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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATGgtaagttgccaggctaggcaatcattcagccttctctgggatagctgtagttttcccaacactgtttttttttgctatttttgcatgcag

Basic information

species Zea mays
transcript GRMZM2G063676_T01
intron # 4
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|21809991|gb|BQ668309.1|BQ668309
EST:     TTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATG                         ATGCTGGAGGAGGAT
genomic: TTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATGgtaagttgcc ... ttgcatgcagATGCTGGAGGAGGAT
EST: gi|67029439|gb|CO458188.1|CO458188
EST:     CACGGGATTGTCACAGTTGATTCAGCTATG                         ATGCTGGAGGAGGATGTGGTAGTTCCAGTCTCATCTGCTAATGAAGCTCCA
genomic: CACGGGATTGTCACAGTTGATTCAGCTATGgtaagttgcc ... ttgcatgcagATGCTGGAGGAGGATGTGGCAGTTCCAGTCTCATCTGCTAATGAAGCTCCA
EST: gi|32931548|gb|CF036360.1|CF036360
EST:     TTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTGTG                         ATGCTGGAGGAGGATGTGGCAGTTCCAGTCTCATCTGCTAATGAAGCTCCA
genomic: TTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATGgtaagttgcc ... ttgcatgcagATGCTGGAGGAGGATGTGGCAGTTCCAGTCTCATCTGCTAATGAAGCTCCA
EST: gi|71307557|gb|DR789997.1|DR789997
EST:     TTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATG                         ATGCTGGAGGAGGATGTGGCAGTTCCAGTCTCATCTGCTAATGAAGCTCCA
genomic: TTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATGgtaagttgcc ... ttgcatgcagATGCTGGAGGAGGATGTGGCAGTTCCAGTCTCATCTGCTAATGAAGCTCCA
EST: gi|18654531|gb|BM499336.1|BM499336
EST:     TTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATG                         ATGCTGGAGGAGGATGTGGCAGTTCCAGTCTCATCTGCTAATGAAGCTCCA
genomic: TTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATGgtaagttgcc ... ttgcatgcagATGCTGGAGGAGGATGTGGCAGTTCCAGTCTCATCTGCTAATGAAGCTCCA
EST: gi|31355297|gb|CD439654.1|CD439654
EST:     TTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATG                         ATGCTGGAGGAGGATGTGGCAGTTCCAGTCTCATCTGCTAATGAAGCTCCA
genomic: TTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATGgtaagttgcc ... ttgcatgcagATGCTGGAGGAGGATGTGGCAGTTCCAGTCTCATCTGCTAATGAAGCTCCA
EST: gi|18654532|gb|BM499337.1|BM499337
EST:     TTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATG                         ATGCTGGAGGAGGATGTGGCAGTTCCAGTCTCATCTGCTAATGAAGCTCCA
genomic: TTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATGgtaagttgcc ... ttgcatgcagATGCTGGAGGAGGATGTGGCAGTTCCAGTCTCATCTGCTAATGAAGCTCCA
EST: gi|32933060|gb|CF037872.1|CF037872
EST:     TTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGGTTCAGCTGTG                         ATGCTGGAGGAGGATGCGGCAGTTCCAGTCTCATCTGCTAATGAAGCTCCA
genomic: TTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATGgtaagttgcc ... ttgcatgcagATGCTGGAGGAGGATGTGGCAGTTCCAGTCTCATCTGCTAATGAAGCTCCA
EST: gi|18654538|gb|BM499343.1|BM499343
EST:     TTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATG                         ATGCTGGAGGAGGATGTGGCAGTTCCAGTCTCATCTGCTAATGAAGCTCCA
genomic: TTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATGgtaagttgcc ... ttgcatgcagATGCTGGAGGAGGATGTGGCAGTTCCAGTCTCATCTGCTAATGAAGCTCCA

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: 353

ATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATGgtaagttgcc ... ttgcatgcagATGCTGGAGGAGGATGTGGCAGTTCCAGTCTCATCTGCTAATGAAGCTCCAAAGGATACTACAAAGATGGACACAGATGATGCACCAAGTGATCCTGTCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 119

ATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATGgtaagttgcc ... ttgcatgcagATGCTGGAGGAGGATGTGGCAGTTCCAGTCTCATCTGCTAATGAAGCTCCAAAGGATACTACAAAGATGGACACAGATGATGCACCAAGTGATCCTGTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

ATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATGgtaagttgcc ... ttgcatgcagATGCTGGAGGAGGATGTGGCAGTTCCAGTCTCATCTGCTAATGAAGCTCCAAAGGATACTACAAAGATGGACACAGATGATGCACCAAGTGATCCTGTCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 171

ATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATGgtaagttgcc ... ttgcatgcagATGCTGGAGGAGGATGTGGCAGTTCCAGTCTCATCTGCTAATGAAGCTCCAAAGGATACTACAAAGATGGACACAGATGATGCACCAAGTGATCCTGTCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATGgtaagttgccaggctaggcaatcattcagccttctctgggatagctgtagttttcccaacactgtttttttttgctatttttgcatgcag

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