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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAACCTTCATCACCTCTGATGCCGTTGTTGTTGACGCCAAGGTGGCTGAGCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAGgtacatgaggttgatggtttacttgttaagaaatgggaatggtggtgttaatttgtgtcggttttctttttcag

Basic information

species Zea mays
transcript GRMZM2G015989_T03
intron # 3
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|32847806|gb|CD987487.1|CD987487
EST:     GCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAG                         GTTTTGGGTTCTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGA
genomic: GCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAGgtacatgagg ... tctttttcagGTTTTGGGTTCTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGA
EST: gi|9254561|gb|BE345029.1|BE345029
EST:     GCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAG                         GTTTTGGGTTTTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGA
genomic: GCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAGgtacatgagg ... tctttttcagGTTTTGGGTTCTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGA
EST: gi|32935512|gb|CF040324.1|CF040324
EST:     GCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAG                         GTTTTGGGTTCTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGA
genomic: GCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAGgtacatgagg ... tctttttcagGTTTTGGGTTCTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGA
EST: gi|32847822|gb|CD987503.1|CD987503
EST:     GCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAG                         GTTTTGGGTTCTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGGCAGA
genomic: GCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAGgtacatgagg ... tctttttcagGTTTTGGGTTCTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGA
EST: gi|33096671|gb|CF056665.1|CF056665
EST:     GCAAGCACCATCATCTCCTGCAAACCCAATGGTAATGGGTGGTGGCTCAG                         GTTTTGGGTTCTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGA
genomic: GCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAGgtacatgagg ... tctttttcagGTTTTGGGTTCTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGA
EST: gi|211490744|gb|FL282860.1|FL282860
EST:     GCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAG                         GTTTTGGGTTCTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGA
genomic: GCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAGgtacatgagg ... tctttttcagGTTTTGGGTTCTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGA
EST: gi|9952879|gb|BE639462.1|BE639462
EST:     GCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAG                         GTTTTGGGTTTTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGA
genomic: GCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAGgtacatgagg ... tctttttcagGTTTTGGGTTCTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGA
EST: gi|8318787|gb|BE025427.1|BE025427
EST:     GCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAG                         GTTTTGGGTTTTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGA
genomic: GCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAGgtacatgagg ... tctttttcagGTTTTGGGTTCTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGA
EST: gi|4573038|gb|AI586687.1|AI586687
EST:     GCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAG                         GTTTTGGGTTCTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGA
genomic: GCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAGgtacatgagg ... tctttttcagGTTTTGGGTTCTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGA
EST: gi|9952880|gb|BE639463.1|BE639463
EST:     GCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAG                         GTTTTGGGTTCTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGA
genomic: GCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAGgtacatgagg ... tctttttcagGTTTTGGGTTCTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGA

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: 49 (upstream exon), 49 (downstream exon)
Score: 436

AAAACCTTCATCACCTCTGATGCCGTTGTTGTTGACGCCAAGGTGGCTGAGCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAGgtacatgagg ... tctttttcagGTTTTGGGTTCTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGAATCTTAGTTTCGAGATATAATAATAAATTGGATGATGTTAGTTTCGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 228

AAAACCTTCATCACCTCTGATGCCGTTGTTGTTGACGCCAAGGTGGCTGAGCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAGgtacatgagg ... tctttttcagGTTTTGGGTTCTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGAATCTTAGTTTCGAGATATAATAATAAATTGGATGATGTTAGTTTCGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 342

AAAACCTTCATCACCTCTGATGCCGTTGTTGTTGACGCCAAGGTGGCTGAGCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAGgtacatgagg ... tctttttcagGTTTTGGGTTCTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGAATCTTAGTTTCGAGATATAATAATAAATTGGATGATGTTAGTTTCGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 373

AAAACCTTCATCACCTCTGATGCCGTTGTTGTTGACGCCAAGGTGGCTGAGCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAGgtacatgagg ... tctttttcagGTTTTGGGTTCTAAATTGTTCAGCTGCCCTTCGTTCCATCGCAGCGACAGAATCTTAGTTTCGAGATATAATAATAAATTGGATGATGTTAGTTTCGAGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAACCTTCATCACCTCTGATGCCGTTGTTGTTGACGCCAAGGTGGCTGAGCAAGCACCATCATCTCCTGCAAACCCAATGGCAATGGGTGGTGGCTCAGgtacatgaggttgatggtttacttgttaagaaatgggaatggtggtgttaatttgtgtcggttttctttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG