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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTCAGTTCACAGTATAAGATTACCAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAGgtatctatttactacccttattttgtatttcgatatactctaattatagggccctttgcatttgtgaagttaacttatgtcttctatatcatatcag

Basic information

species Zea mays
transcript GRMZM5G864266_T01
intron # 28
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G864266_T01 (Zea mays), 5'ss of exon 28
lower sequence: LOC_Os07g06950.1 (Oryza sativa), 5'ss of exon 26
GTGTCAGTTCACAGTATAAGATTACCAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAGgtatctatttactacccttattt----tgtat-ttcgatatactctaattatagggccctttgcatttgtgaagtt-aacttatgtcttctatatcatatcag---------------
||||||||||||||||| || || ||||| ||||||||||| || |||||||| |||||||| ||| | ||||||| | |||    |||||||||    ||| | ||| | || ||| | ||||        |||  |||   ||||| |||||||| | | | | |    || |               
GTGTCAGTTCACAGTATTAGGTTGCCAAAGAACAGCACTGTCGGTGATGTGCTAAATGATATAAAATCAAAGgtatatttttgtaccccttatttatggtgtgtattccacattctccagttattctatttgttggttttacaaagtttaacttatgccctatgtgtgccttcggctattaccaaaccag
















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|61118763|gb|DN559724.1|DN559724
EST:     TACCAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAG                         GTTGAGTTGTCTCATACCAATGCTGAGCTAAGATTACTTGAGGTCTTTTAT
genomic: TACCAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAGgtatctattt ... atcatatcagGTTGAGTTGTCTCATACCAATGCTGAGCTAAGATTACTTGAGGTCTTTTAT
EST: gi|78106266|gb|DV524684.1|DV524684
EST:     CAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAG                         GTTGAGTTGTCTCATACCAATGCTGAGCTAAGATTACTTGAGGTCTTTTAT
genomic: CAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAGgtatctattt ... atcatatcagGTTGAGTTGTCTCATACCAATGCTGAGCTAAGATTACTTGAGGTCTTTTAT
EST: gi|76909980|gb|DV163634.1|DV163634
EST:     TACCAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAG                         GTTGAGTTGTCTCATACCAATGCTGAGCTAAGATTACTTGAGGTCTTTTAT
genomic: TACCAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAGgtatctattt ... atcatatcagGTTGAGTTGTCTCATACCAATGCTGAGCTAAGATTACTTGAGGTCTTTTAT
EST: gi|60394863|gb|DN227732.1|DN227732
EST:     TACCAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAG                         GTTGAGTTGTCTCATACCAATGCTGAGCTAAGATTACTTGAGGTCTTTTAT
genomic: TACCAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAGgtatctattt ... atcatatcagGTTGAGTTGTCTCATACCAATGCTGAGCTAAGATTACTTGAGGTCTTTTAT
EST: gi|211394943|gb|FL031667.1|FL031667
EST:     TACCAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAG                         GTTGAGTTGTCTCATACCAATGCTGAGCTAAGATTACTTGAGGTCTTTTAT
genomic: TACCAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAGgtatctattt ... atcatatcagGTTGAGTTGTCTCATACCAATGCTGAGCTAAGATTACTTGAGGTCTTTTAT
EST: gi|67020350|gb|CO449099.1|CO449099
EST:     GTGCTGAATGATATCAAAACGAA-                         GTTGAGTTGTCTCATACCAATGCTGAGCTAAGATTACTTGAGGTCTTTTAT
genomic: GTGCTGAATGATATCAAAACGAAGgtatctattt ... atcatatcagGTTGAGTTGTCTCATACCAATGCTGAGCTAAGATTACTTGAGGTCTTTTAT

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: 189

GTGTCAGTTCACAGTATAAGATTACCAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAGgtatctattt ... atcatatcagGTTGAGTTGTCTCATACCAATGCTGAGCTAAGATTACTTGAGGTCTTTTATCACAAGATATACAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 85

GTGTCAGTTCACAGTATAAGATTACCAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAGgtatctattt ... atcatatcagGTTGAGTTGTCTCATACCAATGCTGAGCTAAGATTACTTGAGGTCTTTTATCACAAGATATACAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 80

GTGTCAGTTCACAGTATAAGATTACCAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAGgtatctattt ... atcatatcagGTTGAGTTGTCTCATACCAATGCTGAGCTAAGATTACTTGAGGTCTTTTATCACAAGATATACAAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 81

GTGTCAGTTCACAGTATAAGATTACCAAAAAACAGCACTGTTGGCGATGTGCTGAATGATATCAAAACGAAGgtatctattt ... atcatatcagGTTGAGTTGTCTCATACCAATGCTGAGCTAAGATTACTTGAGGTCTTTTATCACAAGATATACAAG