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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGACACAAACCAAAGAACTTCCAAATGACAAGTCAACAAAACCAAATATGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAGgtaaattctacctggtactttgctttcctaggacacatgttatcctctgtataagtatctttaactttcttttattcttaactcacttgcatccag

Basic information

species Zea mays
transcript GRMZM2G014902_T01
intron # 9
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|32925267|gb|CF030079.1|CF030079
EST:     TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAG                         AATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
genomic: TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAGgtaaattcta ... ttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
EST: gi|32926189|gb|CF031001.1|CF031001
EST:     TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAG                         AATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
genomic: TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAGgtaaattcta ... ttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
EST: gi|32926366|gb|CF031178.1|CF031178
EST:     TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAG                         AATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
genomic: TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAGgtaaattcta ... ttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
EST: gi|32926438|gb|CF031250.1|CF031250
EST:     TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAG                         AATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
genomic: TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAGgtaaattcta ... ttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
EST: gi|32942473|gb|CF047292.1|CF047292
EST:     TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAG                         AATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
genomic: TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAGgtaaattcta ... ttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
EST: gi|33098829|gb|CF058789.1|CF058789
EST:     TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAG                         AATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
genomic: TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAGgtaaattcta ... ttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
EST: gi|32925180|gb|CF029992.1|CF029992
EST:     TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCGTCTCTTCAG                         AATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
genomic: TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAGgtaaattcta ... ttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
EST: gi|33099128|gb|CF059088.1|CF059088
EST:     TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAG                         AATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
genomic: TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAGgtaaattcta ... ttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
EST: gi|32924981|gb|CF029793.1|CF029793
EST:     TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAG                         AATTTTCAAAGGAAGGAGTTGTCTGAAAAAAGAAGTCGCTCGGAAGTTCTT
genomic: TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAGgtaaattcta ... ttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
EST: gi|32849850|gb|CD989531.1|CD989531
EST:     GCATGTAAAAATGGTAGGCAATGCATCTCTTCAG                         AATTTTCAAAGGAAGGAGTTGTCTGANAAAGGAAGTCGCTCGGAAGTTCTT
genomic: GCATGTAAAAATGGTAGGCGATGCATCTCTTCAGgtaaattcta ... ttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
EST: gi|32924953|gb|CF029765.1|CF029765
EST:     TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAG                         AATTTTCAAAGGAAGGAGTTGTCTGAAAAAAGAAGTCGCTCGGAAGTTCTT
genomic: TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAGgtaaattcta ... ttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
EST: gi|32925264|gb|CF030076.1|CF030076
EST:     TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAG                         AATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
genomic: TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAGgtaaattcta ... ttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
EST: gi|32925917|gb|CF030729.1|CF030729
EST:     TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAG                         AATTTTCAAAGGAAGGAGTTGTCTGAAAAAAGAAGTCGCTCGGAAGTTCTT
genomic: TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAGgtaaattcta ... ttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
EST: gi|32926220|gb|CF031032.1|CF031032
EST:     GCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCCATCTCTTCAG                         AATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
genomic: GCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATG-CATCTCTTCAGgtaaattcta ... ttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
EST: gi|166631598|gb|EG276963.1|EG276963
EST:     TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAG                         AATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGT
genomic: TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAGgtaaattcta ... ttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGT
EST: gi|32938678|gb|CF043497.1|CF043497
EST:     TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAG                         AATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
genomic: TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAGgtaaattcta ... ttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
EST: gi|194716803|gb|FK933962.1|FK933962
EST:     TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAG                         AATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT
genomic: TGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAGgtaaattcta ... ttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTT

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: 47 (upstream exon), 49 (downstream exon)
Score: 129

CGAGACACAAACCAAAGAACTTCCAAATGACAAGTCAACAAAACCAAATATGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAGgtaaattcta ... ttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTTAATCTCTTCCGTGATGCCCCATCTGCATCATTTTCTTCAGTTAACAAAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 100

CGAGACACAAACCAAAGAACTTCCAAATGACAAGTCAACAAAACCAAATATGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAGgtaaattcta ... ttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTTAATCTCTTCCGTGATGCCCCATCTGCATCATTTTCTTCAGTTAACAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 145

CGAGACACAAACCAAAGAACTTCCAAATGACAAGTCAACAAAACCAAATATGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAGgtaaattcta ... ttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTTAATCTCTTCCGTGATGCCCCATCTGCATCATTTTCTTCAGTTAACAAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 119

CGAGACACAAACCAAAGAACTTCCAAATGACAAGTCAACAAAACCAAATATGCCCTTGAGCAATGGGCATGTAAAAATGGTAGGCGATGCATCTCTTCAGgtaaattcta ... ttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTTAATCTCTTCCGTGATGCCCCATCTGCATCATTTTCTTCAGTTAACAAAA