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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGGGTTCAAGGCGGCGGGTATCTACAGTGGGTTGCGTGCCAAAGGCGAGAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctccggtttcctattagttgtcgttttggataaggttcgagtcaaacttataaaattttggctacaaataactattttgttatttaattttag...

Basic information

species Zea mays
transcript GRMZM2G044237_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044237_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g17120.1 (Oryza sativa), 5'ss of exon 2
AAGGGGTTCAAGGCGGCGGGTATCTACAGTGGGTTGCGTGCCAAAGGCGAGAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctccggtttcctattagttgtcgttttggataaggttcgagtcaaacttataaaattttggctacaaataactattttgttatttaattttag
||||||||||||||||||||||||||| | ||  |||| ||||| ||||||||||| ||| | || ||||||||||||||||||||||||||||| || ||||    ||        |  ||  |  ||  ||        ||   ||       |  | | ||  | || ||  |     | | ||||     | | ||
AAGGGGTTCAAGGCGGCGGGTATCTACGGCGGTCTGCGCGCCAAGGGCGAGAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGGgtaaaggctatcaccaacactttctattcagttcactcgtagtagcagaagtttcttcagagttcagacttcagtttcacttctcgttaccatttctcag
















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|89755796|gb|DY686083.1|DY686083
EST:     GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAG                         GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
genomic: GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
EST: gi|71298836|gb|DR785405.1|DR785405
EST:     GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAG                         GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
genomic: GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
EST: gi|74242073|gb|DT649987.1|DT649987
EST:     GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAG                         GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
genomic: GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
EST: gi|149095151|gb|EE180766.2|EE180766
EST:     GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAG                         GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
genomic: GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
EST: gi|148956344|gb|EC902151.2|EC902151
EST:     GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAG                         GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
genomic: GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
EST: gi|148938791|gb|EC883128.2|EC883128
EST:     GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAG                         GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
genomic: GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
EST: gi|78092275|gb|DV520649.1|DV520649
EST:     GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAG                         GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
genomic: GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
EST: gi|149000193|gb|EE037335.2|EE037335
EST:     GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAG                         GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
genomic: GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
EST: gi|149009106|gb|EE041258.2|EE041258
EST:     GAAGCCTGACTTGGCACTGGTCGCCTGCCACGTCCACGCCACTGTACCAC                         GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
genomic: GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
EST: gi|148932140|gb|EC875563.2|EC875563
EST:     GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAG                         GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
genomic: GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
EST: gi|211453339|gb|FL002421.1|FL002421
EST:     GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAG                         GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
genomic: GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
EST: gi|28873422|gb|CB329414.1|CB329414
EST:     GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAG                         GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
genomic: GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
EST: gi|149071265|gb|EE159660.2|EE159660
EST:     GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAG                         GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
genomic: GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
EST: gi|71446471|gb|DR827521.1|DR827521
EST:     GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAG                         GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
genomic: GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
EST: gi|148930889|gb|EC873334.2|EC873334
EST:     GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAG                         GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
genomic: GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
EST: gi|148972816|gb|EE023801.2|EE023801
EST:     GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAG                         GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
genomic: GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
EST: gi|149110343|gb|EE190365.2|EE190365
EST:     GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAG                         GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
genomic: GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
EST: gi|20301290|gb|BQ164233.1|BQ164233
EST:     GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAG                         GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
genomic: GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
EST: gi|149084216|gb|EE173633.2|EE173633
EST:     GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCCACGCCACTGTAGCAG                         GAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC
genomic: GAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGC

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), 49 (downstream exon)
Score: 217

AAGGGGTTCAAGGCGGCGGGTATCTACAGTGGGTTGCGTGCCAAAGGCGAGAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 211

AAGGGGTTCAAGGCGGCGGGTATCTACAGTGGGTTGCGTGCCAAAGGCGAGAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 178

AAGGGGTTCAAGGCGGCGGGTATCTACAGTGGGTTGCGTGCCAAAGGCGAGAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

AAGGGGTTCAAGGCGGCGGGTATCTACAGTGGGTTGCGTGCCAAAGGCGAGAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctc ... cccatttcagGAGCATTTACAACAAACGTCGTAGCCGCCGCACCTGTTTTGTATTGCAAGCATGTCCTTAGTACATCGAAAACA