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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtctccgtcacctgatcgcatagtgtttgctatgtttaccttagaccatattttttttccgtgtaattttgagaccacttgacatgttagttt...

Basic information

species Zea mays
transcript GRMZM2G046587_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046587_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g47600.1 (Oryza sativa), 5'ss of exon 6
GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtctccgtcacctgatcgcatagtgtttgctatgtttaccttagaccatattttttttccgtgtaatt-ttgagaccacttgacatgttagttt--
||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||| ||||||||  | |    || |||  |  | || |  | |||     |   |  ||   ||||  ||  || |   | | ||  |      |  | |  | |   |    
GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaat---cccatcatgtccttgctttttttttagagaggggaaattcctccatccttggttacatggaagttgcttttgttagataaggtttccatgctt
















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|211537734|gb|FL105292.1|FL105292
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTT
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|19351061|gb|BM895593.1|BM895593
EST:     GGTGTTTCTTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGCAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATT
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCG-AGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATT
EST: gi|32849179|gb|CD988860.1|CD988860
EST:     GGTGTTTCTTGCGAGCTCGTGCTATTTGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|88756535|gb|DY540676.1|DY540676
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|13126709|gb|BG317279.1|BG317279
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|32924525|gb|CF029337.1|CF029337
EST:     GGTGTTTCTTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|18168735|gb|BM338575.1|BM338575
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|76016905|gb|DT944075.1|DT944075
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGGGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|149099848|gb|EE185900.2|EE185900
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|74244614|gb|DT652528.1|DT652528
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|13126527|gb|BG317097.1|BG317097
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGTAATAGTATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAA
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAG-AA-AG-ATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAA
EST: gi|17931649|gb|BM268609.1|BM268609
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|60337363|gb|DN204336.1|DN204336
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|32924252|gb|CF029064.1|CF029064
EST:     GGTGTTTCTTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|60348368|gb|DN215341.1|DN215341
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|16919746|gb|BM074334.1|BM074334
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|16377933|gb|BI992193.1|BI992193
EST:     TTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: TTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|32831285|gb|CD970963.1|CD970963
EST:     GGTGTTTCTTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|13491080|gb|BG517844.1|BG517844
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|74244615|gb|DT652529.1|DT652529
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|13126526|gb|BG317096.1|BG317096
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|9732830|gb|BE511582.1|BE511582
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|32851273|gb|CD990954.1|CD990954
EST:     GGTGTTTCTTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|60354612|gb|DN221585.1|DN221585
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
EST: gi|149099849|gb|EE185901.2|EE185901
EST:     GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG                         GGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC
genomic: GGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTC

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: 45 (upstream exon), 29 (downstream exon)
Score: 96

GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTCCGTCACTACACGGACATCACGGACCTCCCACCGCATCGCCTTCAAGAGA


Block sizes: 48 (upstream exon), 29 (downstream exon)
Score: 92

GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTCCGTCACTACACGGACATCACGGACCTCCCACCGCATCGCCTTCAAGAGA


Block sizes: 48 (upstream exon), 29 (downstream exon)
Score: 31

GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTCCGTCACTACACGGACATCACGGACCTCCCACCGCATCGCCTTCAAGAGA


Block sizes: 49 (upstream exon), 29 (downstream exon)
Score: 200

GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtc ... acatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTCCGTCACTACACGGACATCACGGACCTCCCACCGCATCGCCTTCAAGAGA