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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtttgtaaatagcttctgttttgatcaaatttctgctgttccctttacacataactgagcaagaccccatttcaatgcacttaaaaagagagatttcttctgcttatgttattttgtattcttccaaagctcacctcagtaataaacacatgtaattttcccacagGTTGTAGAACTGTTCCCATCTTCCCGGGGCTTGGAAGTTACATGGTCCAGTGTGGTAAAGATCGGACAATCGCTGTACCGTGAGGCTCCTGGAAACGACC

Basic information

species Zea mays
transcript GRMZM2G454952_T01
intron # 12
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|211257055|gb|FK955913.1|FK955913
EST:     CATACATGCCATTGCCAAACGAGGAGATCATTAGTAAGGTTCAAAAGCAG                         GTTGTAGAACTGTTCCCATCTTCCCGGGGCTTGGAAGTTACATGGTCCAGT
genomic: CATACATGCCATTGCCAAACGAGGAGATCATTAGTAAGGTTCAAAAGCAGgtaggtttgt ... tttcccacagGTTGTAGAACTGTTCCCATCTTCCCGGGGCTTGGAAGTTACATGGTCCAGT
EST: gi|78109524|gb|DV527940.1|DV527940
EST:     CATACATGCCATTGCCAAACGAGGAGATCATTAGTAAGGTTCAAAAGCAG                         GTTGTAGAACTGTTCCCATCTTCCCGGGGCTTGGAAGTTACATGGTCCAGT
genomic: CATACATGCCATTGCCAAACGAGGAGATCATTAGTAAGGTTCAAAAGCAGgtaggtttgt ... tttcccacagGTTGTAGAACTGTTCCCATCTTCCCGGGGCTTGGAAGTTACATGGTCCAGT
EST: gi|7137692|gb|AW499222.1|AW499222
EST:     CATACATGCCATTGCCAAACGAGGAGATCATTAGTAAGGTTCAAAAGCAG                         GTTGTAGAACTGTTCCCATCTTCCCGGGGCTTGGAAGTTACATGGTCCAGT
genomic: CATACATGCCATTGCCAAACGAGGAGATCATTAGTAAGGTTCAAAAGCAGgtaggtttgt ... tttcccacagGTTGTAGAACTGTTCCCATCTTCCCGGGGCTTGGAAGTTACATGGTCCAGT

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: 103

AGCTGTGCTGACTCCTGGAGATCCATACATGCCATTGCCAAACGAGGAGATCATTAGTAAGGTTCAAAAGCAGgtaggtttgt ... tttcccacagGTTGTAGAACTGTTCCCATCTTCCCGGGGCTTGGAAGTTACATGGTCCAGTGTGGTAAAGATCGGACAATCGCTGTACCGTGAGGCTCCTGGAAACGACC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 122

AGCTGTGCTGACTCCTGGAGATCCATACATGCCATTGCCAAACGAGGAGATCATTAGTAAGGTTCAAAAGCAGgtaggtttgt ... tttcccacagGTTGTAGAACTGTTCCCATCTTCCCGGGGCTTGGAAGTTACATGGTCCAGTGTGGTAAAGATCGGACAATCGCTGTACCGTGAGGCTCCTGGAAACGACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

AGCTGTGCTGACTCCTGGAGATCCATACATGCCATTGCCAAACGAGGAGATCATTAGTAAGGTTCAAAAGCAGgtaggtttgt ... tttcccacagGTTGTAGAACTGTTCCCATCTTCCCGGGGCTTGGAAGTTACATGGTCCAGTGTGGTAAAGATCGGACAATCGCTGTACCGTGAGGCTCCTGGAAACGACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 414

AGCTGTGCTGACTCCTGGAGATCCATACATGCCATTGCCAAACGAGGAGATCATTAGTAAGGTTCAAAAGCAGgtaggtttgt ... tttcccacagGTTGTAGAACTGTTCCCATCTTCCCGGGGCTTGGAAGTTACATGGTCCAGTGTGGTAAAGATCGGACAATCGCTGTACCGTGAGGCTCCTGGAAACGACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtattcttccaaagctcacctcagtaataaacacatgtaattttcccacagGTTGTAGAACTGTTCCCATCTTCCCGGGGCTTGGAAGTTACATGGTCCAGTGTGGTAAAGATCGGACAATCGCTGTACCGTGAGGCTCCTGGAAACGACC
                agctcac  putative branch site (score: 414)
                                            ttttcccac  putative PPT
                                      atgtaatttt  TA-rich tract