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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctttccctcatgtggccgtttttcttgtcttctgctgctgctgcttcctgatcatttcatagttgtttatggtggtctatcttttacaagatt...

Basic information

species Zea mays
transcript GRMZM2G009021_T01
intron # 4
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|37396358|gb|CF635468.1|CF635468
EST:     GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAA                         CGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
genomic: GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
EST: gi|30087497|gb|CB885703.1|CB885703
EST:     GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAA                         CGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
genomic: GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
EST: gi|211120475|gb|FL454283.1|FL454283
EST:     CTGATGACACTGTATTGACCTGCTCACGTGGCTTCGACAA                         CGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
genomic: CTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
EST: gi|29945970|gb|CB815912.1|CB815912
EST:     GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAA                         CGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
genomic: GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGC
EST: gi|211502290|gb|FL183062.1|FL183062
EST:     GGCGATATTCCTGATGACACTGTATTGACCTGCTCACGTGGCTTCGACAA                         CGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTAT
genomic: GGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTAT

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), 48 (downstream exon)
Score: 140

ATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGCAGAACTCGGATGCTGCTTGCTGCATCGAGGCGGTAGATTGACCATCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 66

ATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGCAGAACTCGGATGCTGCTTGCTGCATCGAGGCGGTAGATTGACCATCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 112

ATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGCAGAACTCGGATGCTGCTTGCTGCATCGAGGCGGTAGATTGACCATCCAG


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

ATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGTTTCGACAAgtaagctctt ... tatcaaacagCGCACTGGAGTTTCTATCAACATGCAAGATTGCAAATCTGACTATTAGAGCAGAACTCGGATGCTGCTTGCTGCATCGAGGCGGTAGATTGACCATCCAG