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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGCTCCCTCGTCCGGGCTCCTCCGCTCAAGTCGAGGAGTGCAGTGCGCTGTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAGgtaaacccacagctactacctgtgtgcttcgtaagacctatctatgcctgcacccaccagcacagggatatgtaccggcctgctcgtttcagctggaaca...

Basic information

species Zea mays
transcript GRMZM2G156218_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|211323100|gb|FL366933.1|FL366933
EST:     GTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAG                         CTTGTCCTAGAGGTGAAAGAACGGCTAGCAAGGGAGCACCCAAGCCTCCCC
genomic: GTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAGgtaaacccac ... ctgtgtgaagCTTGTCCTAGAGGTGAAAGAACGGCTAGCAAGGGAGCACCCAGGCCTCCCC
EST: gi|148937334|gb|EC881515.2|EC881515
EST:     GTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAG                         CTTGTCCTAGAGGTGAAAGAACGGCTAGCAAGGGAGCACCCAGGCCTCCCC
genomic: GTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAGgtaaacccac ... ctgtgtgaagCTTGTCCTAGAGGTGAAAGAACGGCTAGCAAGGGAGCACCCAGGCCTCCCC
EST: gi|211253175|gb|FL345473.1|FL345473
EST:     GTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAG                         CTTGTCCTAGAGGTGAAAGAACGGCTAGCAAGGGAGCACCCAAGCCTCCCC
genomic: GTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAGgtaaacccac ... ctgtgtgaagCTTGTCCTAGAGGTGAAAGAACGGCTAGCAAGGGAGCACCCAGGCCTCCCC
EST: gi|71438317|gb|DR819367.1|DR819367
EST:     GTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAG                         CTTGTCCTAGAGGTGAAAGAACGGCTAGCAAGGGAGCACCCAGGCCTCCCC
genomic: GTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAGgtaaacccac ... ctgtgtgaagCTTGTCCTAGAGGTGAAAGAACGGCTAGCAAGGGAGCACCCAGGCCTCCCC

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: 46 (upstream exon), 49 (downstream exon)
Score: 66

CCGCTCCCTCGTCCGGGCTCCTCCGCTCAAGTCGAGGAGTGCAGTGCGCTGTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAGgtaaacccac ... ctgtgtgaagCTTGTCCTAGAGGTGAAAGAACGGCTAGCAAGGGAGCACCCAGGCCTCCCCACGGGCAGGAACGGGAGGGACGATGACGACATGGTCCTCTGGTTCCTAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 77

CCGCTCCCTCGTCCGGGCTCCTCCGCTCAAGTCGAGGAGTGCAGTGCGCTGTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAGgtaaacccac ... ctgtgtgaagCTTGTCCTAGAGGTGAAAGAACGGCTAGCAAGGGAGCACCCAGGCCTCCCCACGGGCAGGAACGGGAGGGACGATGACGACATGGTCCTCTGGTTCCTAA


Block sizes: 28 (upstream exon), 47 (downstream exon)
Score: 26

CCGCTCCCTCGTCCGGGCTCCTCCGCTCAAGTCGAGGAGTGCAGTGCGCTGTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAGgtaaacccac ... ctgtgtgaagCTTGTCCTAGAGGTGAAAGAACGGCTAGCAAGGGAGCACCCAGGCCTCCCCACGGGCAGGAACGGGAGGGACGATGACGACATGGTCCTCTGGTTCCTAA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 143

CCGCTCCCTCGTCCGGGCTCCTCCGCTCAAGTCGAGGAGTGCAGTGCGCTGTCCAAGCGCCGCCCCGCCAGGAGCCAGCGGTGCCACCTCCACCTCCAAGgtaaacccac ... ctgtgtgaagCTTGTCCTAGAGGTGAAAGAACGGCTAGCAAGGGAGCACCCAGGCCTCCCCACGGGCAGGAACGGGAGGGACGATGACGACATGGTCCTCTGGTTCCTAA