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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTATGTGTTGTTGGGGTTGCACGCACCCCAATGGGCGGTTTCCTTGGTGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccgaatcttctctgcatttacatccgagctctgaacatggtcatggctgggggctgttag

Basic information

species Zea mays
transcript GRMZM5G866758_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G866758_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 3
ATGTATGTGTTGTTGGGGTTGCACGCACCCCAATGGGCGGTTTCCTTGGTGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccgaatcttctc------tgcatttacatccgagctctgaacatggtcatggctgggggctgttag------------
||||||||||||||||||||||||||||||| ||||| |||||||| |||||| ||||| ||||| | ||||| |||||||| || |||| |||| ||||||| | | | ||||||||      || || |  |   |  || | |||      ||  ||     |  | ||            
ATGTATGTGTTGTTGGGGTTGCACGCACCCCTATGGGTGGTTTCCTAGGTGCCCTGTCTTCCTTGTCAGCTACCAAACTTGGTTCCATAGCAATTGAAGgtgataccagtatcttctcatatgctgtatgtgtaattgttcttttaacccaaatataactaacatc-atcagtgtggtgatcag
















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|101395310|gb|EB819585.1|EB819585
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|78087735|gb|DV516128.1|DV516128
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|148991412|gb|EE032913.2|EE032913
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|33771209|gb|CF273388.1|CF273388
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|148999650|gb|EE036638.2|EE036638
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|149101180|gb|EE187290.2|EE187290
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|149017000|gb|EE045657.2|EE045657
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|211492112|gb|FL334536.1|FL334536
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|211211228|gb|FL354194.1|FL354194
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|211145464|gb|FL359543.1|FL359543
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|76284260|gb|DV023828.1|DV023828
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|32864391|gb|CF004073.1|CF004073
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|211372672|gb|FL327042.1|FL327042
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|149081077|gb|EE170177.2|EE170177
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|148983224|gb|EE029187.2|EE029187
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|148965993|gb|EE016923.2|EE016923
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|93281705|gb|EB673969.1|EB673969
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|149009773|gb|EE041672.2|EE041672
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|211107249|gb|FL258173.1|FL258173
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAA-                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|76017959|gb|DT945129.1|DT945129
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|71327673|gb|DR800451.1|DR800451
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|31353258|gb|CD437615.1|CD437615
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|78091716|gb|DV520090.1|DV520090
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|211107251|gb|FL258175.1|FL258175
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|67042602|gb|CO468857.1|CO468857
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|211107248|gb|FL258172.1|FL258172
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|211033052|gb|FL319725.1|FL319725
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|211195416|gb|FL326468.1|FL326468
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|76921562|gb|DV168618.1|DV168618
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
EST: gi|50324587|gb|CO519713.1|CO519713
EST:     TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAG                         CTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT
genomic: TGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACT

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: 150

ATGTATGTGTTGTTGGGGTTGCACGCACCCCAATGGGCGGTTTCCTTGGTGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACTTTGGAAACGTCTTGAGTGCTAATTTGGGGCAAGCTCCTGCAAGGCAAGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 164

ATGTATGTGTTGTTGGGGTTGCACGCACCCCAATGGGCGGTTTCCTTGGTGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACTTTGGAAACGTCTTGAGTGCTAATTTGGGGCAAGCTCCTGCAAGGCAAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 129

ATGTATGTGTTGTTGGGGTTGCACGCACCCCAATGGGCGGTTTCCTTGGTGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACTTTGGAAACGTCTTGAGTGCTAATTTGGGGCAAGCTCCTGCAAGGCAAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

ATGTATGTGTTGTTGGGGTTGCACGCACCCCAATGGGCGGTTTCCTTGGTGCCTTGTCTCCCTTGCCTGCTACGAAACTTGGCTCTATAGTAATTCAAGgtgagatccg ... gggctgttagCTGCTCTGGAAAGAGCAAACGTGGATCCAGCCCTCGTGCAGGAGGTCTACTTTGGAAACGTCTTGAGTGCTAATTTGGGGCAAGCTCCTGCAAGGCAAGC