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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCGGTTCTCCTGTGTTCGACAAGCTCGAATCCGAACTGGCAAAAGCTATGCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCGgtgcggttttggccttgtgtcgtttattttttgcacaagatgtagatgtttcaggggttcggaatcgcaaggtgctgatatatatagctttatttgctttgtgcgcag

Basic information

species Zea mays
transcript GRMZM2G036861_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036861_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 5'ss of exon 9
CTCGGTTCTCCTGTGTTCGACAAGCTCGAATCCGAACTGGCAAAAGCTATGCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCGgtg-cggttttggccttgtgtcgtttattttttgcacaagatgtagatgtttcaggggttcggaatcgcaaggtgctgatatatatagctttatttgctttgtgcgcag
 | || |||||||| || ||||| || ||  | ||| |||| ||||||||||||||| ||||||| ||||| ||||| ||||| ||||| ||||| || |||    |  ||   ||        ||| ||  |  |     || | ||   |   |  | |  | |     | | |||   |  |||        |   |||||| |||
ATTGGCTCTCCTGTATTTGACAAACTTGAGGCTGAATTGGCGAAAGCTATGCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATCGGCAGTGGATTTGCAGgtaattgaattaatctgcacataattagttgatttattttttgcaaatagct-gtgcatgccaactactttgctactggcctcaatactaactaataacttgtgcccag
















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|211012763|gb|FL448392.1|FL448392
EST:     GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCG                         GGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
genomic: GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCGgtgcggtttt ... ttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
EST: gi|148951093|gb|EC896758.2|EC896758
EST:     GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCG                         GGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
genomic: GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCGgtgcggtttt ... ttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
EST: gi|78109643|gb|DV528059.1|DV528059
EST:     GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCG                         GGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
genomic: GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCGgtgcggtttt ... ttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
EST: gi|76281789|gb|DV021357.1|DV021357
EST:     GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCG                         GGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
genomic: GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCGgtgcggtttt ... ttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
EST: gi|148940355|gb|EC885142.2|EC885142
EST:     GAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCG                         GGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
genomic: GAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCGgtgcggtttt ... ttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
EST: gi|76934910|gb|DV174082.1|DV174082
EST:     ATTGGCAGCGGATTCGCCG                         GGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
genomic: ATTGGCAGCGGATTCGCCGgtgcggtttt ... ttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
EST: gi|149098824|gb|EE184837.2|EE184837
EST:     GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCG                         GGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG
genomic: GCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCGgtgcggtttt ... ttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGG

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: 32 (upstream exon), 47 (downstream exon)
Score: 14

CTCGGTTCTCCTGTGTTCGACAAGCTCGAATCCGAACTGGCAAAAGCTATGCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCGgtgcggtttt ... ttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGGCTGGAAGTGTCAGGACACGGACTAATCGCTCGGGTGGTGTGCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 132

CTCGGTTCTCCTGTGTTCGACAAGCTCGAATCCGAACTGGCAAAAGCTATGCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCGgtgcggtttt ... ttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGGCTGGAAGTGTCAGGACACGGACTAATCGCTCGGGTGGTGTGCAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 77

CTCGGTTCTCCTGTGTTCGACAAGCTCGAATCCGAACTGGCAAAAGCTATGCTTTCTATTCCTGCGAGCAACGGGTTCGAGATTGGCAGCGGATTCGCCGgtgcggtttt ... ttgtgcgcagGGACCGACTTGACAGGAAGTGAGCATAATGATGAGTTTTATATGGATAAGGCTGGAAGTGTCAGGACACGGACTAATCGCTCGGGTGGTGTGCAG