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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCCGCCCCGCTCTCCCACTCGTAGGTGTTCTCCCCGTCTCCGCCCGCACTCGCTCGTCCGCGCGCAGGAAGGTTGACCTGTCGAGGGCCGGCGAACCCGgtaagtaaggtaaccacgctgcttgctgttctcgtggatttcctcctggttcgcacggctctcctgcttcgattcttcggattcggaactgggggaataa...

Basic information

species Zea mays
transcript GRMZM2G107867_T02
intron # 1
splice site 5'
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|148999574|gb|EE036551.2|EE036551
EST:     TCGCTCGTCCGCGCGCAGGAAGGTTGACCTGTCGAGGGCCGGCGAACCCGGTAAGTAAG                 
genomic: TCGCTCGTCCGCGCGCAGGAAGGTTGACCTGTCGAGGGCCGGCGAACCC---------Ggtaagtaagg ... tt
EST: gi|60359581|gb|DN226554.1|DN226554
EST:     AAGGTTGACCTGTCGAGGGCCGGCGAACCCG                         AGTGAAAATGGATGGAAGTAGTAAAGGGAGTGGGCATTCTGAAGCATTAAG
genomic: AAGGTTGACCTGTCGAGGGCCGGCGAACCCGgtaagtaagg ... ttaatggcagAGTGAAAATGGATGGAAGTAGTAAAGGGAGTGGGCATTCTGAAGCATTAAG
EST: gi|71329108|gb|DR801263.1|DR801263
EST:     TCGCTCGTCCGCGCGCAGGAAGGTTGACCTGTCGAGGGCCGGCGAACCCG                         AGTGAAAATGGATGGAAGTAGTAAAGGGAGTGGGCATTCTGAAGCATTAAG
genomic: TCGCTCGTCCGCGCGCAGGAAGGTTGACCTGTCGAGGGCCGGCGAACCCGgtaagtaagg ... ttaatggcagAGTGAAAATGGATGGAAGTAGTAAAGGGAGTGGGCATTCTGAAGCATTAAG
EST: gi|89758870|gb|DY687889.1|DY687889
EST:     TCGCTCGTCCGCGCGCAGGAAGGTTGACCTGTCGAGGGCCGGCGAACCCG                         AGTGAAAATGGATGGAAGTAGTAAAGGGAGTGGGCATTCTGAAGCATTAAG
genomic: TCGCTCGTCCGCGCGCAGGAAGGTTGACCTGTCGAGGGCCGGCGAACCCGgtaagtaagg ... ttaatggcagAGTGAAAATGGATGGAAGTAGTAAAGGGAGTGGGCATTCTGAAGCATTAAG
EST: gi|71447675|gb|DR828725.1|DR828725
EST:     TCGCTCGTCCGCGCGCAGGAAGGTTGACCTGTCGAGGGCCGGCGAACCCG                         AGTGAAAATGGATGGAAGTAGTAAAGGGAGTGGGCATTCTGAAGCATTAAG
genomic: TCGCTCGTCCGCGCGCAGGAAGGTTGACCTGTCGAGGGCCGGCGAACCCGgtaagtaagg ... ttaatggcagAGTGAAAATGGATGGAAGTAGTAAAGGGAGTGGGCATTCTGAAGCATTAAG
EST: gi|58029553|gb|CX724980.1|CX724980
EST:     TCGCTCGTCCGCGCGCAGGAAGGTTGACCTGTCGGGGGCCGGCGAGCCCG                         AGTGAAAATGGATGGAAGTAGTAAAGGGAGTGGGCATTCTGAAGCATTAAG
genomic: TCGCTCGTCCGCGCGCAGGAAGGTTGACCTGTCGAGGGCCGGCGAACCCGgtaagtaagg ... ttaatggcagAGTGAAAATGGATGGAAGTAGTAAAGGGAGTGGGCATTCTGAAGCATTAAG
EST: gi|211440534|gb|FL230371.1|FL230371
EST:     TCGCTCGTCCGCGCGCAGGAAGGTTGACCTGTCGAGGGCCGGCGAACCCG                         AGTGAAAATGGATGGAAGTAGTAAAGGGAGTGGGCATTCTGAAGCATTAAG
genomic: TCGCTCGTCCGCGCGCAGGAAGGTTGACCTGTCGAGGGCCGGCGAACCCGgtaagtaagg ... ttaatggcagAGTGAAAATGGATGGAAGTAGTAAAGGGAGTGGGCATTCTGAAGCATTAAG
EST: gi|71437399|gb|DR818449.1|DR818449
EST:     CGCTCGTCCGCGCGCAGGAAGGTTGACCTGTCGAGGGCCGGCGAACCCG                         AGTGAAAATGGATGGAAGTAGTAAAGGGAGTGGGCATTCTGAAGCATTAAG
genomic: CGCTCGTCCGCGCGCAGGAAGGTTGACCTGTCGAGGGCCGGCGAACCCGgtaagtaagg ... ttaatggcagAGTGAAAATGGATGGAAGTAGTAAAGGGAGTGGGCATTCTGAAGCATTAAG
EST: gi|211427353|gb|FL101766.1|FL101766
EST:     TCGCTCGTCCGCGCGCAGGAAGGTTGACCTGTCGAGGGCCGGCGAACCCGGTAAGTAAG                 
genomic: TCGCTCGTCCGCGCGCAGGAAGGTTGACCTGTCGAGGGCCGGCGAACCC---------Ggtaagtaagg ... tt

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: 42 (upstream exon), 49 (downstream exon)
Score: 27

CTCCGCCCCGCTCTCCCACTCGTAGGTGTTCTCCCCGTCTCCGCCCGCACTCGCTCGTCCGCGCGCAGGAAGGTTGACCTGTCGAGGGCCGGCGAACCCGgtaagtaagg ... ttaatggcagAGTGAAAATGGATGGAAGTAGTAAAGGGAGTGGGCATTCTGAAGCATTAAGGAACTACAACCTGGGAAGAACTTTAGGTATCGGTACATTTGGAAAAGTG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 36

CTCCGCCCCGCTCTCCCACTCGTAGGTGTTCTCCCCGTCTCCGCCCGCACTCGCTCGTCCGCGCGCAGGAAGGTTGACCTGTCGAGGGCCGGCGAACCCGgtaagtaagg ... ttaatggcagAGTGAAAATGGATGGAAGTAGTAAAGGGAGTGGGCATTCTGAAGCATTAAGGAACTACAACCTGGGAAGAACTTTAGGTATCGGTACATTTGGAAAAGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 46

CTCCGCCCCGCTCTCCCACTCGTAGGTGTTCTCCCCGTCTCCGCCCGCACTCGCTCGTCCGCGCGCAGGAAGGTTGACCTGTCGAGGGCCGGCGAACCCGgtaagtaagg ... ttaatggcagAGTGAAAATGGATGGAAGTAGTAAAGGGAGTGGGCATTCTGAAGCATTAAGGAACTACAACCTGGGAAGAACTTTAGGTATCGGTACATTTGGAAAAGTG


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

CTCCGCCCCGCTCTCCCACTCGTAGGTGTTCTCCCCGTCTCCGCCCGCACTCGCTCGTCCGCGCGCAGGAAGGTTGACCTGTCGAGGGCCGGCGAACCCGgtaagtaagg ... ttaatggcagAGTGAAAATGGATGGAAGTAGTAAAGGGAGTGGGCATTCTGAAGCATTAAGGAACTACAACCTGGGAAGAACTTTAGGTATCGGTACATTTGGAAAAGTG