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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCGACTGCACAAATTGCAACCACTGGAATGGTCGCGCTTAGTTATGTACAGAAAGTTTCTGAAAAGgcgagtttttttcatatcatttttaatacttacatttttttgctttaatagcagcttcattacataagaaattgtgtgcag

Basic information

species Zea mays
transcript GRMZM2G120876_T01
intron # 8
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|84977313|gb|DW475735.1|DW475735
EST:     CAACCACTGGAATGGTCGCGCTTAGTTATGTACAGAAAGTTTCTGAAAAG                         GATTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACA
genomic: CAACCACTGGAATGGTCGCGCTTAGTTATGTACAGAAAGTTTCTGAAAAGgcgagttttt ... ttgtgtgcagGTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACA
EST: gi|149101278|gb|EE187391.2|EE187391
EST:     CAACCACTGGAATGGTCGCGCTTAGTTATGTACAGAAAGTTTCTGAAAAG                         GTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACA
genomic: CAACCACTGGAATGGTCGCGCTTAGTTATGTACAGAAAGTTTCTGAAAAGgcgagttttt ... ttgtgtgcagGTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACA
EST: gi|18660880|gb|BM501096.1|BM501096
EST:     CAACCACTGGAATGGTCGCGCTTAGTTATGTACAGAAAGTTTCTGAAAAG                         GTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACA
genomic: CAACCACTGGAATGGTCGCGCTTAGTTATGTACAGAAAGTTTCTGAAAAGgcgagttttt ... ttgtgtgcagGTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACA
EST: gi|211134090|gb|FL422145.1|FL422145
EST:     CAACCACTGGAATGGTCGCGCTTAGTTATGTACAGAAAGTTTCTGAAAAG                         GTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACA
genomic: CAACCACTGGAATGGTCGCGCTTAGTTATGTACAGAAAGTTTCTGAAAAGgcgagttttt ... ttgtgtgcagGTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACA
EST: gi|211538850|gb|FL377090.1|FL377090
EST:     CAACCACTGGAATGGTCGCGCTTAGTTATGTACAGAAAGTTTCTGAAAAG                         GTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACA
genomic: CAACCACTGGAATGGTCGCGCTTAGTTATGTACAGAAAGTTTCTGAAAAGgcgagttttt ... ttgtgtgcagGTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACA
EST: gi|211045137|gb|FL385512.1|FL385512
EST:     CAACCACTGGAATGGTCGCGCTWAGTTATGTACAGAAAGTTTCTGAAAAG                         GTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACA
genomic: CAACCACTGGAATGGTCGCGCTTAGTTATGTACAGAAAGTTTCTGAAAAGgcgagttttt ... ttgtgtgcagGTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACA

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: 199

GTTGCGACTGCACAAATTGCAACCACTGGAATGGTCGCGCTTAGTTATGTACAGAAAGTTTCTGAAAAGgcgagttttt ... ttgtgtgcagGTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 96

GTTGCGACTGCACAAATTGCAACCACTGGAATGGTCGCGCTTAGTTATGTACAGAAAGTTTCTGAAAAGgcgagttttt ... ttgtgtgcagGTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

GTTGCGACTGCACAAATTGCAACCACTGGAATGGTCGCGCTTAGTTATGTACAGAAAGTTTCTGAAAAGgcgagttttt ... ttgtgtgcagGTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 87

GTTGCGACTGCACAAATTGCAACCACTGGAATGGTCGCGCTTAGTTATGTACAGAAAGTTTCTGAAAAGgcgagttttt ... ttgtgtgcagGTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAG