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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGCCATGGCGGCGCCAGGTCGAGCGGCGCTCCTGGCCGCCGCGCTCCTGTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcctttcgcggccccaccgtctcgttcgctctgcttcatccgctgattaagttttgttccgcgtcgggtggcag

Basic information

species Zea mays
transcript GRMZM2G020943_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|149005168|gb|EE039704.2|EE039704
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|211160636|gb|FL114499.1|FL114499
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGGCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|78114597|gb|DV532985.1|DV532985
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|91056271|gb|EB166689.1|EB166689
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGAAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|76912974|gb|DV164954.1|DV164954
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|211159050|gb|FL114492.1|FL114492
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGGCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|211160632|gb|FL114495.1|FL114495
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|31360064|gb|CD444421.1|CD444421
EST:     GTTCGGCACTTTCTTCCCATCCGCGTGCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGGCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|71764659|gb|DR962596.1|DR962596
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|211160637|gb|FL114500.1|FL114500
EST:     TTCGGCACTTTCTTCCCATCCGCGTCCTCTGCRATCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
genomic: TTCGGCACTTTCTTCCCATCCGCGTCCTCTGC-GTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|211160639|gb|FL114502.1|FL114502
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGGCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|149099000|gb|EE185013.2|EE185013
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|148958537|gb|EC904780.2|EC904780
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|211160642|gb|FL114505.1|FL114505
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGGCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|211160646|gb|FL114509.1|FL114509
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|211160635|gb|FL114498.1|FL114498
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGGCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|78118043|gb|DV536430.1|DV536430
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|89759931|gb|DY688587.1|DY688587
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|211160643|gb|FL114506.1|FL114506
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGGCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|74241599|gb|DT649513.1|DT649513
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|211162232|gb|FL114510.1|FL114510
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGGCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|149076865|gb|EE165521.2|EE165521
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|211160633|gb|FL114496.1|FL114496
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGGCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|211160640|gb|FL114503.1|FL114503
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         N
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcag-
EST: gi|211160640|gb|FL114503.1|FL114503
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         N
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcag-
EST: gi|211159051|gb|FL114493.1|FL114493
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|211160644|gb|FL114507.1|FL114507
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGGCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|71325268|gb|DR799321.1|DR799321
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|211162233|gb|FL114511.1|FL114511
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGGCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC
EST: gi|211160638|gb|FL114501.1|FL114501
EST:     GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAA                         GGATTGCGGGCAGGCTCCTGTCCACCACGGCGTCGGCAGTGGCCAAGCAGC
genomic: GTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGC

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: 48

GCGGCCATGGCGGCGCCAGGTCGAGCGGCGCTCCTGGCCGCCGCGCTCCTGTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 30

GCGGCCATGGCGGCGCCAGGTCGAGCGGCGCTCCTGGCCGCCGCGCTCCTGTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG


Block sizes: 42 (upstream exon), 35 (downstream exon)
Score: 4

GCGGCCATGGCGGCGCCAGGTCGAGCGGCGCTCCTGGCCGCCGCGCTCCTGTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 62

GCGGCCATGGCGGCGCCAGGTCGAGCGGCGCTCCTGGCCGCCGCGCTCCTGTTCGGCACTTTCTTCCCATCCGCGTCCTCTGCGTCCTCGTACCCCGCAAgtgagctcct ... cgggtggcagGGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG