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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcgtacatctagacctagaggagttctcatgctcatgcgtacgtacatgacatgcggcgttgccagttgccaccgctcactatcccggccccctctcttaatttgctgctcttcattcagCTCAAGGCGCTGAGGCAGGAGAACGTGCGGCTGAACGAGCACAAGGGCAAGTCCAGGTGGGACGACAAGCCCGCGGCGCAGGCGCAGGCGGCGTCCCACC

Basic information

species Zea mays
transcript GRMZM2G179465_T03
intron # 2
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|211132788|gb|FL136694.1|FL136694
EST:     AGGACGAGCACGAGGACGCCCTCGCCAGGATCCATGTCCTCGACGCCCAG                         CTCAAGGCGCTGAGGCAGGAGAACGTGCGGCTGAACGAGCACAAGG
genomic: AGGACGAGCACGAGGACGCCCTCGCCAGGATCCATGTCCTCGACGCCCAGgtatgtcgta ... cttcattcagCTCAAGGCGCTGAGGCAGGAGAACGTGCGGCTGAACGAGCACAAGG




















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: 48 (upstream exon), 48 (downstream exon)
Score: 254

GGCGGCGCTCCGGGAGCGGGAAGCCGTGGAGGCGGTCCTTGACGACGTGGAGGACGAGCACGAGGACGCCCTCGCCAGGATCCATGTCCTCGACGCCCAGgtatgtcgta ... cttcattcagCTCAAGGCGCTGAGGCAGGAGAACGTGCGGCTGAACGAGCACAAGGGCAAGTCCAGGTGGGACGACAAGCCCGCGGCGCAGGCGCAGGCGGCGTCCCACC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 27

GGCGGCGCTCCGGGAGCGGGAAGCCGTGGAGGCGGTCCTTGACGACGTGGAGGACGAGCACGAGGACGCCCTCGCCAGGATCCATGTCCTCGACGCCCAGgtatgtcgta ... cttcattcagCTCAAGGCGCTGAGGCAGGAGAACGTGCGGCTGAACGAGCACAAGGGCAAGTCCAGGTGGGACGACAAGCCCGCGGCGCAGGCGCAGGCGGCGTCCCACC


Block sizes: 44 (upstream exon), 43 (downstream exon)
Score: 19

GGCGGCGCTCCGGGAGCGGGAAGCCGTGGAGGCGGTCCTTGACGACGTGGAGGACGAGCACGAGGACGCCCTCGCCAGGATCCATGTCCTCGACGCCCAGgtatgtcgta ... cttcattcagCTCAAGGCGCTGAGGCAGGAGAACGTGCGGCTGAACGAGCACAAGGGCAAGTCCAGGTGGGACGACAAGCCCGCGGCGCAGGCGCAGGCGGCGTCCCACC


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 67

GGCGGCGCTCCGGGAGCGGGAAGCCGTGGAGGCGGTCCTTGACGACGTGGAGGACGAGCACGAGGACGCCCTCGCCAGGATCCATGTCCTCGACGCCCAGgtatgtcgta ... cttcattcagCTCAAGGCGCTGAGGCAGGAGAACGTGCGGCTGAACGAGCACAAGGGCAAGTCCAGGTGGGACGACAAGCCCGCGGCGCAGGCGCAGGCGGCGTCCCACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgccaccgctcactatcccggccccctctcttaatttgctgctcttcattcagCTCAAGGCGCTGAGGCAGGAGAACGTGCGGCTGAACGAGCACAAGGGCAAGTCCAGGTGGGACGACAAGCCCGCGGCGCAGGCGCAGGCGGCGTCCCACC
                              tcttaat  putative branch site (score: 67)
                                           ctcttcattc  putative PPT
                              tcttaattt  TA-rich tract