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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGTCGCCCTCCCCATCTCACGCCGGCAGCAGACGCTCCCTTCCCGCCGTCGCGAGTCCCCGCGGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAGgtactcggtgcggcgtgagagtgctttgtacgctcacttttaagatcgttctccggtctccgctagcgatatgcatatgttgtttatcttattacactta...

Basic information

species Zea mays
transcript GRMZM2G072091_T01
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|76936315|gb|DV174671.1|DV174671
EST:     CGCGAGTCCCCGCGGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAG                         TTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGAAACGAGTGATT
genomic: CGCGAGTCCCCGCGGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAGgtactcggtg ... tcaaccttagTTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGAAACGAGTGATT
EST: gi|211319361|gb|FL167949.1|FL167949
EST:     CGCGAGTSCCCGCGGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAG                         TTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGAAACGAGTGATT
genomic: CGCGAGTCCCCGCGGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAGgtactcggtg ... tcaaccttagTTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGAAACGAGTGATT
EST: gi|211319359|gb|FL167947.1|FL167947
EST:     GGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAG                         TTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGAAACGAGTGATT
genomic: GGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAGgtactcggtg ... tcaaccttagTTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGAAACGAGTGATT
EST: gi|89247632|gb|DY619418.1|DY619418
EST:     CGCGAGTCCCCGCGGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAG                         TTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGAAACGAGTGATT
genomic: CGCGAGTCCCCGCGGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAGgtactcggtg ... tcaaccttagTTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGAAACGAGTGATT
EST: gi|76016703|gb|DT943873.1|DT943873
EST:     CGCGAGTCCCCGCGGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAG                         TTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGAAACGAGTGATT
genomic: CGCGAGTCCCCGCGGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAGgtactcggtg ... tcaaccttagTTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGAAACGAGTGATT
EST: gi|211319362|gb|FL167950.1|FL167950
EST:     CGCGAGTCCCCGCGGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAG                         TTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGAAACGAATGATT
genomic: CGCGAGTCCCCGCGGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAGgtactcggtg ... tcaaccttagTTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGAAACGAGTGATT
EST: gi|71309767|gb|DR791165.1|DR791165
EST:     CGCGAGTCCCCGCGGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAG                         TTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGGAACGAGTGATT
genomic: CGCGAGTCCCCGCGGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAGgtactcggtg ... tcaaccttagTTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGAAACGAGTGATT
EST: gi|71443889|gb|DR824939.1|DR824939
EST:     CGCGAGTCCCCGCGGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAG                         TTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGAAACGAGTGATT
genomic: CGCGAGTCCCCGCGGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAGgtactcggtg ... tcaaccttagTTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGAAACGAGTGATT
EST: gi|71446386|gb|DR827436.1|DR827436
EST:     CGCGAGTCCCCGCGGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAG                         TTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGAAACGAGTGATT
genomic: CGCGAGTCCCCGCGGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAGgtactcggtg ... tcaaccttagTTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGAAACGAGTGATT

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: 22 (upstream exon), 49 (downstream exon)
Score: 3

CCGTCGCCCTCCCCATCTCACGCCGGCAGCAGACGCTCCCTTCCCGCCGTCGCGAGTCCCCGCGGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAGgtactcggtg ... tcaaccttagTTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGAAACGAGTGATTCTCCACATGTGGTTTGCTTTGGTGAATTGCTAATTGACTTCGTCCCAAC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 9

CCGTCGCCCTCCCCATCTCACGCCGGCAGCAGACGCTCCCTTCCCGCCGTCGCGAGTCCCCGCGGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAGgtactcggtg ... tcaaccttagTTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGAAACGAGTGATTCTCCACATGTGGTTTGCTTTGGTGAATTGCTAATTGACTTCGTCCCAAC


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 21

CCGTCGCCCTCCCCATCTCACGCCGGCAGCAGACGCTCCCTTCCCGCCGTCGCGAGTCCCCGCGGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAGgtactcggtg ... tcaaccttagTTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGAAACGAGTGATTCTCCACATGTGGTTTGCTTTGGTGAATTGCTAATTGACTTCGTCCCAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 40

CCGTCGCCCTCCCCATCTCACGCCGGCAGCAGACGCTCCCTTCCCGCCGTCGCGAGTCCCCGCGGCGTTGTCTCTGCCGCGCCGCTACGGACACGCGCAGgtactcggtg ... tcaaccttagTTCCAACAAAGGCGATCGTAAACAGTGATGGCATCCCTGAAACGAGTGATTCTCCACATGTGGTTTGCTTTGGTGAATTGCTAATTGACTTCGTCCCAAC