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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGgtgaggctttctttctctgcggcaaacagtgaattggaggctccatcgtggcggtcttgctcgggtgctgatcctgtggcatgacttgactatctgcag

Basic information

species Zea mays
transcript GRMZM2G080375_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080375_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 5'ss of exon 3
GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGgtgaggctttctttctctgcggcaaacagtgaattgga----ggctccatcgtggc---ggtcttgctcgggtg--ctgatcctgtggcatgacttgactatctgcag
||| || ||||||||| | ||||||||||||||||| ||||||||||||  | | ||   | | || ||   | || |    || | ||  |||      || |  ||  | |    | ||  |||||  |    ||  |   | |||
GCAATACTTCGTCAACACTGACGACACCGTCACGCAAAAGgtgaggcttcatctttccatgacgaaaagattactgtaattcggttacagggtgatcatagtttgactgagctaacttaattttgtggtgtttgctgcttgctt-cag
















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|74234373|gb|DT642287.1|DT642287
EST:     GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG                         ATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
genomic: GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGgtgaggcttt ... ctatctgcagATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
EST: gi|211522284|gb|FL320492.1|FL320492
EST:     GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG                         ATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
genomic: GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGgtgaggcttt ... ctatctgcagATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
EST: gi|148940563|gb|EC885365.2|EC885365
EST:     GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG                         ATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
genomic: GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGgtgaggcttt ... ctatctgcagATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
EST: gi|211143668|gb|FL321938.1|FL321938
EST:     GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG                         ATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGC-GGG
genomic: GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGgtgaggcttt ... ctatctgcagATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
EST: gi|149076118|gb|EE164702.2|EE164702
EST:     GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG                         ATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
genomic: GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGgtgaggcttt ... ctatctgcagATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
EST: gi|148941151|gb|EC886025.2|EC886025
EST:     GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG                         ATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
genomic: GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGgtgaggcttt ... ctatctgcagATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
EST: gi|18661967|gb|BM501673.1|BM501673
EST:     GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG                         ATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
genomic: GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGgtgaggcttt ... ctatctgcagATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
EST: gi|76914829|gb|DV165709.1|DV165709
EST:     GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG                         ATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
genomic: GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGgtgaggcttt ... ctatctgcagATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
EST: gi|37416938|gb|CF646120.1|CF646120
EST:     GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG                         ATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
genomic: GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGgtgaggcttt ... ctatctgcagATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
EST: gi|149087521|gb|EE176918.2|EE176918
EST:     GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG                         ATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
genomic: GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGgtgaggcttt ... ctatctgcagATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
EST: gi|76290797|gb|DV030365.1|DV030365
EST:     GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG                         ATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
genomic: GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGgtgaggcttt ... ctatctgcagATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
EST: gi|149111238|gb|EE294735.2|EE294735
EST:     GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG                         ATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
genomic: GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGgtgaggcttt ... ctatctgcagATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
EST: gi|76913985|gb|DV165359.1|DV165359
EST:     GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG                         ATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
genomic: GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGgtgaggcttt ... ctatctgcagATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
EST: gi|78078027|gb|DV506442.1|DV506442
EST:     GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG                         ATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
genomic: GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGgtgaggcttt ... ctatctgcagATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
EST: gi|148935767|gb|EC879810.2|EC879810
EST:     GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG                         ATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
genomic: GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGgtgaggcttt ... ctatctgcagATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
EST: gi|87153260|gb|DY398049.1|DY398049
EST:     GACACCGTCACGCAGAAG                         ATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG
genomic: GACACCGTCACGCAGAAGgtgaggcttt ... ctatctgcagATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGG

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: 41 (upstream exon), 48 (downstream exon)
Score: 40

GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGgtgaggcttt ... ctatctgcagATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGGCCACGGCAGCGGGTGTACTTCCAGTCCGATGAGGTGAACGCCGCCATTG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 473

GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGgtgaggcttt ... ctatctgcagATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGGCCACGGCAGCGGGTGTACTTCCAGTCCGATGAGGTGAACGCCGCCATTG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 455

GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGgtgaggcttt ... ctatctgcagATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGGCCACGGCAGCGGGTGTACTTCCAGTCCGATGAGGTGAACGCCGCCATTG


Block sizes: 41 (upstream exon), 47 (downstream exon)
Score: 115

GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGgtgaggcttt ... ctatctgcagATTGTTGTTCATAAGACCAGTGCCAGGGGCACCCACTTCCGGCGTGCCGGGCCACGGCAGCGGGTGTACTTCCAGTCCGATGAGGTGAACGCCGCCATTG