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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAGgtacattgttgctactttaattgttttctgcttcacactaccttagcacgtcctgcaccttgtgactttgactcatttcttctaatttgatatataatat...

Basic information

species Zea mays
transcript GRMZM2G138125_T03
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138125_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os04g59624.3 (Oryza sativa), 5'ss of exon 10
CGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAGgta--------cattgttgctactttaattgttttctgcttcacactaccttagcacgtcctgcaccttgtgactttgactcatttcttctaatttgatatataatat
|  || |||||| | ||||| ||  | || ||||| || || || |||||||||||||||||| ||||||||||          ||| ||| ||  |||||  || | ||||| | | |     ||  |         ||||||| ||||    |||  |    ||||| |||       
CAAAATCTTGTTAGCGAGGGACACAACGTCTTAATCTTCTCGCAAACTCGTAAAATGCTAAACATTATTCAGgtgataaagtctattcttgttatgttaatctttgtttgctttatagtcatacagttctgtgattttcttgtgattttggtatattgtt----atttgttatcct----
















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|28873896|gb|CB329825.1|CB329825
EST:     ATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAG                         GAAGCTATAATATTAGAGGGCTATGCGTTTTTGCGCATTGATGGCACCACC
genomic: ATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAGgtacattgtt ... attgtaacagGAAGCTATAATATTAGAGGGCTATGCGTTTTTGCGCATTGATGGCACCACC
EST: gi|67035224|gb|CO463757.1|CO463757
EST:     ATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAG                         GAAGCTATAATATTAGAGGGCTATGCGTTTTTGCGCATTGATGGCACCACC
genomic: ATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAGgtacattgtt ... attgtaacagGAAGCTATAATATTAGAGGGCTATGCGTTTTTGCGCATTGATGGCACCACC
EST: gi|28987103|gb|CB351465.1|CB351465
EST:     ATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAG                         GAAGCTATAATATTAGAGGGCTATGCGTTTTTGCGCATTGATGGCACCACC
genomic: ATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAGgtacattgtt ... attgtaacagGAAGCTATAATATTAGAGGGCTATGCGTTTTTGCGCATTGATGGCACCACC
EST: gi|94475969|gb|EB704927.1|EB704927
EST:     ATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAG                         GAAGCTATAATATTAGAGGGCTATGCGTTTTTGCGCATTGATGGCACCACC
genomic: ATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAGgtacattgtt ... attgtaacagGAAGCTATAATATTAGAGGGCTATGCGTTTTTGCGCATTGATGGCACCACC
EST: gi|31909131|gb|CD650765.1|CD650765
EST:     ATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAG                         GAAGCTATAATATTAGAGGGCTATGCGTTTTTGCGCATTGATGGCACCACC
genomic: ATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAGgtacattgtt ... attgtaacagGAAGCTATAATATTAGAGGGCTATGCGTTTTTGCGCATTGATGGCACCACC
EST: gi|28930971|gb|CB334332.1|CB334332
EST:     ATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAG                         GAAGCTATAATATTAGAGGGCTATGCGTTTTTGCGCATTGATGGCACCACC
genomic: ATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAGgtacattgtt ... attgtaacagGAAGCTATAATATTAGAGGGCTATGCGTTTTTGCGCATTGATGGCACCACC

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: 241

CGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAGgtacattgtt ... attgtaacagGAAGCTATAATATTAGAGGGCTATGCGTTTTTGCGCATTGATGGCACCACCAAGGTTTCTGACCGGGAAAGGATTGTGAAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 23

CGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAGgtacattgtt ... attgtaacagGAAGCTATAATATTAGAGGGCTATGCGTTTTTGCGCATTGATGGCACCACCAAGGTTTCTGACCGGGAAAGGATTGTGAAG


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

CGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAGgtacattgtt ... attgtaacagGAAGCTATAATATTAGAGGGCTATGCGTTTTTGCGCATTGATGGCACCACCAAGGTTTCTGACCGGGAAAGGATTGTGAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 60

CGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAGgtacattgtt ... attgtaacagGAAGCTATAATATTAGAGGGCTATGCGTTTTTGCGCATTGATGGCACCACCAAGGTTTCTGACCGGGAAAGGATTGTGAAG