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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcgcttataatatccacccatattcctgttccacaagcatgcacgtgctttgaattaccgtcctatttcttaccactttcccttctgtagCAAACTAACATGTATGGTGTGTCAAATGGCGACTTTGGTTCCG

Basic information

species Zea mays
transcript GRMZM2G363460_T05
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|31354170|gb|CD438527.1|CD438527
EST:     GGGCAATTAACAGTTCATGGAGAGCCTCTCAG                         CAAACTAACATGTATGGTGTGTCAAATGGCGACTTTGGTTCCG
genomic: GGGCAATTAACAGTTCATGGAGAGCCTCTCAGgtatgcgctt ... ccttctgtagCAAACTAACATGTATGGTGTGTCAAATGGCGACTTTGGTTCCG
EST: gi|20300876|gb|BQ163819.1|BQ163819
EST:     GGGCAATTAACAGNTCATGGAGAGCCTCTCAG                         CAAACTAACAT
genomic: GGGCAATTAACAGTTCATGGAGAGCCTCTCAGgtatgcgctt ... ccttctgtagCAAACTAACAT
EST: gi|31355282|gb|CD439639.1|CD439639
EST:     GGGCAATTAACAGTTCATGGAGAGCCTCTCAG                         CAAACTAACATGTATGGTGTGTCAAATGGCGACTTTGGTTCCG
genomic: GGGCAATTAACAGTTCATGGAGAGCCTCTCAGgtatgcgctt ... ccttctgtagCAAACTAACATGTATGGTGTGTCAAATGGCGACTTTGGTTCCG

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: 131

GGGCAATTAACAGTTCATGGAGAGCCTCTCAGgtatgcgctt ... ccttctgtagCAAACTAACATGTATGGTGTGTCAAATGGCGACTTTGGTTCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 208

GGGCAATTAACAGTTCATGGAGAGCCTCTCAGgtatgcgctt ... ccttctgtagCAAACTAACATGTATGGTGTGTCAAATGGCGACTTTGGTTCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 229

GGGCAATTAACAGTTCATGGAGAGCCTCTCAGgtatgcgctt ... ccttctgtagCAAACTAACATGTATGGTGTGTCAAATGGCGACTTTGGTTCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

GGGCAATTAACAGTTCATGGAGAGCCTCTCAGgtatgcgctt ... ccttctgtagCAAACTAACATGTATGGTGTGTCAAATGGCGACTTTGGTTCCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcatgcacgtgctttgaattaccgtcctatttcttaccactttcccttctgtagCAAACTAACATGTATGGTGTGTCAAATGGCGACTTTGGTTCCG
                               ttcttac  putative branch site (score: 169)
                      ccgtcctatttcttac  CT-rich tract
             tttgaatta  TA-rich tract