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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtccattttacacacactcaaaatttgcagatgccatgagaaccttttaattgcttactacatcatgcttttcctggccttcccattccaatacttgctgtagaactagttgcactgttttgtgcagttacatcaaggccatattaataattagtctcctgttttccgtttacagGATTTTGGGAGTGCGATTCATGGCGTTGATACAG

Basic information

species Zea mays
transcript GRMZM2G421829_T01
intron # 11
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|76017890|gb|DT945060.1|DT945060
EST:     CTCATATGGATCTGGATATGATGAATGACTATGAAGTGAAGGAATGCAAC                         GATTTTGGGAGTGCGATTCATGGCGTTGATACAG
genomic: CTCATATGGATCTGGATATGATGAATGACTATGAAGTGAAGGAATGCAACgtgagtccat ... ccgtttacagGATTTTGGGAGTGCGATTCATGGCGTTGATACAG




















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), 34 (downstream exon)
Score: 200

CGCGTCTGCTACGGGAGATAATTCTGGCTTCCAAGAAAACAACACGGGTTCTCATATGGATCTGGATATGATGAATGACTATGAAGTGAAGGAATGCAACgtgagtccat ... ccgtttacagGATTTTGGGAGTGCGATTCATGGCGTTGATACAG


Block sizes: 47 (upstream exon), 34 (downstream exon)
Score: 83

CGCGTCTGCTACGGGAGATAATTCTGGCTTCCAAGAAAACAACACGGGTTCTCATATGGATCTGGATATGATGAATGACTATGAAGTGAAGGAATGCAACgtgagtccat ... ccgtttacagGATTTTGGGAGTGCGATTCATGGCGTTGATACAG


Block sizes: 49 (upstream exon), 34 (downstream exon)
Score: 90

CGCGTCTGCTACGGGAGATAATTCTGGCTTCCAAGAAAACAACACGGGTTCTCATATGGATCTGGATATGATGAATGACTATGAAGTGAAGGAATGCAACgtgagtccat ... ccgtttacagGATTTTGGGAGTGCGATTCATGGCGTTGATACAG


Block sizes: 46 (upstream exon), 34 (downstream exon)
Score: 90

CGCGTCTGCTACGGGAGATAATTCTGGCTTCCAAGAAAACAACACGGGTTCTCATATGGATCTGGATATGATGAATGACTATGAAGTGAAGGAATGCAACgtgagtccat ... ccgtttacagGATTTTGGGAGTGCGATTCATGGCGTTGATACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcagttacatcaaggccatattaataattagtctcctgttttccgtttacagGATTTTGGGAGTGCGATTCATGGCGTTGATACAG
                     tattaat  putative branch site (score: 90)
                                  tctcctgttttccgtt  putative PPT
                    atattaataattagtc  TA-rich tract