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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGCTGAAATTTTGGTGTCCTTGCTCAGCCATGGGTAGTAGGAGgtatgcagtgctttaccttctgtagcggtcgacaattttgtttatgatacatcatgacatgatcaatgcaaaattggcag

Basic information

species Zea mays
transcript GRMZM2G013625_T04
intron # 1
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|78115431|gb|DV533819.1|DV533819
EST:     GGCTGAAATTTTGGTGTCCTTGCTCAGCCATGGGTAGTAGGAG                         ATATGACATTGATACGAGGAGATGTGGGATCCACTCAAGACCAACCAAATC
genomic: GGCTGAAATTTTGGTGTCCTTGCTCAGCCATGGGTAGTAGGAGgtatgcagtg ... aaattggcagATATGACATTGATACGAGGAGATGTGGGATCCACTCAAGACCAACCAAATC
EST: gi|71767635|gb|DR965572.1|DR965572
EST:     AGGCTGAAATTTTGGTGTCCTTGCTCAGCCATGGGTAGTAGGAG                         ATATGACATTGATACGAGGAGATGTGGGATCCACTCAAGACCAACCAAATC
genomic: AGGCTGAAATTTTGGTGTCCTTGCTCAGCCATGGGTAGTAGGAGgtatgcagtg ... aaattggcagATATGACATTGATACGAGGAGATGTGGGATCCACTCAAGACCAACCAAATC
EST: gi|91053085|gb|EB163503.1|EB163503
EST:     AGGCTGAAATTTTGGTGTCCTTGCTCAGCCATGGGTAGTAGGAG                         ATATGACATTGATACGAGGAGATGTGGGATCCACTCAAGACCAACCAAATC
genomic: AGGCTGAAATTTTGGTGTCCTTGCTCAGCCATGGGTAGTAGGAGgtatgcagtg ... aaattggcagATATGACATTGATACGAGGAGATGTGGGATCCACTCAAGACCAACCAAATC

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: 43 (upstream exon), 48 (downstream exon)
Score: 187

CAGGCTGAAATTTTGGTGTCCTTGCTCAGCCATGGGTAGTAGGAGgtatgcagtg ... aaattggcagATATGACATTGATACGAGGAGATGTGGGATCCACTCAAGACCAACCAAATCAATGTATCTGGATGCTCAACAAATCGTCAGCTGCCAAACTAGAGTGGGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 300

CAGGCTGAAATTTTGGTGTCCTTGCTCAGCCATGGGTAGTAGGAGgtatgcagtg ... aaattggcagATATGACATTGATACGAGGAGATGTGGGATCCACTCAAGACCAACCAAATCAATGTATCTGGATGCTCAACAAATCGTCAGCTGCCAAACTAGAGTGGGA


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 178

CAGGCTGAAATTTTGGTGTCCTTGCTCAGCCATGGGTAGTAGGAGgtatgcagtg ... aaattggcagATATGACATTGATACGAGGAGATGTGGGATCCACTCAAGACCAACCAAATCAATGTATCTGGATGCTCAACAAATCGTCAGCTGCCAAACTAGAGTGGGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 298

CAGGCTGAAATTTTGGTGTCCTTGCTCAGCCATGGGTAGTAGGAGgtatgcagtg ... aaattggcagATATGACATTGATACGAGGAGATGTGGGATCCACTCAAGACCAACCAAATCAATGTATCTGGATGCTCAACAAATCGTCAGCTGCCAAACTAGAGTGGGA