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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCAAGCATCACTTGAGCGGGATGATGAGgtatattcagatttactgtttatattcattgtatcatttcgaattgaactgaacagattggtgtttgatgtttttctctggttattatatctgccgcag

Basic information

species Zea mays
transcript GRMZM2G096107_T01
intron # 18
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|211224174|gb|FL079362.1|FL079362
EST:     GCTCAAGCATCACTTGAGCGGGATGATGAG                         GATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCCTCCCTTCGC
genomic: GCTCAAGCATCACTTGAGCGGGATGATGAGgtatattcag ... tctgccgcagGATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCCTCCCTTCGC
EST: gi|18174696|gb|BM350084.1|BM350084
EST:     AGGCTCAAGCATCACTTGAGCGGGATGATGAG                         GATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCCTCCCTTCGC
genomic: AGGCTCAAGCATCACTTGAGCGGGATGATGAGgtatattcag ... tctgccgcagGATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCCTCCCTTCGC
EST: gi|211480244|gb|FK978298.1|FK978298
EST:     GCTCAAGCATCACTTGAGCGGGATGATGAG                         GATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCC
genomic: GCTCAAGCATCACTTGAGCGGGATGATGAGgtatattcag ... tctgccgcagGATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCC
EST: gi|61119063|gb|DN560024.1|DN560024
EST:     GCTCAAGCATCACTTGAGCGGGATGATGAG                         GATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCTTCCCTTCGC
genomic: GCTCAAGCATCACTTGAGCGGGATGATGAGgtatattcag ... tctgccgcagGATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCCTCCCTTCGC
EST: gi|211224176|gb|FL079364.1|FL079364
EST:     GCTCAAGCATCACTTGAGCGGGATGATGAG                         GATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCCTCCCTTCGC
genomic: GCTCAAGCATCACTTGAGCGGGATGATGAGgtatattcag ... tctgccgcagGATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCCTCCCTTCGC
EST: gi|211224178|gb|FL079366.1|FL079366
EST:     GCTCAAGCATCACTTGAGCGGGATGATGAG                         GATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCCTCCCTTCGC
genomic: GCTCAAGCATCACTTGAGCGGGATGATGAGgtatattcag ... tctgccgcagGATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCCTCCCTTCGC
EST: gi|211224177|gb|FL079365.1|FL079365
EST:     GCTCAAGCATCACTTGAGCGGGATGATGAG                         GATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCCTCCCTTCGC
genomic: GCTCAAGCATCACTTGAGCGGGATGATGAGgtatattcag ... tctgccgcagGATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCCTCCCTTCGC
EST: gi|28986412|gb|CB351123.1|CB351123
EST:     AGGCTCAAGCATCACTTGAGCGGGATGATGAG                         GATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCCTCCCTTCGC
genomic: AGGCTCAAGCATCACTTGAGCGGGATGATGAGgtatattcag ... tctgccgcagGATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCCTCCCTTCGC
EST: gi|32931280|gb|CF036092.1|CF036092
EST:     GCTCAAGCATCACTTGAGCGGGATGATGAG                         GATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCTTCCCTTCGC
genomic: GCTCAAGCATCACTTGAGCGGGATGATGAGgtatattcag ... tctgccgcagGATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCCTCCCTTCGC

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), 47 (downstream exon)
Score: 105

GCTCAAGCATCACTTGAGCGGGATGATGAGgtatattcag ... tctgccgcagGATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCCTCCCTTCGCCTTGGAGACGACCAAGAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 75

GCTCAAGCATCACTTGAGCGGGATGATGAGgtatattcag ... tctgccgcagGATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCCTCCCTTCGCCTTGGAGACGACCAAGAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 72

GCTCAAGCATCACTTGAGCGGGATGATGAGgtatattcag ... tctgccgcagGATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCCTCCCTTCGCCTTGGAGACGACCAAGAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 107

GCTCAAGCATCACTTGAGCGGGATGATGAGgtatattcag ... tctgccgcagGATGTATATTTTGATGATGAATCTGCAGAGGTAGTAATCTCCTCCCTTCGCCTTGGAGACGACCAAGAAAG