAAGAATCGATGTCGCAAGAGCTAGTGGTTGAGTGTGA
EST: gi|113701833|gb|EE679337.1|EE679337
EST:     CAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAG                         ATTATCAAAGATGGAAGAATCCATGTCGCAAGAGCTAGTGGTTGAGTGTGA
genomic: CAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAGgtaaatatca ... cttttctcagATTATCAAAGATGGAAGAATCGATGTCGCAAGAGCTAGTGGTTGAGTGTGA
EST: gi|32932425|gb|CF037237.1|CF037237
EST:     CAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAG                         ATTATCAAAGATGGAAGAATCGATGTCCCAAGAGCTAGTGGTTGAGCGTGA
genomic: CAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAGgtaaatatca ... cttttctcagATTATCAAAGATGGAAGAATCGATGTCGCAAGAGCTAGTGGTTGAGTGTGA
EST: gi|71772591|gb|DR970520.1|DR970520
EST:     CAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAG                         ATTATCAAAGATGGAAGAATCGATGTCGCAAGAGCTAGTGGTTGAGTGTGA
genomic: CAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAGgtaaatatca ... cttttctcagATTATCAAAGATGGAAGAATCGATGTCGCAAGAGCTAGTGGTTGAGTGTGA

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: 46 (upstream exon), 48 (downstream exon)
Score: 124

GACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAGgtaaatatca ... cttttctcagATTATCAAAGATGGAAGAATCGATGTCGCAAGAGCTAGTGGTTGAGTGTGACAAGAACAAGTCTTTGACAGAGAGG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 42

GACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAGgtaaatatca ... cttttctcagATTATCAAAGATGGAAGAATCGATGTCGCAAGAGCTAGTGGTTGAGTGTGACAAGAACAAGTCTTTGACAGAGAGG


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

GACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAGgtaaatatca ... cttttctcagATTATCAAAGATGGAAGAATCGATGTCGCAAGAGCTAGTGGTTGAGTGTGACAAGAACAAGTCTTTGACAGAGAGG


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

GACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAGgtaaatatca ... cttttctcagATTATCAAAGATGGAAGAATCGATGTCGCAAGAGCTAGTGGTTGAGTGTGACAAGAACAAGTCTTTGACAGAGAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAGgtaaatatcagcgtattaccgttgggcaaccaacaattactatatgtcgatggtattttacgagatctaataattgaacaaagttcaaacttaaaaacat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaacaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaaaaca