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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTACAAAGATTGACTTCCGGCAAACATCTGATGGCCAGCTAATAACTGAAAgttagtaccatatagcttatttctttccacatgctttagtttcttgtctccactacaatgtcttgactaaaaacatccgtgtgcag

Basic information

species Zea mays
transcript GRMZM2G095778_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095778_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g53810.1 (Oryza sativa), 5'ss of exon 9
GGTACAAAGATTGACTTCCGGCAAACATCTGATGGCCAGCTAATAACTGAAAgttagtaccatatagcttatttctttccacatgctttagtttcttgtctccactacaatgtcttgactaaaaacatccgtgtgcag
||||||||||| |||||||||||||| |||||||||||||| ||||||||||||||||| | ||| || |  ||  |||  |||| ||    || ||    |    | ||  | |||||    ||| ||  |||||||
GGTACAAAGATCGACTTCCGGCAAACCTCTGATGGCCAGCTCATAACTGAAAgttagtatcgtat-gcctgattggttctgcatggttagaatttttacacctgacaaaa-atgttgacatggaacgtctttgtgcag
















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|76015881|gb|DT943051.1|DT943051
EST:     TACAAAGATTGACTTCCGGCAAACATCTGATGGCCAGCTAATAACTGAAA                         TTGATGGCAAACAAATTGGCACTGTCCAGAGCAAAGATCTTTGCA
genomic: TACAAAGATTGACTTCCGGCAAACATCTGATGGCCAGCTAATAACTGAAAgttagtacca ... ccgtgtgcagTTGATGGCAAACAAATTGGCACTGTCCAGAGCAAAGATCTTTGCA
EST: gi|37377338|gb|CF625266.1|CF625266
EST:     TACAAAGATTGACTTCCGGCAAACATCTGATGGCCAGCTAATAACTGAAA                         TTGATGGCAAACAAATTGGCACTGTCCAGAGCAAAGATCTTTGCA
genomic: TACAAAGATTGACTTCCGGCAAACATCTGATGGCCAGCTAATAACTGAAAgttagtacca ... ccgtgtgcagTTGATGGCAAACAAATTGGCACTGTCCAGAGCAAAGATCTTTGCA
EST: gi|211482002|gb|FL392969.1|FL392969
EST:     TACAAAGATTGACTTCCGGCAAACATCTGATGGCCAGCTAATAACTGAAA                         TTGATGGCAAACAAATTGGCACTGTCCAGAGCAAAGATCTTTGCA
genomic: TACAAAGATTGACTTCCGGCAAACATCTGATGGCCAGCTAATAACTGAAAgttagtacca ... ccgtgtgcagTTGATGGCAAACAAATTGGCACTGTCCAGAGCAAAGATCTTTGCA
EST: gi|211430121|gb|FL449154.1|FL449154
EST:     TACAAAGATTGACTTCCGGCAAACATCTGATGGCCAGCTAATACCTGAAA                         TTGATGGCAAACAAATTGGCACTGTCCAGAGCAGAGATCTTTGCA
genomic: TACAAAGATTGACTTCCGGCAAACATCTGATGGCCAGCTAATAACTGAAAgttagtacca ... ccgtgtgcagTTGATGGCAAACAAATTGGCACTGTCCAGAGCAAAGATCTTTGCA
EST: gi|78116956|gb|DV535343.1|DV535343
EST:     TACAAAGATTGACTTCCGGCAAACATCTGATGGCCAGCTAATAACTGAAA                         TTGATGGCAAACAAATTGGCACTGTCCAGAGCAAAGATCTTTGCA
genomic: TACAAAGATTGACTTCCGGCAAACATCTGATGGCCAGCTAATAACTGAAAgttagtacca ... ccgtgtgcagTTGATGGCAAACAAATTGGCACTGTCCAGAGCAAAGATCTTTGCA
EST: gi|211522635|gb|FL444079.1|FL444079
EST:     GACTTCCGGCAAACATCTGATGGCCAGCTAATAACTGAAA                         TTGATGGCAAACAAATTGGCACTGTCCAGAGCAAAGATCTTTGCA
genomic: GACTTCCGGCAAACATCTGATGGCCAGCTAATAACTGAAAgttagtacca ... ccgtgtgcagTTGATGGCAAACAAATTGGCACTGTCCAGAGCAAAGATCTTTGCA
EST: gi|89760691|gb|DY689000.1|DY689000
EST:     TACAAAGATTGACTTCCGGCAAACATCTGATGGCCAGCTAATAACTGAAA                         TTGATGGCAAACAAATTGGCACTGTCCAGAGCAAAGATCTTTGCA
genomic: TACAAAGATTGACTTCCGGCAAACATCTGATGGCCAGCTAATAACTGAAAgttagtacca ... ccgtgtgcagTTGATGGCAAACAAATTGGCACTGTCCAGAGCAAAGATCTTTGCA

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), 44 (downstream exon)
Score: 123

GGTACAAAGATTGACTTCCGGCAAACATCTGATGGCCAGCTAATAACTGAAAgttagtacca ... ccgtgtgcagTTGATGGCAAACAAATTGGCACTGTCCAGAGCAAAGATCTTTGCA


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 122

GGTACAAAGATTGACTTCCGGCAAACATCTGATGGCCAGCTAATAACTGAAAgttagtacca ... ccgtgtgcagTTGATGGCAAACAAATTGGCACTGTCCAGAGCAAAGATCTTTGCA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 138

GGTACAAAGATTGACTTCCGGCAAACATCTGATGGCCAGCTAATAACTGAAAgttagtacca ... ccgtgtgcagTTGATGGCAAACAAATTGGCACTGTCCAGAGCAAAGATCTTTGCA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 105

GGTACAAAGATTGACTTCCGGCAAACATCTGATGGCCAGCTAATAACTGAAAgttagtacca ... ccgtgtgcagTTGATGGCAAACAAATTGGCACTGTCCAGAGCAAAGATCTTTGCA