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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGTTTCCACCAAGAATGGCACGCAAGGACACCTGCACCTACTCGACAACTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAGgtaaatgaggtcccactgaactgtaactctgcaggcactttaatgcttgatctcattgagtctaccaatttgaaaactttgcag

Basic information

species Zea mays
transcript GRMZM2G066578_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066578_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os10g33250.2 (Oryza sativa), 5'ss of exon 9
ACAGTTTCCACCAAGAATGGCACGCAAGGACACCTGCACCTACTCGACAACTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAGgta--aatgaggtcccactgaactgtaactctgcaggcactttaatgcttgatctcattgagtctaccaatttgaaaactttgcag-------
||| ||||| ||||  |||| ||||||||||| ||||| ||||||||||||||||||||||| |||||| ||||| || ||||||||||| || || ||||||  | | |   ||   |||| |   | ||   ||   |       ||| |  | ||  | ||    |||||   ||||||           
ACAATTTCCTCCAAAGATGGTACGCAAGGACAGCTGCAGCTACTCGACAACTCCTGCAATGGCTGTACCAAAAACGCTGCAGAATGTGCATTCATGCGAGgtagtagtaataacctgttgaaat---aatccagagattcagacgaacttcacatgatctaatcacaaaatttttgaactttttttttgacag
















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|211117536|gb|FL480259.1|FL480259
EST:     CTCCTGCAATGGTTGTGCCTAAAACACTACAGAATGTGCACTCCTGTGAG                         AATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTT
genomic: CTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAGgtaaatgagg ... aactttgcagAATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTT
EST: gi|76018387|gb|DT945557.1|DT945557
EST:     CTCCTGCAATGGTTGTACCTAAAACCCTACAGAATGTGCACTCCTGTGAG                         AATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTT
genomic: CTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAGgtaaatgagg ... aactttgcagAATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTT
EST: gi|84970225|gb|DW468575.1|DW468575
EST:     CTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAG                         AATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTT
genomic: CTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAGgtaaatgagg ... aactttgcagAATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTT
EST: gi|211362136|gb|FL332732.1|FL332732
EST:     CTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAG                         AATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTT
genomic: CTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAGgtaaatgagg ... aactttgcagAATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTT
EST: gi|6827258|gb|AW330901.1|AW330901
EST:     CTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAG                         AATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTT
genomic: CTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAGgtaaatgagg ... aactttgcagAATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTT
EST: gi|78091932|gb|DV520306.1|DV520306
EST:     CTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAG                         AATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTT
genomic: CTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAGgtaaatgagg ... aactttgcagAATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTT
EST: gi|211355369|gb|FL034995.1|FL034995
EST:     CTCCTGCAATGGTTGTGCCTAAAACACTACAGAATGTGCACTCCTGTGAG                         AATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTT
genomic: CTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAGgtaaatgagg ... aactttgcagAATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTT
EST: gi|211355370|gb|FL034996.1|FL034996
EST:     CTCCTGCAATGGTTGTGCCTAAAACACTACAGAATGTGCACTCCTGTGAG                         AATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCT
genomic: CTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAGgtaaatgagg ... aactttgcagAATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCT
EST: gi|78180792|gb|DV551165.1|DV551165
EST:     CTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAG                         AATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTT
genomic: CTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAGgtaaatgagg ... aactttgcagAATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTT
EST: gi|89757800|gb|DY687246.1|DY687246
EST:     CTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAG                         AATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTT
genomic: CTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAGgtaaatgagg ... aactttgcagAATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTT
EST: gi|78179861|gb|DV550234.1|DV550234
EST:     CTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAG                         AATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTT
genomic: CTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAGgtaaatgagg ... aactttgcagAATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTT

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 2 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 99

ACAGTTTCCACCAAGAATGGCACGCAAGGACACCTGCACCTACTCGACAACTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAGgtaaatgagg ... aactttgcagAATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTTCATGCATTGGAGGGATGGAACGAGCATGAGTGTGGGGACATCGTGCTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1466

ACAGTTTCCACCAAGAATGGCACGCAAGGACACCTGCACCTACTCGACAACTCCTGCAATGGTTGTACCTAAAACACTACAGAATGTGCACTCCTGTGAGgtaaatgagg ... aactttgcagAATTGGCTGCCAAGGAGGGTCATGAGTGCATGGCGCATTGCTGGAATGGTTCATGCATTGGAGGGATGGAACGAGCATGAGTGTGGGGACATCGTGCTAG




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