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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatcacattacatgtacagttataggtgcaccaagccatttcttgctgtatctagtaaagaacgctgtgtaaaaatgcaaccaagcagcagcataatataaattgtgactgttttacttttttttcagGCAGAGATTGTCCAAACATGTCGAAGTATGGAGAAACCAGTCATTGTCGCTACAAATATGTTGGAAAGCATGATTGACCATCCTACTCCCACTAGGGCAG

Basic information

species Zea mays
transcript GRMZM2G033526_T02
intron # 7
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|60341691|gb|DN208664.1|DN208664
EST:     GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAG                         GCAGAGATTGTCCAAACATGTCGAAGTATGGAGAAACCAGTCATTGTCGCT
genomic: GTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... tttttttcagGCAGAGATTGTCCAAACATGTCGAAGTATGGAGAAACCAGTCATTGTCGCT
EST: gi|20208070|gb|BQ134159.1|BQ134159
EST:     TGAGGATGTTCCTTTGCTACAG                         GCAGAGATTGTCCAAACATGTCGAAGCATGGAGAAACCAGTCATTGTCGCT
genomic: TGAGGATGTTCCTTTGCTACAGgtgagatcac ... tttttttcagGCAGAGATTGTCCAAACATGTCGAAGTATGGAGAAACCAGTCATTGTCGCT

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: 486

GCAATGGTGGCGCGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... tttttttcagGCAGAGATTGTCCAAACATGTCGAAGTATGGAGAAACCAGTCATTGTCGCTACAAATATGTTGGAAAGCATGATTGACCATCCTACTCCCACTAGGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 254

GCAATGGTGGCGCGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... tttttttcagGCAGAGATTGTCCAAACATGTCGAAGTATGGAGAAACCAGTCATTGTCGCTACAAATATGTTGGAAAGCATGATTGACCATCCTACTCCCACTAGGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 258

GCAATGGTGGCGCGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... tttttttcagGCAGAGATTGTCCAAACATGTCGAAGTATGGAGAAACCAGTCATTGTCGCTACAAATATGTTGGAAAGCATGATTGACCATCCTACTCCCACTAGGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1160

GCAATGGTGGCGCGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcac ... tttttttcagGCAGAGATTGTCCAAACATGTCGAAGTATGGAGAAACCAGTCATTGTCGCTACAAATATGTTGGAAAGCATGATTGACCATCCTACTCCCACTAGGGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgcaaccaagcagcagcataatataaattgtgactgttttacttttttttcagGCAGAGATTGTCCAAACATGTCGAAGTATGGAGAAACCAGTCATTGTCGCTACAAATATGTTGGAAAGCATGATTGACCATCCTACTCCCACTAGGGCAG
                                   ctgttttacttttttt  CT-rich tract
                   ataatataaattgtga  TA-rich tract