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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAGCTCCGCCCGTCGCTCCTCCTCCCCGCCACACTGCTCCCGTCGTCGTCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgcttgctcgctggcactcccatcccatgcaccagccaccacctctgttgatgacttgattcctaattaattaccttggcgacagcag

Basic information

species Zea mays
transcript GRMZM2G070605_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|149095141|gb|EE180755.2|EE180755
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|76914837|gb|DV165713.1|DV165713
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|149013546|gb|EE043037.2|EE043037
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|101394747|gb|EB819306.1|EB819306
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|148966890|gb|EE018012.2|EE018012
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|149075192|gb|EE163691.2|EE163691
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|148986357|gb|EE030094.2|EE030094
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|149000807|gb|EE038032.2|EE038032
EST:     TCGCAGGGCGCCAGGAGGCACACGCCATGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAGGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|149075125|gb|EE163618.2|EE163618
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|211407726|gb|FL367074.1|FL367074
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|149112153|gb|EE191267.2|EE191267
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|91050012|gb|EB160430.1|EB160430
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|149026859|gb|EE046212.2|EE046212
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|149097452|gb|EE183315.2|EE183315
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|149015293|gb|EE045098.2|EE045098
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|71766326|gb|DR964263.1|DR964263
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCTTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|211475706|gb|FL352571.1|FL352571
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|78077772|gb|DV506204.1|DV506204
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG

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), 48 (downstream exon)
Score: 46

GCCAGCTCCGCCCGTCGCTCCTCCTCCCCGCCACACTGCTCCCGTCGTCGTCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1019

GCCAGCTCCGCCCGTCGCTCCTCCTCCCCGCCACACTGCTCCCGTCGTCGTCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 15

GCCAGCTCCGCCCGTCGCTCCTCCTCCCCGCCACACTGCTCCCGTCGTCGTCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 484

GCCAGCTCCGCCCGTCGCTCCTCCTCCCCGCCACACTGCTCCCGTCGTCGTCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG