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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGACGCGAGAAGTCGAGGCGCCGCTGCTTGCTAGGACCGAGCTTCAGGAAGTCTCCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAGgtaccattcgatctctccgccttccggtctctgcgtcctcccggtcgacctacataatcatgcagttttctctgccttcggattctttttagcgttttaa...

Basic information

species Zea mays
transcript GRMZM2G063676_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|211188060|gb|FK976795.1|FK976795
EST:     AGTCTGCCAACGGCCCCGGCGCCGGCACGGCCTNCCCCGCGCCGCCACAG                         GGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAA
genomic: AGTCT-CCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAGgtaccattcg ... ctgtttgcagGGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAA
EST: gi|148939723|gb|EC884405.2|EC884405
EST:     AAGTCTCCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAG                         GGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAA
genomic: AAGTCTCCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAGgtaccattcg ... ctgtttgcagGGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAA
EST: gi|211188067|gb|FK976802.1|FK976802
EST:     AAGTCTCCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAG                         GGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAA
genomic: AAGTCTCCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAGgtaccattcg ... ctgtttgcagGGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAA
EST: gi|87153021|gb|DY397810.1|DY397810
EST:     AAGTCTCCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAG                         GGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAA
genomic: AAGTCTCCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAGgtaccattcg ... ctgtttgcagGGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAA
EST: gi|18648901|gb|BM497720.1|BM497720
EST:     AAGTCTCCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAG                         GGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAA
genomic: AAGTCTCCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAGgtaccattcg ... ctgtttgcagGGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAA
EST: gi|149112039|gb|EE191205.2|EE191205
EST:     AAGTCTCCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAG                         GGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAA
genomic: AAGTCTCCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAGgtaccattcg ... ctgtttgcagGGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAA
EST: gi|211188064|gb|FK976799.1|FK976799
EST:     AAGTCTCCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAG                         GGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAA
genomic: AAGTCTCCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAGgtaccattcg ... ctgtttgcagGGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAA
EST: gi|87153994|gb|DY398783.1|DY398783
EST:     AAGTCTCCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAG                         GGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAA
genomic: AAGTCTCCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAGgtaccattcg ... ctgtttgcagGGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAA
EST: gi|149078905|gb|EE167723.2|EE167723
EST:     AAGTCTCCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAG                         GGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAA
genomic: AAGTCTCCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAGgtaccattcg ... ctgtttgcagGGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAA

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: 241

GACGACGCGAGAAGTCGAGGCGCCGCTGCTTGCTAGGACCGAGCTTCAGGAAGTCTCCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAGgtaccattcg ... ctgtttgcagGGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAACCGAAGATGAGCGTTGTGGGATTCGATCTCGGCAATGAGAGCTGCATTG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 123

GACGACGCGAGAAGTCGAGGCGCCGCTGCTTGCTAGGACCGAGCTTCAGGAAGTCTCCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAGgtaccattcg ... ctgtttgcagGGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAACCGAAGATGAGCGTTGTGGGATTCGATCTCGGCAATGAGAGCTGCATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 156

GACGACGCGAGAAGTCGAGGCGCCGCTGCTTGCTAGGACCGAGCTTCAGGAAGTCTCCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAGgtaccattcg ... ctgtttgcagGGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAACCGAAGATGAGCGTTGTGGGATTCGATCTCGGCAATGAGAGCTGCATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

GACGACGCGAGAAGTCGAGGCGCCGCTGCTTGCTAGGACCGAGCTTCAGGAAGTCTCCAACGGCCCCGGCGCCGGCACGGCCTGCCCCGCGCCGCCACAGgtaccattcg ... ctgtttgcagGGATTGATTGTGATCAGATCTATTCTGTAGTGGTCAGCGGCTGAGGGTGAACCGAAGATGAGCGTTGTGGGATTCGATCTCGGCAATGAGAGCTGCATTG