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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaattgattcatgcacgtgagttgggtcctcctccatgtgtgctctgcttacaatggcaagctctgtgtgtgcagACGAAACTGTATGAGGAAGACTGGATTGGTTTGAAGACACTGGATGAAGCAGGGCGGGTGAAGTTTGTGTCTGTGCCGGGAGGTCATCTTGGTATCTCCA

Basic information

species Zea mays
transcript GRMZM2G374779_T04
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|166579498|gb|EG058710.1|EG058710
EST:     TTGGTTACTACCCTGATGGAGCCTTTGATCCAGTTCTACCACCTCAGAAG                         ACGAAACTGTATGAGGAAGACTGGATTGGTTT
genomic: TTGGTTACTACCCTGATGGAGCCTTTGATCCAGTTCTACCACCTCAGAAGgtagaattga ... gtgtgtgcagACGAAACTGTATGAGGAAGACTGGATTGGTTT




















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: 47 (upstream exon), 49 (downstream exon)
Score: 99

TTTCAGGATGATGCAGTCCTGATACCACGAGAAACGGCATGGTTTGGTTACTACCCTGATGGAGCCTTTGATCCAGTTCTACCACCTCAGAAGgtagaattga ... gtgtgtgcagACGAAACTGTATGAGGAAGACTGGATTGGTTTGAAGACACTGGATGAAGCAGGGCGGGTGAAGTTTGTGTCTGTGCCGGGAGGTCATCTTGGTATCTCCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 196

TTTCAGGATGATGCAGTCCTGATACCACGAGAAACGGCATGGTTTGGTTACTACCCTGATGGAGCCTTTGATCCAGTTCTACCACCTCAGAAGgtagaattga ... gtgtgtgcagACGAAACTGTATGAGGAAGACTGGATTGGTTTGAAGACACTGGATGAAGCAGGGCGGGTGAAGTTTGTGTCTGTGCCGGGAGGTCATCTTGGTATCTCCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 188

TTTCAGGATGATGCAGTCCTGATACCACGAGAAACGGCATGGTTTGGTTACTACCCTGATGGAGCCTTTGATCCAGTTCTACCACCTCAGAAGgtagaattga ... gtgtgtgcagACGAAACTGTATGAGGAAGACTGGATTGGTTTGAAGACACTGGATGAAGCAGGGCGGGTGAAGTTTGTGTCTGTGCCGGGAGGTCATCTTGGTATCTCCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 137

TTTCAGGATGATGCAGTCCTGATACCACGAGAAACGGCATGGTTTGGTTACTACCCTGATGGAGCCTTTGATCCAGTTCTACCACCTCAGAAGgtagaattga ... gtgtgtgcagACGAAACTGTATGAGGAAGACTGGATTGGTTTGAAGACACTGGATGAAGCAGGGCGGGTGAAGTTTGTGTCTGTGCCGGGAGGTCATCTTGGTATCTCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgggtcctcctccatgtgtgctctgcttacaatggcaagctctgtgtgtgcagACGAAACTGTATGAGGAAGACTGGATTGGTTTGAAGACACTGGATGAAGCAGGGCGGGTGAAGTTTGTGTCTGTGCCGGGAGGTCATCTTGGTATCTCCA
                         tgcttac  putative branch site (score: 137)
                            ttacaat  TA-rich tract