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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGGGATGTTCTGATGTCTATGCATCATTTGATAAGTATGTTGCAGTGGAGAGGTTAGAAGGTGATAATAAGTATCAATCTGAGGAACATGGTCTACAGgtgagttaaacttggcagtgacgtttagagccttaaaatgtcgtttaaaacggtttgtatatgtgtagcatggtaatctggattgtgctgattcacatct...

Basic information

species Zea mays
transcript GRMZM2G071441_T01
intron # 4
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|32934895|gb|CF039707.1|CF039707
EST:     AGAGGTTAGAAGGTGATAATAAGTATCAATCTGAGGAACATGGTCTACAG                         GATGCCAAGAAAGGAATGCTTTTTATTGACTTTCCTCCAGTTCTGCAACTT
genomic: AGAGGTTAGAAGGTGATAATAAGTATCAATCTGAGGAACATGGTCTACAGgtgagttaaa ... tttttttcagGATGCCAAGAAAGGAATGCTTTTTATTGACTTTCCTCCAGTTCTGCAACTT
EST: gi|15590392|gb|BI675008.1|BI675008
EST:     AGAGGTTAGAAGGTGATAATAAGTATCAATCTGAGGAACATGGTCTACAG                         GATGCCAAGAAAGGAATGCTTTTTATCGACTTTCCTCCAGTTCTGCAACTT
genomic: AGAGGTTAGAAGGTGATAATAAGTATCAATCTGAGGAACATGGTCTACAGgtgagttaaa ... tttttttcagGATGCCAAGAAAGGAATGCTTTTTATTGACTTTCCTCCAGTTCTGCAACTT

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: 135

CAAGGGATGTTCTGATGTCTATGCATCATTTGATAAGTATGTTGCAGTGGAGAGGTTAGAAGGTGATAATAAGTATCAATCTGAGGAACATGGTCTACAGgtgagttaaa ... tttttttcagGATGCCAAGAAAGGAATGCTTTTTATTGACTTTCCTCCAGTTCTGCAACTTCAGTTAAAACGGTTTGAATATGATTTTGTGCGGGATACGATGCTCAAG


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

CAAGGGATGTTCTGATGTCTATGCATCATTTGATAAGTATGTTGCAGTGGAGAGGTTAGAAGGTGATAATAAGTATCAATCTGAGGAACATGGTCTACAGgtgagttaaa ... tttttttcagGATGCCAAGAAAGGAATGCTTTTTATTGACTTTCCTCCAGTTCTGCAACTTCAGTTAAAACGGTTTGAATATGATTTTGTGCGGGATACGATGCTCAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 93

CAAGGGATGTTCTGATGTCTATGCATCATTTGATAAGTATGTTGCAGTGGAGAGGTTAGAAGGTGATAATAAGTATCAATCTGAGGAACATGGTCTACAGgtgagttaaa ... tttttttcagGATGCCAAGAAAGGAATGCTTTTTATTGACTTTCCTCCAGTTCTGCAACTTCAGTTAAAACGGTTTGAATATGATTTTGTGCGGGATACGATGCTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 145

CAAGGGATGTTCTGATGTCTATGCATCATTTGATAAGTATGTTGCAGTGGAGAGGTTAGAAGGTGATAATAAGTATCAATCTGAGGAACATGGTCTACAGgtgagttaaa ... tttttttcagGATGCCAAGAAAGGAATGCTTTTTATTGACTTTCCTCCAGTTCTGCAACTTCAGTTAAAACGGTTTGAATATGATTTTGTGCGGGATACGATGCTCAAG