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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggagaaacattatgttttcttccttgctttctttaatttgactatgtgaactatgattttttctaccattttcctaccatcacaattcgaataccaaaaccttgcagGGGCAGTCAGAAAACGGAAG

Basic information

species Zea mays
transcript GRMZM5G846339_T01
intron # 13
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|76915577|gb|DV166042.1|DV166042
EST:     TCGATTCGCAGTGGATCGTTCACCAAGTGGTTCCTTCTCTGGGGAACCAG                         GGGCAGTCAGAAAACGGAAG
genomic: TCGATTCGCAGTGGATCGTTCACCAAGTGGTTCCTTCTCTGGGGAACCAGgtaaggagaa ... aaccttgcagGGGCAGTCAGAAAACGGAAG
EST: gi|211501409|gb|FL138835.1|FL138835
EST:     TCGATTCGCAGTGGATCGKTCACCAAGTGGTTCCTTCTCTGGGGAACCAG                         GGGCAGTCAGAAAACGGAAGGGCGC
genomic: TCGATTCGCAGTGGATCGTTCACCAAGTGGTTCCTTCTCTGGGGAACCAGgtaaggagaa ... aaccttgcagGGGCAGTCAGAAAACGGAAGGGCGC

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: 46 (upstream exon), 47 (downstream exon)
Score: 44

CCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAAGTGGTTCCTTCTCTGGGGAACCAGgtaaggagaa ... aaccttgcagGGGCAGTCAGAAAACGGAAG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 40

CCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAAGTGGTTCCTTCTCTGGGGAACCAGgtaaggagaa ... aaccttgcagGGGCAGTCAGAAAACGGAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 30

CCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAAGTGGTTCCTTCTCTGGGGAACCAGgtaaggagaa ... aaccttgcagGGGCAGTCAGAAAACGGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 107

CCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAAGTGGTTCCTTCTCTGGGGAACCAGgtaaggagaa ... aaccttgcagGGGCAGTCAGAAAACGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgattttttctaccattttcctaccatcacaattcgaataccaaaaccttgcagGGGCAGTCAGAAAACGGAAG
     tttttcta  TA-rich tract