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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCAGCACCACTCCACACCCACACTCCGCCCATCGGCTGCCATGGCGACCAGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAGgtaagctattcgattctgctctcctacaatagtttcgagcagcaatctcatccaatcccgtccgactcaagtcgtctttccctctcttgttacag

Basic information

species Zea mays
transcript GRMZM2G143767_T01
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|6536550|gb|AW224863.1|AW224863
EST:     AGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAG                         GCGCTCTACCTCGCTGCGGCCGCAGGGACTCCGGGTCCCCCACCGCGTGCC
genomic: AGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAGgtaagctatt ... cttgttacagGCGCTCTACCTCGCTGCGGCCGCAGGGTCTCCGGGTCCCCCACCGCGTGCC
EST: gi|211478458|gb|FL136947.1|FL136947
EST:     AGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAG                         GCGCTCTACCTCGCTGCGGCCGCAGGGACTCCGGGTCCCCCACCGCGTGCC
genomic: AGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAGgtaagctatt ... cttgttacagGCGCTCTACCTCGCTGCGGCCGCAGGGTCTCCGGGTCCCCCACCGCGTGCC
EST: gi|211478445|gb|FL136934.1|FL136934
EST:     AGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAG                         GCGCTCTACCTCGCTGCGGCCGCAGGGTCTCCGGGTCCCCCACCGCGTGCC
genomic: AGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAGgtaagctatt ... cttgttacagGCGCTCTACCTCGCTGCGGCCGCAGGGTCTCCGGGTCCCCCACCGCGTGCC
EST: gi|211478452|gb|FL136941.1|FL136941
EST:     AGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAG                         GCGCTCTACCTCGCTGCGGCCGCAGGGACTCCGGGTCCCCCACCGCGTGCC
genomic: AGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAGgtaagctatt ... cttgttacagGCGCTCTACCTCGCTGCGGCCGCAGGGTCTCCGGGTCCCCCACCGCGTGCC
EST: gi|211478451|gb|FL136940.1|FL136940
EST:     AGGGCAGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAG                         GCGCTCTACCTCGCTGCGGCCGCAGGGTCTCCGGGTCCCCCACCGCGTGCC
genomic: AGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAGgtaagctatt ... cttgttacagGCGCTCTACCTCGCTGCGGCCGCAGGGTCTCCGGGTCCCCCACCGCGTGCC
EST: gi|211478456|gb|FL136945.1|FL136945
EST:     AGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAG                         GCGCTCTACCTCGCTGCGGCCGCAGGGACTCCGGGTCCCCCACCGCGTGCC
genomic: AGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAGgtaagctatt ... cttgttacagGCGCTCTACCTCGCTGCGGCCGCAGGGTCTCCGGGTCCCCCACCGCGTGCC
EST: gi|211478450|gb|FL136939.1|FL136939
EST:     AGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAG                         GCGCTCTACCTCGCTGCGGCCGCAGGGACTCCGGGTCCCCCACCGCGTGCC
genomic: AGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAGgtaagctatt ... cttgttacagGCGCTCTACCTCGCTGCGGCCGCAGGGTCTCCGGGTCCCCCACCGCGTGCC
EST: gi|211478447|gb|FL136936.1|FL136936
EST:     AGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAG                         GCGCTCTACCTCGCTGCGGCCGCAGGGTCTCCGGGTCCCCCACCGCGTGCC
genomic: AGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAGgtaagctatt ... cttgttacagGCGCTCTACCTCGCTGCGGCCGCAGGGTCTCCGGGTCCCCCACCGCGTGCC
EST: gi|211478453|gb|FL136942.1|FL136942
EST:     AGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAG                         GCGCTCTACCTCGCTGCGGCCGCAGGGTCTCCGGGTCCCCCACCGCGTGCC
genomic: AGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAGgtaagctatt ... cttgttacagGCGCTCTACCTCGCTGCGGCCGCAGGGTCTCCGGGTCCCCCACCGCGTGCC
EST: gi|211376140|gb|FL136932.1|FL136932
EST:     AGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAG                         GCGCTCTACCTCGCTGCGGCCGCAGGGTCTCCGGGTCCCCCACCGCGTGCC
genomic: AGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAGgtaagctatt ... cttgttacagGCGCTCTACCTCGCTGCGGCCGCAGGGTCTCCGGGTCCCCCACCGCGTGCC
EST: gi|211478444|gb|FL136933.1|FL136933
EST:     AGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAG                         GCGCTCTACCTCGCTGCGGCCGCAGGGACTCCGGGTCCCCCACCGCGTGCC
genomic: AGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAGgtaagctatt ... cttgttacagGCGCTCTACCTCGCTGCGGCCGCAGGGTCTCCGGGTCCCCCACCGCGTGCC

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: 95

GGCAGCACCACTCCACACCCACACTCCGCCCATCGGCTGCCATGGCGACCAGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAGgtaagctatt ... cttgttacagGCGCTCTACCTCGCTGCGGCCGCAGGGTCTCCGGGTCCCCCACCGCGTGCCTCCCCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

GGCAGCACCACTCCACACCCACACTCCGCCCATCGGCTGCCATGGCGACCAGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAGgtaagctatt ... cttgttacagGCGCTCTACCTCGCTGCGGCCGCAGGGTCTCCGGGTCCCCCACCGCGTGCCTCCCCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

GGCAGCACCACTCCACACCCACACTCCGCCCATCGGCTGCCATGGCGACCAGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAGgtaagctatt ... cttgttacagGCGCTCTACCTCGCTGCGGCCGCAGGGTCTCCGGGTCCCCCACCGCGTGCCTCCCCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 88

GGCAGCACCACTCCACACCCACACTCCGCCCATCGGCTGCCATGGCGACCAGGGCGGCGGCGGCAGCCACGCTCACGGCGGCTACGTCCTCTCTTCTTAGgtaagctatt ... cttgttacagGCGCTCTACCTCGCTGCGGCCGCAGGGTCTCCGGGTCCCCCACCGCGTGCCTCCCCAAAG