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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTAGTATTCCGAACGGACAGCCAAAGTTGCTTCTATCTTTCTTACCAGATTATCCGATGCTTAACTTTTTGCTTACTACGACGATATTTCTGTCGgtaagctccagcttcgaattgacttttctgtcgactggattatgaaaagatactcacttcatgacttgtgctgcag

Basic information

species Zea mays
transcript GRMZM2G076394_T01
intron # 14
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|78021364|gb|DV489751.1|DV489751
EST:     CAGATTATCCGATGCTTAACTTTTTGCTTACTACGACGATATTTCTGTCG                         GTATCATTCCGGGTGTTTAAGCTCACAAACGTACTGAAAGAGGCATTTATC
genomic: CAGATTATCCGATGCTTAACTTTTTGCTTACTACGACGATATTTCTGTCGgtaagctcca ... tgtgctgcagGTATCATTCCGGGTGTTTAAGCTCACAAACGTACTGAAAGAGGCATTTATC
EST: gi|12968792|gb|BG265828.1|BG265828
EST:     CAGATTATCCGATGCTTAACTTTTTGCTTACTACGACGATATTTCTGTCG                         GTATCATTCCGGGTGTTTAAGCTCACAAACGTACTGAAAGAGGCATTTATC
genomic: CAGATTATCCGATGCTTAACTTTTTGCTTACTACGACGATATTTCTGTCGgtaagctcca ... tgtgctgcagGTATCATTCCGGGTGTTTAAGCTCACAAACGTACTGAAAGAGGCATTTATC
EST: gi|6056529|gb|AW090919.1|AW090919
EST:     CAGATTATCCGATGCTTAACTTTTTGCTTACTACGACGATATTTCTGTCG                         GTATCATTCCGGGTGTTTAAGCTCACAAACGTACTGAAAGAGGCATTTATC
genomic: CAGATTATCCGATGCTTAACTTTTTGCTTACTACGACGATATTTCTGTCGgtaagctcca ... tgtgctgcagGTATCATTCCGGGTGTTTAAGCTCACAAACGTACTGAAAGAGGCATTTATC
EST: gi|5929073|gb|AW056365.1|AW056365
EST:     CAGATTATCCGATGCTTAACTTTTTGCTTACTACGACGATATTTCTGTCG                         GTATCATTCCGGGTGTTTAAGCTCACAAACGTACTGAAAGAGGCATTTATC
genomic: CAGATTATCCGATGCTTAACTTTTTGCTTACTACGACGATATTTCTGTCGgtaagctcca ... tgtgctgcagGTATCATTCCGGGTGTTTAAGCTCACAAACGTACTGAAAGAGGCATTTATC
EST: gi|5525684|gb|AI861577.1|AI861577
EST:     CAGATTATCCGATGCTTAACTTTTTGCTTACTACGACGATATTTCTGTCG                         GTATCATTCCGGGTGTTTAAGCTCACAAACGTACTGAAAGAGGCATTTATC
genomic: CAGATTATCCGATGCTTAACTTTTTGCTTACTACGACGATATTTCTGTCGgtaagctcca ... tgtgctgcagGTATCATTCCGGGTGTTTAAGCTCACAAACGTACTGAAAGAGGCATTTATC

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: 49 (upstream exon), 48 (downstream exon)
Score: 234

GTCTAGTATTCCGAACGGACAGCCAAAGTTGCTTCTATCTTTCTTACCAGATTATCCGATGCTTAACTTTTTGCTTACTACGACGATATTTCTGTCGgtaagctcca ... tgtgctgcagGTATCATTCCGGGTGTTTAAGCTCACAAACGTACTGAAAGAGGCATTTATCCCCACCAGGGACAACAAGTGTCTATATCAAAATTTTATTGCTGGAGTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 212

GTCTAGTATTCCGAACGGACAGCCAAAGTTGCTTCTATCTTTCTTACCAGATTATCCGATGCTTAACTTTTTGCTTACTACGACGATATTTCTGTCGgtaagctcca ... tgtgctgcagGTATCATTCCGGGTGTTTAAGCTCACAAACGTACTGAAAGAGGCATTTATCCCCACCAGGGACAACAAGTGTCTATATCAAAATTTTATTGCTGGAGTTG


Block sizes: 40 (upstream exon), 10 (downstream exon)
Score: 1

GTCTAGTATTCCGAACGGACAGCCAAAGTTGCTTCTATCTTTCTTACCAGATTATCCGATGCTTAACTTTTTGCTTACTACGACGATATTTCTGTCGgtaagctcca ... tgtgctgcagGTATCATTCCGGGTGTTTAAGCTCACAAACGTACTGAAAGAGGCATTTATCCCCACCAGGGACAACAAGTGTCTATATCAAAATTTTATTGCTGGAGTTG