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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTCGTCCACCTCCACCACTGGTACGGGTCTTGCTACCCTAATTGCGGGGTGGGTGGGATCTCTTCTGAATAAGTTCTCTCGAGACGTAGATCGGCATGgtaacgcttcagaaatgttggattgcacgcagcacgcgtgagcctgtttctatgcagtatgtactcccgattgctgacgcatcgtttgctgctgctattttgatttcctgaag

Basic information

species Zea mays
transcript GRMZM2G009320_T01
intron # 1
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|211285822|gb|FL376863.1|FL376863
EST:     GTGGGTGGGATCTCTTCTGAATAAGTTCTCTCGAGACGTAGATCGGCATG                         TTAGCAAGAAGAAGGATGCCGCG
genomic: GTGGGTGGGATCTCTTCTGAATAAGTTCTCTCGAGACGTAGATCGGCATGgtaacgcttc ... tttcctgaagTTAGCAAGAAGAAGGATGCCGCG
EST: gi|211185368|gb|FL306759.1|FL306759
EST:     GTGGGTGGGATCTCTTCTGAATAAGTTCTCTCGAGACGTAGATCGGCATG                         TTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
genomic: GTGGGTGGGATCTCTTCTGAATAAGTTCTCTCGAGACGTAGATCGGCATGgtaacgcttc ... tttcctgaagTTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
EST: gi|211534809|gb|FL337821.1|FL337821
EST:     NTGGGTGGGATCTCTTCTGAATAAGTTCTCTCGAGACGTAGATCGGCATG                         TTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
genomic: -TGGGTGGGATCTCTTCTGAATAAGTTCTCTCGAGACGTAGATCGGCATGgtaacgcttc ... tttcctgaagTTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
EST: gi|211423743|gb|FL401025.1|FL401025
EST:     TGTGGTGGGATCTCTTCTGAATAAGTTCTCTCGAGACGTAGATCGGCATG                         TTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG
genomic: TG-GGTGGGATCTCTTCTGAATAAGTTCTCTCGAGACGTAGATCGGCATGgtaacgcttc ... tttcctgaagTTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGG

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 3 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 38

GAGTCGTCCACCTCCACCACTGGTACGGGTCTTGCTACCCTAATTGCGGGGTGGGTGGGATCTCTTCTGAATAAGTTCTCTCGAGACGTAGATCGGCATGgtaacgcttc ... tttcctgaagTTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGGCGGCGAAGCCGGCCGCGGCCGCCAAGCCAAAGAAGGCCGCGGCGCTGCC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 3

GAGTCGTCCACCTCCACCACTGGTACGGGTCTTGCTACCCTAATTGCGGGGTGGGTGGGATCTCTTCTGAATAAGTTCTCTCGAGACGTAGATCGGCATGgtaacgcttc ... tttcctgaagTTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGGCGGCGAAGCCGGCCGCGGCCGCCAAGCCAAAGAAGGCCGCGGCGCTGCC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 20

GAGTCGTCCACCTCCACCACTGGTACGGGTCTTGCTACCCTAATTGCGGGGTGGGTGGGATCTCTTCTGAATAAGTTCTCTCGAGACGTAGATCGGCATGgtaacgcttc ... tttcctgaagTTAGCAAGAAGAAGGATGCCGCGGACGGGGCCAAGGAGGCCACAGCGGAGGCGGCGAAGCCGGCCGCGGCCGCCAAGCCAAAGAAGGCCGCGGCGCTGCC