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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttaaattccatccggaatttggtattcatgtcatttcctgttttgttacttatctgcgggtaatgattcgtctgcagCAAACAAGGGGACTAGTTCAACGCCATTCCAGAAATCTCGTGGGTCAAATGATTGCCATG

Basic information

species Zea mays
transcript GRMZM2G110309_T01
intron # 4
splice site 3'
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|32920498|gb|CF025310.1|CF025310
EST:     AAACACGAAGAAGGTTACCGGAAGAGACTCCCATGCTGTCTCTTCGGAAG                         CAAACAAGGGGACTAGTTCAACGCCATTCCAGAAATCTCGTGGGTCAAATG
genomic: AAACACGAAGAAGGTTACCGGAAGAGACTCCCATGCTGTGTCTTTGGAAGgtttgtttaa ... tcgtctgcagCAAACAAGGGGACTAGTTCAACGCCATTCCAGAAATCTCGTGGGTCAAATG
EST: gi|148942281|gb|EC887299.2|EC887299
EST:     AAACACGAAGAAGGTTACCGGAAGAGACTCCCATGCTGTGTCTTTGGAAG                         CAAACAAGGGGACTAGTTCAACGCCATTCCAGAAATCTCGTGGGTCAAATG
genomic: AAACACGAAGAAGGTTACCGGAAGAGACTCCCATGCTGTGTCTTTGGAAGgtttgtttaa ... tcgtctgcagCAAACAAGGGGACTAGTTCAACGCCATTCCAGAAATCTCGTGGGTCAAATG

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), 42 (downstream exon)
Score: 56

GATCGCCATTCAGTTCTAGCATCTGAATTTGGTACCGCACATGGAAAGGGAAACACGAAGAAGGTTACCGGAAGAGACTCCCATGCTGTGTCTTTGGAAGgtttgtttaa ... tcgtctgcagCAAACAAGGGGACTAGTTCAACGCCATTCCAGAAATCTCGTGGGTCAAATGATTGCCATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 275

GATCGCCATTCAGTTCTAGCATCTGAATTTGGTACCGCACATGGAAAGGGAAACACGAAGAAGGTTACCGGAAGAGACTCCCATGCTGTGTCTTTGGAAGgtttgtttaa ... tcgtctgcagCAAACAAGGGGACTAGTTCAACGCCATTCCAGAAATCTCGTGGGTCAAATGATTGCCATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 216

GATCGCCATTCAGTTCTAGCATCTGAATTTGGTACCGCACATGGAAAGGGAAACACGAAGAAGGTTACCGGAAGAGACTCCCATGCTGTGTCTTTGGAAGgtttgtttaa ... tcgtctgcagCAAACAAGGGGACTAGTTCAACGCCATTCCAGAAATCTCGTGGGTCAAATGATTGCCATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 156

GATCGCCATTCAGTTCTAGCATCTGAATTTGGTACCGCACATGGAAAGGGAAACACGAAGAAGGTTACCGGAAGAGACTCCCATGCTGTGTCTTTGGAAGgtttgtttaa ... tcgtctgcagCAAACAAGGGGACTAGTTCAACGCCATTCCAGAAATCTCGTGGGTCAAATGATTGCCATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcatgtcatttcctgttttgttacttatctgcgggtaatgattcgtctgcagCAAACAAGGGGACTAGTTCAACGCCATTCCAGAAATCTCGTGGGTCAAATGATTGCCATG
                                            ttcgtct  CT-rich tract
                  ttttgtta  TA-rich tract