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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGGCGATCGAGAAGTTCCTCCAGTTCCAGGACGCCGTCCCCTGCAAGATCCGCGCCAAGCGCGGGTGCGCCACCCACCCGCGCAGCATCGCCGAGCGGgttcgctgcattcctgctcgctgctactctcgaattcctcgcttggttttaattcccagcccaatccaaaaagagaacgaaagcaaaaaaaaaaaaaaaaaaaaaatgaaaccggttcgtgtcgttgtcgctgtcag

Basic information

species Zea mays
transcript GRMZM2G085467_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085467_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os09g31300.1 (Oryza sativa), 5'ss of exon 2
GGCGGCGATCGAGAAGTTCCTCCAGTTCCAGGACGCCGTCCCCTGCAAGATCCGCGCCAAGCGCGGGTGCGCCACCCACCCGCGCAGCATCGCCGAGCGGgttcgctgcattcct-gctcgctgctactctcgaattcctcgcttggttttaattcccagcccaatccaaaaagagaacgaaagcaaaaaaaaaaaaaaaaaaaaaatgaaaccggttcgtgtcgt-tgtcgctgtcag
||| || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||  |   | | |||  | | |    || |       |  | |  |      ||  |  | |    |        |   |       |    |   |         ||      | |     |||| |  ||||  |||
GGCCGCCATCGAGAAGTTCCTCCAGTTCCAGGACGCCGTCCCCTGCAAGATCCGCGCCAAGCGCGGCTGCGCCACCCACCCCCGCAGCATCGCCGAGCGGgtcagtaccgtaccttacacacgcgcacacctctcgccgccacgcgcacgccatggcatggcgtggcgtggcgtggcgtggcgtggcacgcgatccatttccttcgattcctgagctgaaaatcgtctcccgcttgcag
















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|74237981|gb|DT645895.1|DT645895
EST:     TCCGCGCCAAGCGCGGGTGCGCCACCCACCCGCGCAGCATCGCCGAGCGG                         GTGAGGAGGACGAAGATCAGCGAGCGGATACGGAAGCTGCAGGAGCTCGTG
genomic: TCCGCGCCAAGCGCGGGTGCGCCACCCACCCGCGCAGCATCGCCGAGCGGgttcgctgca ... tcgctgtcagGTGAGGAGGACGAAGATCAGCGAGCGGATACGGAAGCTGCAGGAGCTCGTG
EST: gi|76281063|gb|DV020631.1|DV020631
EST:     TCCGCGCCAAGCGCGGGTGCGCCACCCACCCGCGCAGCATCGCCGAGCGG                         GTGAGGAGGACGAAGATCAGCGAGCGGATACGGAAGCTGCAGGAGCTCGTG
genomic: TCCGCGCCAAGCGCGGGTGCGCCACCCACCCGCGCAGCATCGCCGAGCGGgttcgctgca ... tcgctgtcagGTGAGGAGGACGAAGATCAGCGAGCGGATACGGAAGCTGCAGGAGCTCGTG
EST: gi|149085916|gb|EE175444.2|EE175444
EST:     TCCGCGCCAAGCGCGGGTGCGCCACCCACCCGCGCAGCATCGCCGAGCGG                         GTGAGGAGGACGAAGATCAGCGAGCGGATACGGAAGCTGCAGGAGCTCGTG
genomic: TCCGCGCCAAGCGCGGGTGCGCCACCCACCCGCGCAGCATCGCCGAGCGGgttcgctgca ... tcgctgtcagGTGAGGAGGACGAAGATCAGCGAGCGGATACGGAAGCTGCAGGAGCTCGTG
EST: gi|211103379|gb|FL434747.1|FL434747
EST:     TCCGCGCCAAGCGCGGGTGCGCCACCCACCCGCGCAGCATCGCCGAGCGG                         GTGAGGAGGACGAAGATCAGCGAGCGGATACGGAAGCTGCAGGAGCTCGTG
genomic: TCCGCGCCAAGCGCGGGTGCGCCACCCACCCGCGCAGCATCGCCGAGCGGgttcgctgca ... tcgctgtcagGTGAGGAGGACGAAGATCAGCGAGCGGATACGGAAGCTGCAGGAGCTCGTG

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: 29 (upstream exon), 22 (downstream exon)
Score: 2

GGCGGCGATCGAGAAGTTCCTCCAGTTCCAGGACGCCGTCCCCTGCAAGATCCGCGCCAAGCGCGGGTGCGCCACCCACCCGCGCAGCATCGCCGAGCGGgttcgctgca ... tcgctgtcagGTGAGGAGGACGAAGATCAGCGAGCGGATACGGAAGCTGCAGGAGCTCGTGCCCAACATGGAAAAG


Block sizes: 39 (upstream exon), 27 (downstream exon)
Score: 3

GGCGGCGATCGAGAAGTTCCTCCAGTTCCAGGACGCCGTCCCCTGCAAGATCCGCGCCAAGCGCGGGTGCGCCACCCACCCGCGCAGCATCGCCGAGCGGgttcgctgca ... tcgctgtcagGTGAGGAGGACGAAGATCAGCGAGCGGATACGGAAGCTGCAGGAGCTCGTGCCCAACATGGAAAAG


Block sizes: 45 (upstream exon), 40 (downstream exon)
Score: 15

GGCGGCGATCGAGAAGTTCCTCCAGTTCCAGGACGCCGTCCCCTGCAAGATCCGCGCCAAGCGCGGGTGCGCCACCCACCCGCGCAGCATCGCCGAGCGGgttcgctgca ... tcgctgtcagGTGAGGAGGACGAAGATCAGCGAGCGGATACGGAAGCTGCAGGAGCTCGTGCCCAACATGGAAAAG


Block sizes: 46 (upstream exon), 11 (downstream exon)
Score: 3

GGCGGCGATCGAGAAGTTCCTCCAGTTCCAGGACGCCGTCCCCTGCAAGATCCGCGCCAAGCGCGGGTGCGCCACCCACCCGCGCAGCATCGCCGAGCGGgttcgctgca ... tcgctgtcagGTGAGGAGGACGAAGATCAGCGAGCGGATACGGAAGCTGCAGGAGCTCGTGCCCAACATGGAAAAG