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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCACCTCGCTCCCCTCCAGTGGCCGCCAGCGCGGCTCAGCGGTCCATCCTCCTGACGCCACCTGCAACGGCGTCAGGCGGTGATCCATTCCAACTCGCGgtaagctctacccgtctcgcttgggttgctcgagaccaccaagtccatgcctaaacccaaccttttttccattatatttatatgtacaatactacaattt...

Basic information

species Zea mays
transcript GRMZM2G337311_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|211066926|gb|FK979249.1|FK979249
EST:     TCCTGACGCCACCTGCAACGGCGTCAGGCGGTGATCCATTCCAACTCGCG                         CTCCGTCCTGGCAATCACTTTGGGAAGGTGGTCAGTGGAATAGCTTTGCTT
genomic: TCCTGACGCCACCTGCAACGGCGTCAGGCGGTGATCCATTCCAACTCGCGgtaagctcta ... atttcattagCTCCGTCCTGGCAATCACTTTGGGAAGGTGGTCAGTGGAATAGCTTTGCTT
EST: gi|211066929|gb|FK979252.1|FK979252
EST:     TCCTGACGCCACCTGCAACGGCGTCA-GCGGTGATCCATTCCAACTCGCG                         CTCCGTCCTGGCAATCACTTTGGGAAGGTGGTCAGTGGAATAGCTTTGCTT
genomic: TCCTGACGCCACCTGCAACGGCGTCAGGCGGTGATCCATTCCAACTCGCGgtaagctcta ... atttcattagCTCCGTCCTGGCAATCACTTTGGGAAGGTGGTCAGTGGAATAGCTTTGCTT
EST: gi|211066928|gb|FK979251.1|FK979251
EST:     TCCTGACGCCACCKGCAACGGCGTCAGGCGGTGATCCATTCCAACTCGCG                         CTCCGTCCTGGCAATCACTTTGGGAAGGTGGTCAGTGGAATAGCTTTGCTT
genomic: TCCTGACGCCACCTGCAACGGCGTCAGGCGGTGATCCATTCCAACTCGCGgtaagctcta ... atttcattagCTCCGTCCTGGCAATCACTTTGGGAAGGTGGTCAGTGGAATAGCTTTGCTT
EST: gi|211066927|gb|FK979250.1|FK979250
EST:     TCCTGACGCCACCTGCAACGGCRTCARGCGGTGATCCATTCCAACTCGCG                         CTCCGTCCTGGCAATCACTTTGGGAAGGTGGTCAGTGGAATAGCTTTGCTT
genomic: TCCTGACGCCACCTGCAACGGCGTCAGGCGGTGATCCATTCCAACTCGCGgtaagctcta ... atttcattagCTCCGTCCTGGCAATCACTTTGGGAAGGTGGTCAGTGGAATAGCTTTGCTT

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: 48 (upstream exon), 49 (downstream exon)
Score: 42

CCCACCTCGCTCCCCTCCAGTGGCCGCCAGCGCGGCTCAGCGGTCCATCCTCCTGACGCCACCTGCAACGGCGTCAGGCGGTGATCCATTCCAACTCGCGgtaagctcta ... atttcattagCTCCGTCCTGGCAATCACTTTGGGAAGGTGGTCAGTGGAATAGCTTTGCTTAAAAAGCTTGAAGCAGTTGGTAGTGAAACTGGAAATCCTTCTTATCAAG


Block sizes: 48 (upstream exon), 34 (downstream exon)
Score: 9

CCCACCTCGCTCCCCTCCAGTGGCCGCCAGCGCGGCTCAGCGGTCCATCCTCCTGACGCCACCTGCAACGGCGTCAGGCGGTGATCCATTCCAACTCGCGgtaagctcta ... atttcattagCTCCGTCCTGGCAATCACTTTGGGAAGGTGGTCAGTGGAATAGCTTTGCTTAAAAAGCTTGAAGCAGTTGGTAGTGAAACTGGAAATCCTTCTTATCAAG


Block sizes: 42 (upstream exon), 46 (downstream exon)
Score: 2

CCCACCTCGCTCCCCTCCAGTGGCCGCCAGCGCGGCTCAGCGGTCCATCCTCCTGACGCCACCTGCAACGGCGTCAGGCGGTGATCCATTCCAACTCGCGgtaagctcta ... atttcattagCTCCGTCCTGGCAATCACTTTGGGAAGGTGGTCAGTGGAATAGCTTTGCTTAAAAAGCTTGAAGCAGTTGGTAGTGAAACTGGAAATCCTTCTTATCAAG