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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGAGCTCGGAAACCACGGTGAGCCGCCCGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgtttttctctctttacttcactgtatcaatcatgtggtacatgccttattttgccctgcatttgctctttcgtttgcatggtgtgatttaggtc...

Basic information

species Zea mays
transcript GRMZM2G066440_T01
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|211413817|gb|FL421626.1|FL421626
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211271873|gb|FL420608.1|FL420608
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211453719|gb|FL371690.1|FL371690
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211479925|gb|FL425093.1|FL425093
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211271148|gb|FL388759.1|FL388759
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGNGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211089720|gb|FL375370.1|FL375370
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211273933|gb|FL428371.1|FL428371
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211085797|gb|FL424019.1|FL424019
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAANCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211059644|gb|FL374516.1|FL374516
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|78120608|gb|DV538992.1|DV538992
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211233915|gb|FL394219.1|FL394219
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211210029|gb|FL411366.1|FL411366
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211218085|gb|FL424499.1|FL424499
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211485264|gb|FL406762.1|FL406762
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGNGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|78122609|gb|DV540993.1|DV540993
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACTTTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211450321|gb|FL410319.1|FL410319
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211158229|gb|FL401285.1|FL401285
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211339029|gb|FL403594.1|FL403594
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211204746|gb|FL408304.1|FL408304
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211282425|gb|FL393384.1|FL393384
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211229498|gb|FL371568.1|FL371568
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211179793|gb|FL384665.1|FL384665
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211527411|gb|FL405481.1|FL405481
EST:     CGCAGTATGCACCTCTCTCGGATAA-GGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211487815|gb|FL394402.1|FL394402
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGNGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|149072975|gb|EE161236.2|EE161236
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211374582|gb|FL413733.1|FL413733
EST:     CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT
EST: gi|211521604|gb|FL412478.1|FL412478
EST:     CGCAGNATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAG                         CCACATTATGCATCTGGAGTGAACCTTTCACAAAGNGCTCCTTCCACTAAT
genomic: CGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAAT

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: 139

CGGAGCTCGGAAACCACGGTGAGCCGCCCGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAATCAAGTTTCTCAGGCTGCCAGTGGAAACCAAATGTCGACAGAAGCATATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 89

CGGAGCTCGGAAACCACGGTGAGCCGCCCGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAATCAAGTTTCTCAGGCTGCCAGTGGAAACCAAATGTCGACAGAAGCATATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

CGGAGCTCGGAAACCACGGTGAGCCGCCCGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAATCAAGTTTCTCAGGCTGCCAGTGGAAACCAAATGTCGACAGAAGCATATC


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 166

CGGAGCTCGGAAACCACGGTGAGCCGCCCGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgttt ... ttgtttacagCCACATTATGCATCTGGAGTGAACCTTTCACAAAGTGCTCCTTCCACTAATCAAGTTTCTCAGGCTGCCAGTGGAAACCAAATGTCGACAGAAGCATATC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGAGCTCGGAAACCACGGTGAGCCGCCCGCAGTATGCACCTCTCTCGGATAACAGGGCAAGGAATGACCACTCGGAGgtgcgtgtttttctctctttacttcactgtatcaatcatgtggtacatgccttattttgccctgcatttgctctttcgtttgcatggtgtgatttaggtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA