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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAAGGCCCCATCAAGGATAGGCAGGCTGTTTCTCACAAAGAATGGGCAGCCTGCAAATTCGAAGCCAAAACCAAGGGAGTCTGCCCTGAAACCGTCAGgtacattggaaacgtgaaccactttgcatgctacatggtagtaggcattgctgcccggtatcacttcactggtattaaatcaaatcgtgcagtagctggtcgatgctttcgcaatttgcgagcatcgctaggcatgatgcgatcccatgacatcgatcaacgctcgtattcgtttacag

Basic information

species Zea mays
transcript GRMZM2G323622_T01
intron # 12
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|38687290|gb|CK144321.1|CK144321
EST:     GCCTGCAAATTCGAAGCCAAAACCAAGGGAGTCTGCCCTGAAACCGTCAG                         GTCGCACGACATCTACAGGAAGCCAGGCGACAGGAGGAGGATCTTCAGTGA
genomic: GCCTGCAAATTCGAAGCCAAAACCAAGGGAGTCTGCCCTGAAACCGTCAGgtacattgga ... tcgtttacagGTCGCACGACATCTACAGGAAGCCAGGCGACAGGAGGAGGATCTTCAGTGA
EST: gi|211227434|gb|FL027878.1|FL027878
EST:     GCCTGCCCCTTTTAAGCCAAAACCAAGGGAGTCTGCCCTGAAACCGTCAG                         GTCGCACGACATCTACAGGAAGCCAGGCGACAGGAGGAGGATCTTCAGTGA
genomic: GCCTGCAAATTCGAAGCCAAAACCAAGGGAGTCTGCCCTGAAACCGTCAGgtacattgga ... tcgtttacagGTCGCACGACATCTACAGGAAGCCAGGCGACAGGAGGAGGATCTTCAGTGA
EST: gi|211225387|gb|FL027877.1|FL027877
EST:     GCCTGCAAATTCGAAGCCAAAACCAAGGGAGTCTGCCCTGAAACCGTCAG                         GTCGCACGACATCTACAGGAAGCCAGGCGACAGGAGGAGGATCTTCAGTGA
genomic: GCCTGCAAATTCGAAGCCAAAACCAAGGGAGTCTGCCCTGAAACCGTCAGgtacattgga ... tcgtttacagGTCGCACGACATCTACAGGAAGCCAGGCGACAGGAGGAGGATCTTCAGTGA

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: 48 (upstream exon), 47 (downstream exon)
Score: 151

CAGAAGGCCCCATCAAGGATAGGCAGGCTGTTTCTCACAAAGAATGGGCAGCCTGCAAATTCGAAGCCAAAACCAAGGGAGTCTGCCCTGAAACCGTCAGgtacattgga ... tcgtttacagGTCGCACGACATCTACAGGAAGCCAGGCGACAGGAGGAGGATCTTCAGTGAAACCCCCGAAGAGGCGGTAGAGAAATAAAGAGCATCTGGGGTTTGTCAT


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 20

CAGAAGGCCCCATCAAGGATAGGCAGGCTGTTTCTCACAAAGAATGGGCAGCCTGCAAATTCGAAGCCAAAACCAAGGGAGTCTGCCCTGAAACCGTCAGgtacattgga ... tcgtttacagGTCGCACGACATCTACAGGAAGCCAGGCGACAGGAGGAGGATCTTCAGTGAAACCCCCGAAGAGGCGGTAGAGAAATAAAGAGCATCTGGGGTTTGTCAT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 51

CAGAAGGCCCCATCAAGGATAGGCAGGCTGTTTCTCACAAAGAATGGGCAGCCTGCAAATTCGAAGCCAAAACCAAGGGAGTCTGCCCTGAAACCGTCAGgtacattgga ... tcgtttacagGTCGCACGACATCTACAGGAAGCCAGGCGACAGGAGGAGGATCTTCAGTGAAACCCCCGAAGAGGCGGTAGAGAAATAAAGAGCATCTGGGGTTTGTCAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 75

CAGAAGGCCCCATCAAGGATAGGCAGGCTGTTTCTCACAAAGAATGGGCAGCCTGCAAATTCGAAGCCAAAACCAAGGGAGTCTGCCCTGAAACCGTCAGgtacattgga ... tcgtttacagGTCGCACGACATCTACAGGAAGCCAGGCGACAGGAGGAGGATCTTCAGTGAAACCCCCGAAGAGGCGGTAGAGAAATAAAGAGCATCTGGGGTTTGTCAT