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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCGCGGCGACGCTGGATTCACTTAGATCCAACAGGGTAATCGGCACGGGGCAGCCTCTCCACCCATTCCCGCAGCCGGTTGGGCGAGTCGTCGGTTCAGgtttctttcaagctcctctgctcccttcaattccttcaaattcatgcggtcaagcctacgggaggttctgttgcccgtcccgtagctgcgcgttcctttt...

Basic information

species Zea mays
transcript GRMZM2G082181_T02
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|76915407|gb|DV165971.1|DV165971
EST:     GCAGCCTCTCCACCCATTCCCGCAGCCGGTTGGGCGAGTCGTCGGTTCAG                         ATAATAGACTGGGCGTGTGGATCCAAGAGGTTTGATCCCTTTAATTTGGAT
genomic: GCAGCCTCTCCACCCATTCCCGCAGCCGGTTGGGCGAGTCGTCGGTTCAGgtttctttca ... atcattgcagATAATAGACTGGGCGTGTGGATCCAAGAGGTTTGATCCCTTTAATTTGGAT
EST: gi|22491186|gb|BU051109.1|BU051109
EST:     GCAGCCTCTCCACCCATTCCCGCAGCCGGTTGGGCGAGTCGTCGGCTCAG                         ATAATAGACTGGTGCGTGTGGATCCAAGAGGTTTGATCCCTTTAATTTGGA
genomic: GCAGCCTCTCCACCCATTCCCGCAGCCGGTTGGGCGAGTCGTCGGTTCAGgtttctttca ... atcattgcagATAATAGACTGG-GCGTGTGGATCCAAGAGGTTTGATCCCTTTAATTTGGA
EST: gi|71770031|gb|DR967968.1|DR967968
EST:     GCAGCCTCTCCACCCATTCCCGCAGCCGGTTGGGCGAGTCGTCGGTTCAG                         ATAATAGACTGGGCGTGTGGATCCAAGAGGTTTGATCCCTTTAATTTGGAT
genomic: GCAGCCTCTCCACCCATTCCCGCAGCCGGTTGGGCGAGTCGTCGGTTCAGgtttctttca ... atcattgcagATAATAGACTGGGCGTGTGGATCCAAGAGGTTTGATCCCTTTAATTTGGAT
EST: gi|78089544|gb|DV517918.1|DV517918
EST:     CCCATTCCCGCAGCCGGTTGGGCGAGTCGTCGGTTCAG                         ATAATAGACTGGGCGTGTGGATCCAAGAGGTTTGATCCCTTTAATTTGGAT
genomic: CCCATTCCCGCAGCCGGTTGGGCGAGTCGTCGGTTCAGgtttctttca ... atcattgcagATAATAGACTGGGCGTGTGGATCCAAGAGGTTTGATCCCTTTAATTTGGAT
EST: gi|211504893|gb|FL311457.1|FL311457
EST:     GCAGCCTCTCCACCCATTCCCGCAGCCGGTTGGGCGAGTCGTCGGTTCAG                         ATAATAGACTGGGCGTGYGGATCCAAGAGGTTTGATCCCTTTAATTTGGAT
genomic: GCAGCCTCTCCACCCATTCCCGCAGCCGGTTGGGCGAGTCGTCGGTTCAGgtttctttca ... atcattgcagATAATAGACTGGGCGTGTGGATCCAAGAGGTTTGATCCCTTTAATTTGGAT
EST: gi|87152306|gb|DY397095.1|DY397095
EST:     GCAGCCTCTCCACCCATTCCCGCAGCCGGTTGGGCGAGTCGTCGGCTCAG                         ATAATAGACTGGGCGTGTGGATCCAAGAGGTTTGATCCCTTTAATTTGGAT
genomic: GCAGCCTCTCCACCCATTCCCGCAGCCGGTTGGGCGAGTCGTCGGTTCAGgtttctttca ... atcattgcagATAATAGACTGGGCGTGTGGATCCAAGAGGTTTGATCCCTTTAATTTGGAT
EST: gi|19351393|gb|BM895925.1|BM895925
EST:     GCAGCCTCTCCACCCATTCCCGCAGCCGGTTGGGCGAGTCGGCGGCTCAG                         ATAATAGACTGGGCGTGTGGATCCAAGAGGTTTGATCCCTTTAATTTGGAT
genomic: GCAGCCTCTCCACCCATTCCCGCAGCCGGTTGGGCGAGTCGTCGGTTCAGgtttctttca ... atcattgcagATAATAGACTGGGCGTGTGGATCCAAGAGGTTTGATCCCTTTAATTTGGAT

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), 45 (downstream exon)
Score: 69

CGCGCGGCGACGCTGGATTCACTTAGATCCAACAGGGTAATCGGCACGGGGCAGCCTCTCCACCCATTCCCGCAGCCGGTTGGGCGAGTCGTCGGTTCAGgtttctttca ... atcattgcagATAATAGACTGGGCGTGTGGATCCAAGAGGTTTGATCCCTTTAATTTGGATTGAAGTGCCAGCTTTCGGTCAGGAAGGTGATGCTGGATGATGCTGACGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 69

CGCGCGGCGACGCTGGATTCACTTAGATCCAACAGGGTAATCGGCACGGGGCAGCCTCTCCACCCATTCCCGCAGCCGGTTGGGCGAGTCGTCGGTTCAGgtttctttca ... atcattgcagATAATAGACTGGGCGTGTGGATCCAAGAGGTTTGATCCCTTTAATTTGGATTGAAGTGCCAGCTTTCGGTCAGGAAGGTGATGCTGGATGATGCTGACGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 93

CGCGCGGCGACGCTGGATTCACTTAGATCCAACAGGGTAATCGGCACGGGGCAGCCTCTCCACCCATTCCCGCAGCCGGTTGGGCGAGTCGTCGGTTCAGgtttctttca ... atcattgcagATAATAGACTGGGCGTGTGGATCCAAGAGGTTTGATCCCTTTAATTTGGATTGAAGTGCCAGCTTTCGGTCAGGAAGGTGATGCTGGATGATGCTGACGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 118

CGCGCGGCGACGCTGGATTCACTTAGATCCAACAGGGTAATCGGCACGGGGCAGCCTCTCCACCCATTCCCGCAGCCGGTTGGGCGAGTCGTCGGTTCAGgtttctttca ... atcattgcagATAATAGACTGGGCGTGTGGATCCAAGAGGTTTGATCCCTTTAATTTGGATTGAAGTGCCAGCTTTCGGTCAGGAAGGTGATGCTGGATGATGCTGACGG