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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGAAGCGGGCGCCCCCCGTCGTCGCGTTCCCCCGCGCCCGTAGCGGCGGCGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTGgtacgggtcttgctaccctaattgcggggtgggtgggatctcttctgaataagttctctcgagacgtagatcggcatggtaacgcttcagaaatgttggattgcacgcagcacgcgtgagcctgtttctatgcagtatgtactcccgattgctgacgcatcgtttgctgctgctattttgatttcctgaag

Basic information

species Zea mays
transcript GRMZM2G009320_T02
intron # 1
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|211165892|gb|FL257810.1|FL257810
EST:     CGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTG                         TTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
genomic: CGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTGgtacgggtct ... tttcctgaagTTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
EST: gi|211533149|gb|FL165887.1|FL165887
EST:     CGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTG                         TTAGCAAGAAGAAGGATGCCGCGGACAGGGCCAAGGAGGCCACAGCGGAGG
genomic: CGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTGgtacgggtct ... tttcctgaagTTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
EST: gi|211530143|gb|FL165872.1|FL165872
EST:     CGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTG                         TTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
genomic: CGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTGgtacgggtct ... tttcctgaagTTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
EST: gi|211530144|gb|FL165873.1|FL165873
EST:     CGCSGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTG                         TTNAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGG
genomic: CGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTGgtacgggtct ... tttcctgaagTT-AGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGG
EST: gi|211533145|gb|FL165883.1|FL165883
EST:     CGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTG                         TTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
genomic: CGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTGgtacgggtct ... tttcctgaagTTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
EST: gi|211533148|gb|FL165886.1|FL165886
EST:     CGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTG                         TTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
genomic: CGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTGgtacgggtct ... tttcctgaagTTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
EST: gi|211533143|gb|FL165881.1|FL165881
EST:     CGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTG                         TTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
genomic: CGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTGgtacgggtct ... tttcctgaagTTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
EST: gi|211530145|gb|FL165874.1|FL165874
EST:     CGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTG                         TTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
genomic: CGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTGgtacgggtct ... tttcctgaagTTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
EST: gi|5740068|gb|AI947758.1|AI947758
EST:     CGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTG                         TTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
genomic: CGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTGgtacgggtct ... tttcctgaagTTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
EST: gi|149204962|gb|ES700558.1|ES700558
EST:     CGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTG                         TTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
genomic: CGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTGgtacgggtct ... tttcctgaagTTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
EST: gi|211533141|gb|FL165879.1|FL165879
EST:     CGCCGTCGCCTCGTGCTCGGCCCCGCAGGAGTCGTCCACCTCCACCACTG                         TTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCTGAGG
genomic: CGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTGgtacgggtct ... tttcctgaagTTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG

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 3 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 105

GGGAAGCGGGCGCCCCCCGTCGTCGCGTTCCCCCGCGCCCGTAGCGGCGGCGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTGgtacgggtct ... tttcctgaagTTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGGCGGCGAAGCCGGCCGCGGCCGCCAAGCCAAAGAAGGCCGCGGCGCTGCC


Block sizes: 36 (upstream exon), 49 (downstream exon)
Score: 9

GGGAAGCGGGCGCCCCCCGTCGTCGCGTTCCCCCGCGCCCGTAGCGGCGGCGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTGgtacgggtct ... tttcctgaagTTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGGCGGCGAAGCCGGCCGCGGCCGCCAAGCCAAAGAAGGCCGCGGCGCTGCC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 29

GGGAAGCGGGCGCCCCCCGTCGTCGCGTTCCCCCGCGCCCGTAGCGGCGGCGCCGTCGCCTCGTGCTCGGCCGTGCAGGAGTCGTCCACCTCCACCACTGgtacgggtct ... tttcctgaagTTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGGCGGCGAAGCCGGCCGCGGCCGCCAAGCCAAAGAAGGCCGCGGCGCTGCC