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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTCATCAAGTAGCGCTGGGGAATCGTCTAGTATGGACATTGACAAAGgcaagttgtttgtttctgccctcattttgtaatgatacaccttattgtcaaacttcatttcttgggattatattcttaggacccaaaaagtttcaccctttgtctttgatgatacgcaatacaatatccaaaaggtttgctcgtgtgttaaatgcag

Basic information

species Zea mays
transcript GRMZM2G028733_T01
intron # 15
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|5608231|gb|AI901898.1|AI901898
EST:     GGGAATCGTCTAGTATGGACATTGACAAAG                         CTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTG
genomic: GGGAATCGTCTAGTATGGACATTGACAAAGgcaagttgtt ... ttaaatgcagCTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTG
EST: gi|33094354|gb|CF054348.1|CF054348
EST:     GAGTCATCAAGTAGCGCTGGGGAATCGTCTAGTATGGACATTGACAAAG                         CTGAGTCTTCTCTACCAAAGAAACAATTAACCGGCGCCTATGATTTGGTTG
genomic: GAGTCATCAAGTAGCGCTGGGGAATCGTCTAGTATGGACATTGACAAAGgcaagttgtt ... ttaaatgcagCTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTG
EST: gi|60354780|gb|DN221753.1|DN221753
EST:     GAG---TCAAGTAGCGCTGGGGAATCGTCTAGTATGGACATTGACAAAG                         CTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTG
genomic: GAGTCATCAAGTAGCGCTGGGGAATCGTCTAGTATGGACATTGACAAAGgcaagttgtt ... ttaaatgcagCTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTG
EST: gi|211276333|gb|FL459020.1|FL459020
EST:     GAGTCATCAAGTAGCGCTGGGGAATCGTCTAGTATGGACATTGACAAAG                         CTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTG
genomic: GAGTCATCAAGTAGCGCTGGGGAATCGTCTAGTATGGACATTGACAAAGgcaagttgtt ... ttaaatgcagCTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTG

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: 285

GAGTCATCAAGTAGCGCTGGGGAATCGTCTAGTATGGACATTGACAAAGgcaagttgtt ... ttaaatgcagCTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTGCTGTCTTGACACACAAGGGAAGAAGTGCAGACTCTGGCCACTATGTTGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 148

GAGTCATCAAGTAGCGCTGGGGAATCGTCTAGTATGGACATTGACAAAGgcaagttgtt ... ttaaatgcagCTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTGCTGTCTTGACACACAAGGGAAGAAGTGCAGACTCTGGCCACTATGTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 180

GAGTCATCAAGTAGCGCTGGGGAATCGTCTAGTATGGACATTGACAAAGgcaagttgtt ... ttaaatgcagCTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTGCTGTCTTGACACACAAGGGAAGAAGTGCAGACTCTGGCCACTATGTTGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 188

GAGTCATCAAGTAGCGCTGGGGAATCGTCTAGTATGGACATTGACAAAGgcaagttgtt ... ttaaatgcagCTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTGCTGTCTTGACACACAAGGGAAGAAGTGCAGACTCTGGCCACTATGTTGG