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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattaagcgatgatttttcagactgcaaacatttgctgcattgttcctgctgattttgagctttggtgttacagCTCCCTGATGAAGCCAAAGAGCTGGACAAAGAGCTGCGGCAGATAACCAAGCAGAAAAATGAGGCTGTACGTGGCCAAGATTTCGAGAAG

Basic information

species Zea mays
transcript GRMZM2G001084_T01
intron # 7
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|166681359|gb|EG166862.1|EG166862
EST:     GGCATGCGCAG                         CTCCCTGATGAAGCCAAAGAGCTGGACAAAGAGCTGCGGCAGATAACCAAG
genomic: GGCATGCGCAGgtattaagcg ... ggtgttacagCTCCCTGATGAAGCCAAAGAGCTGGACAAAGAGCTGCGGCAGATAACCAAG
EST: gi|211161958|gb|FL101571.1|FL101571
EST:     TTGACTTGATTGATGAAGCTGGATCTCGTGTTAGGCTGAGGCATGCGCAG                         CTCCCTGATGAAGCCAAAGAGCTGGACAAAGAGCTGCGGCAGATAACCAAG
genomic: TTGACTTGATTGATGAAGCTGGATCTCGTGTTAGGCTGAGGCATGCGCAGgtattaagcg ... ggtgttacagCTCCCTGATGAAGCCAAAGAGCTGGACAAAGAGCTGCGGCAGATAACCAAG
EST: gi|211161957|gb|FL101570.1|FL101570
EST:     TTGACTTGATTGATGAAGCTGGATCTCGTGTTAGGCTGAGGCATGCGCAG                         CTCCCTGATGAAGCCAAAGAGCTGGACAAAGAGCTGCGGCAGAT
genomic: TTGACTTGATTGATGAAGCTGGATCTCGTGTTAGGCTGAGGCATGCGCAGgtattaagcg ... ggtgttacagCTCCCTGATGAAGCCAAAGAGCTGGACAAAGAGCTGCGGCAGAT

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

CGATCGTTTCCTGCCTGACAAAGCCATTGACTTGATTGATGAAGCTGGATCTCGTGTTAGGCTGAGGCATGCGCAGgtattaagcg ... ggtgttacagCTCCCTGATGAAGCCAAAGAGCTGGACAAAGAGCTGCGGCAGATAACCAAGCAGAAAAATGAGGCTGTACGTGGCCAAGATTTCGAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 267

CGATCGTTTCCTGCCTGACAAAGCCATTGACTTGATTGATGAAGCTGGATCTCGTGTTAGGCTGAGGCATGCGCAGgtattaagcg ... ggtgttacagCTCCCTGATGAAGCCAAAGAGCTGGACAAAGAGCTGCGGCAGATAACCAAGCAGAAAAATGAGGCTGTACGTGGCCAAGATTTCGAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 166

CGATCGTTTCCTGCCTGACAAAGCCATTGACTTGATTGATGAAGCTGGATCTCGTGTTAGGCTGAGGCATGCGCAGgtattaagcg ... ggtgttacagCTCCCTGATGAAGCCAAAGAGCTGGACAAAGAGCTGCGGCAGATAACCAAGCAGAAAAATGAGGCTGTACGTGGCCAAGATTTCGAGAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 165

CGATCGTTTCCTGCCTGACAAAGCCATTGACTTGATTGATGAAGCTGGATCTCGTGTTAGGCTGAGGCATGCGCAGgtattaagcg ... ggtgttacagCTCCCTGATGAAGCCAAAGAGCTGGACAAAGAGCTGCGGCAGATAACCAAGCAGAAAAATGAGGCTGTACGTGGCCAAGATTTCGAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agactgcaaacatttgctgcattgttcctgctgattttgagctttggtgttacagCTCCCTGATGAAGCCAAAGAGCTGGACAAAGAGCTGCGGCAGATAACCAAGCAGAAAAATGAGGCTGTACGTGGCCAAGATTTCGAGAAG
                            tgctgat  putative branch site (score: 165)
       aaacattt  TA-rich tract