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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGATGAGTTCAGAATCTGATCCATCACTAAATGCTGAACATCGGAGCATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAGgtaagcatactgttgtgccattgtaattttgtacatgtatttgtttttgacatcatatatttatatgcgagtgtgacatattactttgaaattggcag

Basic information

species Zea mays
transcript GRMZM2G151268_T01
intron # 5
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|12971760|gb|BG267644.1|BG267644
EST:     ATGAGTAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAG                         ACCTATCTCTTCTTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAGgtaagcatac ... aaattggcagACCTATCTCTTCTTCGCAGCAGGCATCAG
EST: gi|4647161|gb|AI622236.1|AI622236
EST:     ATGAGGAGGGCACCATCAGCATCAG-TGGGAATCTGCCTCCTATGGGGAG                         ACCTATCTCTTCTTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAGgtaagcatac ... aaattggcagACCTATCTCTTCTTCGCAGCAGGCATCAG
EST: gi|91049337|gb|EB159755.1|EB159755
EST:     CACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAG                         ACCTATCTCTTCTTCGCAGCAGGCATCAG
genomic: CACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAGgtaagcatac ... aaattggcagACCTATCTCTTCTTCGCAGCAGGCATCAG
EST: gi|32909956|gb|CF014768.1|CF014768
EST:     ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAG                         ACCTATCTCTTCTTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAGgtaagcatac ... aaattggcagACCTATCTCTTCTTCGCAGCAGGCATCAG
EST: gi|60348471|gb|DN215444.1|DN215444
EST:     ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAG                         ACCTATCTCTTCTTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAGgtaagcatac ... aaattggcagACCTATCTCTTCTTCGCAGCAGGCATCAG
EST: gi|74239381|gb|DT647295.1|DT647295
EST:     ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAG                         ACCTATCTTTTCTTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAGgtaagcatac ... aaattggcagACCTATCTCTTCTTCGCAGCAGGCATCAG
EST: gi|21809549|gb|BQ667867.1|BQ667867
EST:     ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAG                         ACCTATCTCTTCTTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAGgtaagcatac ... aaattggcagACCTATCTCTTCTTCGCAGCAGGCATCAG
EST: gi|47961828|gb|CN844537.1|CN844537
EST:     ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAG                         ACCTATTTCTTCTTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAGgtaagcatac ... aaattggcagACCTATCTCTTCTTCGCAGCAGGCATCAG
EST: gi|74239382|gb|DT647296.1|DT647296
EST:     ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAG                         ACCTATCTCTTCTTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAGgtaagcatac ... aaattggcagACCTATCTCTTCTTCGCAGCAGGCATCAG
EST: gi|94478768|gb|EB707726.1|EB707726
EST:     CACCCTCAGCATCAGATGGGAATCTGCCTCCTATGGGGAG                         ACCTATCTCTTCTTCGCAGCAGGCATCAG
genomic: CACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAGgtaagcatac ... aaattggcagACCTATCTCTTCTTCGCAGCAGGCATCAG
EST: gi|60399998|gb|DN232805.1|DN232805
EST:     TCAGCATCATTTGGGAATCTGCCTCCTATGGGGAG                         ACCTATCTCTTCTTTGCAGCAGGCATCAG
genomic: TCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAGgtaagcatac ... aaattggcagACCTATCTCTTCTTCGCAGCAGGCATCAG
EST: gi|15323531|gb|BI478753.1|BI478753
EST:     ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAG                         ACCTATCTCTTCTTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAGgtaagcatac ... aaattggcagACCTATCTCTTCTTCGCAGCAGGCATCAG
EST: gi|211191649|gb|FL029190.1|FL029190
EST:     ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCCCCTAT--GGAG                         ACCTATCTCTTCTTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAGgtaagcatac ... aaattggcagACCTATCTCTTCTTCGCAGCAGGCATCAG
EST: gi|60400202|gb|DN233009.1|DN233009
EST:     ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAG                         ACCTATCTCTTCTTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAGgtaagcatac ... aaattggcagACCTATCTCTTCTTCGCAGCAGGCATCAG
EST: gi|45847355|gb|CN071298.1|CN071298
EST:     ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAG                         ACCTATCTCTTCTTCGCAGCAGGCATCAG
genomic: ATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAGgtaagcatac ... aaattggcagACCTATCTCTTCTTCGCAGCAGGCATCAG

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: 479

GGATGATGAGTTCAGAATCTGATCCATCACTAAATGCTGAACATCGGAGCATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAGgtaagcatac ... aaattggcagACCTATCTCTTCTTCGCAGCAGGCATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 163

GGATGATGAGTTCAGAATCTGATCCATCACTAAATGCTGAACATCGGAGCATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAGgtaagcatac ... aaattggcagACCTATCTCTTCTTCGCAGCAGGCATCAG


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

GGATGATGAGTTCAGAATCTGATCCATCACTAAATGCTGAACATCGGAGCATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAGgtaagcatac ... aaattggcagACCTATCTCTTCTTCGCAGCAGGCATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 244

GGATGATGAGTTCAGAATCTGATCCATCACTAAATGCTGAACATCGGAGCATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAGgtaagcatac ... aaattggcagACCTATCTCTTCTTCGCAGCAGGCATCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGATGAGTTCAGAATCTGATCCATCACTAAATGCTGAACATCGGAGCATGAGGAGGGCACCATCAGCATCAGTTGGGAATCTGCCTCCTATGGGGAGgtaagcatactgttgtgccattgtaattttgtacatgtatttgtttttgacatcatatatttatatgcgagtgtgacatattactttgaaattggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG