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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGATTGTGCTCCTCCTCGTCGCTGCTGCCGTACTCGCCTGCGCGGGCGGTGCGCGCGGGTTCTACCTCCCGGGCGTCGCCCCCGCCGGTTTCCTCAAGgtccgtccctcctttgtttttcttcttcctctgtgtttttcttttgtgtttttgctacgtgcgtcggtttgttgatctcggtaagtcctccactcaccccgctccgagcctgtgtggattgcag

Basic information

species Zea mays
transcript GRMZM2G409104_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|78110631|gb|DV529039.1|DV529039
EST:     GTGCGCGCGGGTTCTACCTCCCGGGCGTCGCCCCCGCCGGTTTCCTCAAG                         AAGGACCCGCTCGCCGTGAAGGTGAATCAGCTGAGCTCCATCAAGACGCAG
genomic: GTGCGCGCGGGTTCTACCTCCCGGGCGTCGCCCCCGCCGGTTTCCTCAAGgtccgtccct ... tggattgcagAAGGACCCGCTCGCCGTGAAGGTGAATCAGCTGAGCTCCATCAAGACGCAG
EST: gi|148965278|gb|EE016081.2|EE016081
EST:     GTGCGCGCGGGTTCTACCTCCCGGGCGTCGCCCCCGCCGGTTTCCTCAAG                         AAGGACCCGCTCGCCGTGAAGGTGAATCAGCTGAGCTCCATCAAGACGCAG
genomic: GTGCGCGCGGGTTCTACCTCCCGGGCGTCGCCCCCGCCGGTTTCCTCAAGgtccgtccct ... tggattgcagAAGGACCCGCTCGCCGTGAAGGTGAATCAGCTGAGCTCCATCAAGACGCAG
EST: gi|88752328|gb|DY536469.1|DY536469
EST:     GTGCGCGCGGGTTCTACCTCCCGGGCGTCGCCCCCGCCGGTTCCCTCAAG                         AAGGACCCGCTCGCCGTGAAGGTGAATCAGCTGAGCTCCATCAAGACGCAG
genomic: GTGCGCGCGGGTTCTACCTCCCGGGCGTCGCCCCCGCCGGTTTCCTCAAGgtccgtccct ... tggattgcagAAGGACCCGCTCGCCGTGAAGGTGAATCAGCTGAGCTCCATCAAGACGCAG
EST: gi|89250725|gb|DY622511.1|DY622511
EST:     GTGCGCGCGGGTTCTACCTCCCGGGCGTCGCCCCCGCCGGTTTCCTCAAG                         AAGGACCCGCTCGCCGTGAAGGTGAATCAGCTGAGCTCCATCAAGACGCAG
genomic: GTGCGCGCGGGTTCTACCTCCCGGGCGTCGCCCCCGCCGGTTTCCTCAAGgtccgtccct ... tggattgcagAAGGACCCGCTCGCCGTGAAGGTGAATCAGCTGAGCTCCATCAAGACGCAG
EST: gi|101390012|gb|EB816938.1|EB816938
EST:     GTGCGCGCGGGTTCTACCTCCCGGGCGTCGCCCCCGCCGGTTTCCTCAAG                         AAGGACCCGCTCGCCGTGAAGGTGAATCAGCTGAGCTCCATCAAGACGCAG
genomic: GTGCGCGCGGGTTCTACCTCCCGGGCGTCGCCCCCGCCGGTTTCCTCAAGgtccgtccct ... tggattgcagAAGGACCCGCTCGCCGTGAAGGTGAATCAGCTGAGCTCCATCAAGACGCAG
EST: gi|149013945|gb|EE043446.2|EE043446
EST:     GTGCGCGCGGGTTCTACCTCCCGGGCGTCGCCCCCGCCGGTTTCCTCAAG                         AAGGACCCGCTCGCCGTGAAGGTGAATCAGCTGAGCTCCATCAAGACGCAG
genomic: GTGCGCGCGGGTTCTACCTCCCGGGCGTCGCCCCCGCCGGTTTCCTCAAGgtccgtccct ... tggattgcagAAGGACCCGCTCGCCGTGAAGGTGAATCAGCTGAGCTCCATCAAGACGCAG
EST: gi|149102922|gb|EE288273.2|EE288273
EST:     GTGCGCGCGGGTTCTACCTCCCGGGCGTCGCCCCCGCCGGTTTCCTCAAG                         AAGGACCCGCTCGCCGTGAAGGTGAATCAGCTGAGCTCCATCAAGACGCAG
genomic: GTGCGCGCGGGTTCTACCTCCCGGGCGTCGCCCCCGCCGGTTTCCTCAAGgtccgtccct ... tggattgcagAAGGACCCGCTCGCCGTGAAGGTGAATCAGCTGAGCTCCATCAAGACGCAG
EST: gi|149096266|gb|EE181975.2|EE181975
EST:     GTGCGCGCGGGTTCTACCTCCCGGGCGTCGCCCCCGCCGGTTTCCTCAAG                         AAGGACCCGCTCGCCGTGAAGGTGAATCAGCTGAGCTCCATCAAGACGCAG
genomic: GTGCGCGCGGGTTCTACCTCCCGGGCGTCGCCCCCGCCGGTTTCCTCAAGgtccgtccct ... tggattgcagAAGGACCCGCTCGCCGTGAAGGTGAATCAGCTGAGCTCCATCAAGACGCAG

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: 55

GGTGATTGTGCTCCTCCTCGTCGCTGCTGCCGTACTCGCCTGCGCGGGCGGTGCGCGCGGGTTCTACCTCCCGGGCGTCGCCCCCGCCGGTTTCCTCAAGgtccgtccct ... tggattgcagAAGGACCCGCTCGCCGTGAAGGTGAATCAGCTGAGCTCCATCAAGACGCAGCTGCCCTACTCCTACTACTCCCTCCCCTTCTGCAGGCCGGGCACAATCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 74

GGTGATTGTGCTCCTCCTCGTCGCTGCTGCCGTACTCGCCTGCGCGGGCGGTGCGCGCGGGTTCTACCTCCCGGGCGTCGCCCCCGCCGGTTTCCTCAAGgtccgtccct ... tggattgcagAAGGACCCGCTCGCCGTGAAGGTGAATCAGCTGAGCTCCATCAAGACGCAGCTGCCCTACTCCTACTACTCCCTCCCCTTCTGCAGGCCGGGCACAATCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 99

GGTGATTGTGCTCCTCCTCGTCGCTGCTGCCGTACTCGCCTGCGCGGGCGGTGCGCGCGGGTTCTACCTCCCGGGCGTCGCCCCCGCCGGTTTCCTCAAGgtccgtccct ... tggattgcagAAGGACCCGCTCGCCGTGAAGGTGAATCAGCTGAGCTCCATCAAGACGCAGCTGCCCTACTCCTACTACTCCCTCCCCTTCTGCAGGCCGGGCACAATCG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 86

GGTGATTGTGCTCCTCCTCGTCGCTGCTGCCGTACTCGCCTGCGCGGGCGGTGCGCGCGGGTTCTACCTCCCGGGCGTCGCCCCCGCCGGTTTCCTCAAGgtccgtccct ... tggattgcagAAGGACCCGCTCGCCGTGAAGGTGAATCAGCTGAGCTCCATCAAGACGCAGCTGCCCTACTCCTACTACTCCCTCCCCTTCTGCAGGCCGGGCACAATCG