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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGTTGGCATCGCTGGCTCCTGCTCCGACTTCCTCGACTACCTCTATTCTTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagttcatatcttctccatcctaccctgcctggctgaacgtctgaacctgaacgccttcgcctactgcacgatgtcgtatgcag

Basic information

species Zea mays
transcript GRMZM5G824597_T02
intron # 2
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|211495258|gb|FL115225.1|FL115225
EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
EST: gi|94476029|gb|EB704987.1|EB704987
EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTGGTGGCTACCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCA
EST: gi|211495257|gb|FL115224.1|FL115224
EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
EST: gi|94479640|gb|EB708598.1|EB708598
EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
EST: gi|211495259|gb|FL115226.1|FL115226
EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
EST: gi|94476028|gb|EB704986.1|EB704986
EST:     CCGCGGCCCTAG                         GTCCTGATTCTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: CCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
EST: gi|211498135|gb|FL115228.1|FL115228
EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
EST: gi|166453393|gb|EG139875.1|EG139875
EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
EST: gi|211498137|gb|FL115230.1|FL115230
EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
EST: gi|211498138|gb|FL115231.1|FL115231
EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
EST: gi|211498134|gb|FL115227.1|FL115227
EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
EST: gi|211498136|gb|FL115229.1|FL115229
EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
EST: gi|94476020|gb|EB704978.1|EB704978
EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
EST: gi|94479639|gb|EB708597.1|EB708597
EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
EST: gi|76283433|gb|DV023001.1|DV023001
EST:     TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAG                         GTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA
genomic: TTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCA

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: 31

GACGTTGGCATCGCTGGCTCCTGCTCCGACTTCCTCGACTACCTCTATTCTTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCATCACTCTCTCTCTCGATAGAGTTGCCGCATCTGCGCTCAAAGATGTCAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 49

GACGTTGGCATCGCTGGCTCCTGCTCCGACTTCCTCGACTACCTCTATTCTTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCATCACTCTCTCTCTCGATAGAGTTGCCGCATCTGCGCTCAAAGATGTCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 63

GACGTTGGCATCGCTGGCTCCTGCTCCGACTTCCTCGACTACCTCTATTCTTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCATCACTCTCTCTCTCGATAGAGTTGCCGCATCTGCGCTCAAAGATGTCAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 27

GACGTTGGCATCGCTGGCTCCTGCTCCGACTTCCTCGACTACCTCTATTCTTCCTTGTCTTCCGACCAAGTCAGGCTCTTCTTCCCTGCCGCGGCCCTAGgtattcagtt ... tcgtatgcagGTCCTGATACTGCTGAGCTTGTGGCTACCAAGGCAAAGGGACTACCTCGCATCACTCTCTCTCTCGATAGAGTTGCCGCATCTGCGCTCAAAGATGTCAT