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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatccatgcacatacatttgatcgatcagcagctgattatgattgctggcttctgaacttttaattcgattttcttctgcgcagAACCAGTATGCGGCCGTGTTCTCGAGTATCGTGTCGAGAGCCGCGACGCTGGAGGTGCTATCAACCGGCGTGGCTGGGAACTACAATGGTGCATTGCAAG

Basic information

species Zea mays
transcript GRMZM2G122897_T01
intron # 3
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|101382676|gb|EB813392.1|EB813392
EST:     CCGTCGTCATCATGACCCATGCCAACCTCGTCGAAATCCTCATGGACGTG                         AACCAGTATGCGGCCGTGTTCTCGAGTATCGTGTCGAGAGCCGCGACGCTG
genomic: CCGTCGTCATCATGACCCATGCCAACCTCGTCGAAATCCTCATGGACGTGgtatgatcca ... ttctgcgcagAACCAGTATGCGGCCGTGTTCTCGAGTATCGTGTCGAGAGCCGCGACGCTG




















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), 48 (downstream exon)
Score: 152

GCTCGGGCCCAAGCCGTACGGGCTCAACTCGGAGGCGTCGCGTGACAGCGCCGTCGTCATCATGACCCATGCCAACCTCGTCGAAATCCTCATGGACGTGgtatgatcca ... ttctgcgcagAACCAGTATGCGGCCGTGTTCTCGAGTATCGTGTCGAGAGCCGCGACGCTGGAGGTGCTATCAACCGGCGTGGCTGGGAACTACAATGGTGCATTGCAAG


Block sizes: 41 (upstream exon), 47 (downstream exon)
Score: 22

GCTCGGGCCCAAGCCGTACGGGCTCAACTCGGAGGCGTCGCGTGACAGCGCCGTCGTCATCATGACCCATGCCAACCTCGTCGAAATCCTCATGGACGTGgtatgatcca ... ttctgcgcagAACCAGTATGCGGCCGTGTTCTCGAGTATCGTGTCGAGAGCCGCGACGCTGGAGGTGCTATCAACCGGCGTGGCTGGGAACTACAATGGTGCATTGCAAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 66

GCTCGGGCCCAAGCCGTACGGGCTCAACTCGGAGGCGTCGCGTGACAGCGCCGTCGTCATCATGACCCATGCCAACCTCGTCGAAATCCTCATGGACGTGgtatgatcca ... ttctgcgcagAACCAGTATGCGGCCGTGTTCTCGAGTATCGTGTCGAGAGCCGCGACGCTGGAGGTGCTATCAACCGGCGTGGCTGGGAACTACAATGGTGCATTGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagctgattatgattgctggcttctgaacttttaattcgattttcttctgcgcagAACCAGTATGCGGCCGTGTTCTCGAGTATCGTGTCGAGAGCCGCGACGCTGGAGGTGCTATCAACCGGCGTGGCTGGGAACTACAATGGTGCATTGCAAG
                             ttttaat  putative branch site (score: 66)
                                   ttcgattttcttct  CT-rich tract
                             ttttaattcgatttt  TA-rich tract