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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtcaatgtgcaattctcatactgcactgttagtgcaatttcttctattattacgccacgtgcatgtccaaatcattagagatatctgtagttgt...

Basic information

species Zea mays
transcript GRMZM2G011575_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011575_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os11g13694.1 (Oryza sativa), 5'ss of exon 11
GACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgt--caatgtgcaattctcatactgcactgttagtgcaatttcttctattattacgccacgtgcatgtccaaat-cattagagata-tctgtagttgt
|| || || |||||||| || ||||| || |||||||||||||| |||||||| |||||||| |||| ||||||| ||||||||||| || || |||| | | | | || | || | || | | | |||||| || | | |||| || | | | ||||
GATAAATACATGCAAAACAGGCTAGTAAGGCTAGTATGTGTTTTCCTACAGAGTCTCATTCGAAACAAGATAATAAATGgtgagtgtaccatcatgtaattttttt-ttaccaaaataccgtcatgtatttggtagat---ctgcgtgcaattctatttacattctgtattctgtttggttgg

upper sequence: GRMZM2G011575_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA10G00610.1 (Glycine max), 5'ss of exon 11
GACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtcaatgtgcaattctcatactgcactgttagtgcaatttcttctattattacgccacgtgcatgtccaaatcattaga-gatatctgtagttgt-
|| || || ||||| || | || |||||||| || ||||||||||| || |||||||||||||||| || || ||||||||| | | | || || | ||| | | | |||| | | | | | ||| | ||| |||| | | ||||
GATAAATACATGCAGAACCGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAACATTATTAATGgtgagt-ttacccagttgggacattattgaattgtaacattattgtctttaaaaaatgtaggtccctagtaaagaaaagaaaagaagataaat-tgtttgtt

upper sequence: GRMZM2G011575_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA02G00750.1 (Glycine max), 5'ss of exon 11
GACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgt---caatgtgcaattctcatactgcactgttagtgcaatttcttctattattacgccacgtgcatgtccaaatcattagagatatctgtagttgt
|| || || ||||| || || || |||||||| || ||||||||||| || |||||||||||||||| || || ||||||||| | || | | ||| | | || | ||| || || ||| | | | | | | ||| | || | |||
GATAAATACATGCAGAACAGGCTTGTGAGACTTGTCTGTGTTTTTCTGCAAAGCCTCATTCGGAACAATATTATTAATGgtgagtttacccagttggacattattgaattgtaacattattgt--ctttaaaaattgtaggtctctagtaaaggaaagaaaggaagataaattgtttgtta-

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|24765764|gb|CA400923.1|CA400923
EST:     ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATG                         TGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
genomic: ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
EST: gi|148930025|gb|EE285908.2|EE285908
EST:     ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATG                         TGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
genomic: ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
EST: gi|211108201|gb|FL028207.1|FL028207
EST:     CTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAATATG                         TGCAAGATCTCTTCGTGGARGTGCAAGCATTTTGCATCGCCTTCTCGCGA
genomic: CTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAG-ATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGA
EST: gi|89251017|gb|DY622803.1|DY622803
EST:     ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATG                         TGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
genomic: ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
EST: gi|211108200|gb|FL028206.1|FL028206
EST:     CTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAATATG                         TGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGA
genomic: CTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAG-ATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGA
EST: gi|113701502|gb|EE679006.1|EE679006
EST:     ATTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATG                         TGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
genomic: ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
EST: gi|40303841|gb|CK348228.1|CK348228
EST:     ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATG                         TGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
genomic: ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
EST: gi|71769411|gb|DR967348.1|DR967348
EST:     ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATG                         TGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
genomic: ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
EST: gi|91049014|gb|EB159432.1|EB159432
EST:     ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATG                         TGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
genomic: ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
EST: gi|74239167|gb|DT647081.1|DT647081
EST:     ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATG                         TGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA
genomic: ACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAA

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), 49 (downstream exon)
Score: 63

GACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAATAAGGGAGGCAGTGGGGTTGTTCAGGCTCCTGAAATCTCTAGAATGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 43

GACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAATAAGGGAGGCAGTGGGGTTGTTCAGGCTCCTGAAATCTCTAGAATGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 62

GACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAATAAGGGAGGCAGTGGGGTTGTTCAGGCTCCTGAAATCTCTAGAATGAAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 28

GACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAGAGCCTCATTCGGAACAGGATAATAGATGgtgagtgtca ... ttgtgtgcagTGCAAGATCTCTTCGTGGAGGTGCAAGCATTTTGCATCGCCTTCTCGCGAATAAGGGAGGCAGTGGGGTTGTTCAGGCTCCTGAAATCTCTAGAATGAAG