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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagagcaccccggccgcccgtctctctctctatatctctctctgattatgatggattcgtcataatgctcaatgaagGTCGCTGCCAAGAGGATCGCCGCCGGCAAGTGGGGCTGCAACAGCGGCCAAGCCTGCGTCTCGCCGGACTACGTCGTCACTACCAAATCGTTCGCGCCAA

Basic information

species Zea mays
transcript GRMZM2G103546_T01
intron # 5
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|78082053|gb|DV510465.1|DV510465
EST:     AGCTCGGTGGCAAATGCCCTGTCGTCGTCGACTCCGACGTCAACCTCCAC                         GTCGCTGCCAAGAGGATCGCCGCCGGCAAGTGGGGCTGCAACAGCGGCCAA
genomic: AGCTCGGTGGCAAATGCCCTGTCGTCGTCGACTCCGACGTCAACCTCCACgtaaagagca ... ctcaatgaagGTCGCTGCCAAGAGGATCGCCGCCGGCAAGTGGGGCTGCAACAGCGGCCAA
EST: gi|71439164|gb|DR820214.1|DR820214
EST:     AGCTCGGTGGCAAATGCCCTGTCGTCGTCGACTCCGACGTCAACCTCCAC                         GTCGCTGCCAAGAGGATCGCCGCCGGCAAGTGGGGCTGCAACAGCGGCCAA
genomic: AGCTCGGTGGCAAATGCCCTGTCGTCGTCGACTCCGACGTCAACCTCCACgtaaagagca ... ctcaatgaagGTCGCTGCCAAGAGGATCGCCGCCGGCAAGTGGGGCTGCAACAGCGGCCAA

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: 45 (upstream exon), 49 (downstream exon)
Score: 12

ACGCATCGTCATGTCCTACGCTGCCAAGCACCTGACGCCCGTGGTCTTGGAGCTCGGTGGCAAATGCCCTGTCGTCGTCGACTCCGACGTCAACCTCCACgtaaagagca ... ctcaatgaagGTCGCTGCCAAGAGGATCGCCGCCGGCAAGTGGGGCTGCAACAGCGGCCAAGCCTGCGTCTCGCCGGACTACGTCGTCACTACCAAATCGTTCGCGCCAA


Block sizes: 39 (upstream exon), 25 (downstream exon)
Score: 2

ACGCATCGTCATGTCCTACGCTGCCAAGCACCTGACGCCCGTGGTCTTGGAGCTCGGTGGCAAATGCCCTGTCGTCGTCGACTCCGACGTCAACCTCCACgtaaagagca ... ctcaatgaagGTCGCTGCCAAGAGGATCGCCGCCGGCAAGTGGGGCTGCAACAGCGGCCAAGCCTGCGTCTCGCCGGACTACGTCGTCACTACCAAATCGTTCGCGCCAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 43

ACGCATCGTCATGTCCTACGCTGCCAAGCACCTGACGCCCGTGGTCTTGGAGCTCGGTGGCAAATGCCCTGTCGTCGTCGACTCCGACGTCAACCTCCACgtaaagagca ... ctcaatgaagGTCGCTGCCAAGAGGATCGCCGCCGGCAAGTGGGGCTGCAACAGCGGCCAAGCCTGCGTCTCGCCGGACTACGTCGTCACTACCAAATCGTTCGCGCCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctctctatatctctctctgattatgatggattcgtcataatgctcaatgaagGTCGCTGCCAAGAGGATCGCCGCCGGCAAGTGGGGCTGCAACAGCGGCCAAGCCTGCGTCTCGCCGGACTACGTCGTCACTACCAAATCGTTCGCGCCAA
                 ctctgat  putative branch site (score: 43)
                      attatgat  TA-rich tract