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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagtggtggtttgtcttggggatatgtttaagtgaaccattctgttcaagacctgcttaatttgtttcactaaacaaatactaattctgactaaactgtggaaccttttcagATGGTTTAAACCTGCTGCAGAATCTTTTGTGAAAGTACCGTTCCTTGGAGCCGTTTCGCATCTTACTCTGGCAGTTTGCCCATTTTGCGTTGCATTTGCT

Basic information

species Zea mays
transcript GRMZM2G165351_T04
intron # 6
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|32848065|gb|CD987746.1|CD987746
EST:     GGTCTACAAACATGCTTGGTGGCTCTGTTGTCAAG                         ATGGTTTAAACCTGCTGCAGAATCTTTTGTGAAAGTA
genomic: GGTCTACAAACATGCTTGGTGGCTCTGTTATCAAGgtacagtggt ... accttttcagATGGTTTAAACCTGCTGCAGAATCTTTTGTGAAAGTA




















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), 49 (downstream exon)
Score: 235

GGTCTACAAACATGCTTGGTGGCTCTGTTATCAAGgtacagtggt ... accttttcagATGGTTTAAACCTGCTGCAGAATCTTTTGTGAAAGTACCGTTCCTTGGAGCCGTTTCGCATCTTACTCTGGCAGTTTGCCCATTTTGCGTTGCATTTGCT


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

GGTCTACAAACATGCTTGGTGGCTCTGTTATCAAGgtacagtggt ... accttttcagATGGTTTAAACCTGCTGCAGAATCTTTTGTGAAAGTACCGTTCCTTGGAGCCGTTTCGCATCTTACTCTGGCAGTTTGCCCATTTTGCGTTGCATTTGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 261

GGTCTACAAACATGCTTGGTGGCTCTGTTATCAAGgtacagtggt ... accttttcagATGGTTTAAACCTGCTGCAGAATCTTTTGTGAAAGTACCGTTCCTTGGAGCCGTTTCGCATCTTACTCTGGCAGTTTGCCCATTTTGCGTTGCATTTGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 201

GGTCTACAAACATGCTTGGTGGCTCTGTTATCAAGgtacagtggt ... accttttcagATGGTTTAAACCTGCTGCAGAATCTTTTGTGAAAGTACCGTTCCTTGGAGCCGTTTCGCATCTTACTCTGGCAGTTTGCCCATTTTGCGTTGCATTTGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatttgtttcactaaacaaatactaattctgactaaactgtggaaccttttcagATGGTTTAAACCTGCTGCAGAATCTTTTGTGAAAGTACCGTTCCTTGGAGCCGTTTCGCATCTTACTCTGGCAGTTTGCCCATTTTGCGTTGCATTTGCT
                                              ccttttc  CT-rich tract
             taaacaaatactaatt  TA-rich tract