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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtcaacctaatcttaacatgtttatcatgccgattgcaaactgtgaagctcttttttttatatcactcag

Basic information

species Zea mays
transcript GRMZM2G011068_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011068_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g44590.3 (Oryza sativa), 5'ss of exon 2
AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtcaac-ctaatcttaacatgtt---tatcatgccgattgcaaa----ctgtgaagctcttttttttatatcactcag
             || |||||||||||||| ||||||| |||||||||||| |  |||||||| ||  ||||||| || ||||| ||||||||||  | |||  |||   || |    | | |||| ||| | |||     ||| |      | ||| | | ||||||||
------------GGAAGGAGTGGCTAGCACTTCTGGACAATTCACATTCAACACATCTCTAGCCTCGTTGCACACCTATCTTGGTGgtaaatgtcctcgctatccttgctatatgatgtttgatgctgatagaaaagaaagtgtaataagactctttatgtgtcactcag

upper sequence: GRMZM2G011068_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g44590.2 (Oryza sativa), 5'ss of exon 2
AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtcaac-ctaatcttaacatg---tttatcatgccgattgcaaac----tgtgaagctcttttttttatatcactcag
||||| | |  | || |||||||||||||| ||||||| |||||||||||| |  |||||||| ||  ||||||| || ||||| ||||||||||  | |||  |||   ||    | | | |||| ||| | |||     ||| |      | ||| | | ||||||||
AGATACCGACAGGGAAGGAGTGGCTAGCACTTCTGGACAATTCACATTCAACACATCTCTAGCCTCGTTGCACACCTATCTTGGTGgtaaatgtcctcgctatccttgctatatgatgtttgatgctgatagaaaagaaagtgtaataagactctttatgtgtcactcag
















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|211144537|gb|FL166805.1|FL166805
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|71766061|gb|DR963998.1|DR963998
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|211143112|gb|FL166799.1|FL166799
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|211144535|gb|FL166803.1|FL166803
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|71448594|gb|DR829644.1|DR829644
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|71436330|gb|DR817380.1|DR817380
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|31664610|gb|CD573543.1|CD573543
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|211143111|gb|FL166798.1|FL166798
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|211144538|gb|FL166806.1|FL166806
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|211144536|gb|FL166804.1|FL166804
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACGATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|211144532|gb|FL166800.1|FL166800
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|211144533|gb|FL166801.1|FL166801
EST:     CCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATANCCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATC
genomic: CCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATA-CCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATC
EST: gi|211143110|gb|FL166797.1|FL166797
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|76288774|gb|DV028342.1|DV028342
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC

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: 48 (upstream exon), 47 (downstream exon)
Score: 76

AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCCTCAACTTGCCAATGTTTTATCTTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 42

AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCCTCAACTTGCCAATGTTTTATCTTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 52

AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCCTCAACTTGCCAATGTTTTATCTTCAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 55

AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCCTCAACTTGCCAATGTTTTATCTTCAAG