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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGACCGGATGGGAGGAGTACACTCTCATCCATAACCCGGAGTCATTTTTCAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTGgtgagttcattgtttagtagactgcctttttctatccaaccaaactcttaacccttcaacctcaagcaggctttcctccaaaatctgtcatattttgtgg...

Basic information

species Zea mays
transcript GRMZM2G080650_T01
intron # 2
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|88756488|gb|DY540629.1|DY540629
EST:     CAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTG                         GCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCA
genomic: CAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTGgtgagttcat ... cggtactcagGCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCA
EST: gi|71438579|gb|DR819629.1|DR819629
EST:     CAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTG                         GCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCA
genomic: CAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTGgtgagttcat ... cggtactcagGCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCA
EST: gi|71427833|gb|DR808883.1|DR808883
EST:     CAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTG                         GCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCA
genomic: CAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTGgtgagttcat ... cggtactcagGCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCA
EST: gi|71773835|gb|DR971726.1|DR971726
EST:     CAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTG                         GCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCA
genomic: CAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTGgtgagttcat ... cggtactcagGCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCA
EST: gi|148941140|gb|EC886011.2|EC886011
EST:     CAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTG                         GCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCA
genomic: CAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTGgtgagttcat ... cggtactcagGCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCA
EST: gi|71440434|gb|DR821484.1|DR821484
EST:     CAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTG                         GCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCA
genomic: CAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTGgtgagttcat ... cggtactcagGCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCA
EST: gi|148940548|gb|EC885350.2|EC885350
EST:     CAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTG                         GCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCA
genomic: CAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTGgtgagttcat ... cggtactcagGCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCA
EST: gi|101401656|gb|EB822492.1|EB822492
EST:     CAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTG                         GCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCA
genomic: CAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTGgtgagttcat ... cggtactcagGCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCA
EST: gi|78092000|gb|DV520374.1|DV520374
EST:     CAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTG                         GCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCA
genomic: CAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTGgtgagttcat ... cggtactcagGCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCA

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), 49 (downstream exon)
Score: 27

ATGACCGGATGGGAGGAGTACACTCTCATCCATAACCCGGAGTCATTTTTCAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTGgtgagttcat ... cggtactcagGCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCAAGAAAGGCGACTATGTCTTCGTCTCAGCAGCATCAGGAGCCGTTGGTCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 116

ATGACCGGATGGGAGGAGTACACTCTCATCCATAACCCGGAGTCATTTTTCAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTGgtgagttcat ... cggtactcagGCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCAAGAAAGGCGACTATGTCTTCGTCTCAGCAGCATCAGGAGCCGTTGGTCA


Block sizes: 43 (upstream exon), 46 (downstream exon)
Score: 62

ATGACCGGATGGGAGGAGTACACTCTCATCCATAACCCGGAGTCATTTTTCAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTGgtgagttcat ... cggtactcagGCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCAAGAAAGGCGACTATGTCTTCGTCTCAGCAGCATCAGGAGCCGTTGGTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 118

ATGACCGGATGGGAGGAGTACACTCTCATCCATAACCCGGAGTCATTTTTCAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTGgtgagttcat ... cggtactcagGCATGCCGGGCCTTACTGCTTGGGCTGGATTTTTCGATGTGGGCAAGCCCAAGAAAGGCGACTATGTCTTCGTCTCAGCAGCATCAGGAGCCGTTGGTCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGACCGGATGGGAGGAGTACACTCTCATCCATAACCCGGAGTCATTTTTCAAGATCAAGCATCCTGAATTGCCTCTGTCCTACTACACAGGCGTTCTTGgtgagttcattgtttagtagactgcctttttctatccaaccaaactcttaacccttcaacctcaagcaggctttcctccaaaatctgtcatattttgtgg

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