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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctcctgctgcacctgcactgtcgttttaggccggggtttcagaattgcaacaagactactacatgagagctagctgaccaaatcttcttgcttttcttcttcttctgctgccagCTTCCATGCATCATGTGGCTCGCAATCTACAAGCCCAAACGGTTCAGCCTCTCATGGTTCACCAACTGG

Basic information

species Zea mays
transcript GRMZM2G127328_T01
intron # 5
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|211256088|gb|FL474859.1|FL474859
EST:     CGGATTCGCGTTCGCGCCAACAACNTATTTC                         TTTCCATGCATCATGTGGCTCGCAATCTACAAGCCCAAACGGTTCAGCCTC
genomic: CGGATTCGCGTTCGCGCCCACAACCTATTTCgtaagctcct ... ctgctgccagCTTCCATGCATCATGTGGCTCGCAATCTACAAGCCCAAACGGTTCAGCCTC
EST: gi|24934362|gb|CA452580.1|CA452580
EST:     GGCTGCTCAGCTTCTTCGGCGGATTCGCGTTCGCGCCCACAACCTATTTC                         CTTCCGTGCATCATGTGGCTCGCAATCTACAAGCCCAAACGGTTCAGCCTC
genomic: GGCTGCTCAGCTTCTTCGGCGGATTCGCGTTCGCGCCCACAACCTATTTCgtaagctcct ... ctgctgccagCTTCCATGCATCATGTGGCTCGCAATCTACAAGCCCAAACGGTTCAGCCTC
EST: gi|32840328|gb|CD980009.1|CD980009
EST:     GGCTGCTCAGCTTCTTCGGCGGATTCGCGTTCGCACCCACAACCTATTTC                         CTTCCCTGCATCATGTGGCTCGCAATCTACAAGCCCAAACGGTTCAGGCCT
genomic: GGCTGCTCAGCTTCTTCGGCGGATTCGCGTTCGCGCCCACAACCTATTTCgtaagctcct ... ctgctgccagCTTCCATGCATCATGTGGCTCGCAATCTACAAGCCCAAACGGTTCA-GCCT

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 179

CGTTCACAATGTTCATAGCCATCACGTTTCCCTTCTTCGACGGGCTGCTCAGCTTCTTCGGCGGATTCGCGTTCGCGCCCACAACCTATTTCgtaagctcct ... ctgctgccagCTTCCATGCATCATGTGGCTCGCAATCTACAAGCCCAAACGGTTCAGCCTCTCATGGTTCACCAACTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 127

CGTTCACAATGTTCATAGCCATCACGTTTCCCTTCTTCGACGGGCTGCTCAGCTTCTTCGGCGGATTCGCGTTCGCGCCCACAACCTATTTCgtaagctcct ... ctgctgccagCTTCCATGCATCATGTGGCTCGCAATCTACAAGCCCAAACGGTTCAGCCTCTCATGGTTCACCAACTGG


Block sizes: 34 (upstream exon), 46 (downstream exon)
Score: 2

CGTTCACAATGTTCATAGCCATCACGTTTCCCTTCTTCGACGGGCTGCTCAGCTTCTTCGGCGGATTCGCGTTCGCGCCCACAACCTATTTCgtaagctcct ... ctgctgccagCTTCCATGCATCATGTGGCTCGCAATCTACAAGCCCAAACGGTTCAGCCTCTCATGGTTCACCAACTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatgagagctagctgaccaaatcttcttgcttttcttcttcttctgctgccagCTTCCATGCATCATGTGGCTCGCAATCTACAAGCCCAAACGGTTCAGCCTCTCATGGTTCACCAACTGG
            agctgac  putative branch site (score: 2)
                       tcttcttgcttttctt  putative PPT
                    aaatctt  TA-rich tract