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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaagagtgttgcattcatcaatttatttgacctgttttttttttgtcaatacattataaaccaagatcttttcttctggattttctatcagCGCCAATCTCAAAGGCTGCCATAATTGGTGTTGCTGTGGGTGGACTTGTTATCCTCCTGATGATCTTAGTAGCTGTATGCAGGCCACACCATCCACCTGC

Basic information

species Zea mays
transcript GRMZM5G809695_T03
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G809695_T03 (Zea mays), 3'ss of exon 22
lower sequence: LOC_Os06g10230.1 (Oryza sativa), 3'ss of exon 23
gtaagaagagtgttgcattcatcaatttatttgacctgttttttttttgtcaatacattataaaccaagatcttttcttctggattttctat-cagCGCCAATCTCAAAGGCTGCCATAATTGGTGTTGCTGTGGGTGGACTTGTTATCCTCCTGATGATCTTAGTAGCTGTATGCAGGCCACACCATCCACCTGC
|||| ||   | || |||||||      || | || |  ||||||  |  | | | |    ||  |||  | |  |   ||  ||||| | | |||| | ||||||||||||||| ||| ||||  |||| |||||||| ||||||||||||||||||||||||||||| || |||||||| ||   |||||||| 
gtaacaaa--tattccattcat------atcttacataattttttcataccta-atagacaaagtcaacttttcgttacctacattttatttgcagCACTAATCTCAAAGGCTGCAATACTTGGAATTGCCGTGGGTGGGCTTGTTATCCTCCTGATGATCTTAGTAGCGGTCTGCAGGCCTCATAGTCCACCTGT
















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|71769229|gb|DR967166.1|DR967166
EST:     TGGATATTGGCTTGGTTCTTCATGTCGTTCCACTGGCCACCGAGACAAAC                         CGCCAATCTCAAAGGCTGCCATAATTGGTGTTGCTGTGGGTGGACTTGTTA
genomic: TGGATATTGGCTTGGTTCTTCATGTCGTTCCACTGGCCACCGAGACAAACgtaagaagag ... tttctatcagCGCCAATCTCAAAGGCTGCCATAATTGGTGTTGCTGTGGGTGGACTTGTTA
EST: gi|211021287|gb|FL334113.1|FL334113
EST:     TGGATATTGGCTTGGTTCTTCATGTCGTTCCACTGGCCACCGAGACAAAC                         CGCCAATCTCAAAGGCTGCCATAATTGGTGTTGCTGTGGGTGGACTTGTTA
genomic: TGGATATTGGCTTGGTTCTTCATGTCGTTCCACTGGCCACCGAGACAAACgtaagaagag ... tttctatcagCGCCAATCTCAAAGGCTGCCATAATTGGTGTTGCTGTGGGTGGACTTGTTA
EST: gi|211538240|gb|FL353975.1|FL353975
EST:     TGGATATTGGCTTGGTTCTTCATGTCGTTCCACTGGCCACCGAGACAAAC                         CGCCAATCTCAAAGGCTGCCATAATTGGTGTTGCYGTGGGTGGACTTGTTA
genomic: TGGATATTGGCTTGGTTCTTCATGTCGTTCCACTGGCCACCGAGACAAACgtaagaagag ... tttctatcagCGCCAATCTCAAAGGCTGCCATAATTGGTGTTGCTGTGGGTGGACTTGTTA
EST: gi|28873715|gb|CB329664.1|CB329664
EST:     TGGATATTGGCTTGGTTCTTCATGTCGTTCCACTGGCCACCGAGACAAAC                         CGCCAATCTCAAAGGCTGCCATAATTGGTGTTGCTGTGGGTGGACTTGTTA
genomic: TGGATATTGGCTTGGTTCTTCATGTCGTTCCACTGGCCACCGAGACAAACgtaagaagag ... tttctatcagCGCCAATCTCAAAGGCTGCCATAATTGGTGTTGCTGTGGGTGGACTTGTTA
EST: gi|211403947|gb|FL320399.1|FL320399
EST:     TGGATATTGGCTTGGTTCTTCATGTCGTTCCACTGGCCACCGAGACAAAC                         CGCCAATCTCAAAGGCTGCCATAATTGGTGTTGCTGTGGGTGGACTTGTTA
genomic: TGGATATTGGCTTGGTTCTTCATGTCGTTCCACTGGCCACCGAGACAAACgtaagaagag ... tttctatcagCGCCAATCTCAAAGGCTGCCATAATTGGTGTTGCTGTGGGTGGACTTGTTA
EST: gi|32164946|gb|CD670264.1|CD670264
EST:     TGGATATTGGCTTGGTTCTTCATGTCGTTCCACTGGCCACCGAGACAAAC                         CGCCAATCTCAAAGGCTGCCATAATTGGCGTTGCTGTGGGTGGACTTGTTA
genomic: TGGATATTGGCTTGGTTCTTCATGTCGTTCCACTGGCCACCGAGACAAACgtaagaagag ... tttctatcagCGCCAATCTCAAAGGCTGCCATAATTGGTGTTGCTGTGGGTGGACTTGTTA

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: 1982

CTTTTTAGGTAATCCTGGACTCTGTGGATATTGGCTTGGTTCTTCATGTCGTTCCACTGGCCACCGAGACAAACgtaagaagag ... tttctatcagCGCCAATCTCAAAGGCTGCCATAATTGGTGTTGCTGTGGGTGGACTTGTTATCCTCCTGATGATCTTAGTAGCTGTATGCAGGCCACACCATCCACCTGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 80

CTTTTTAGGTAATCCTGGACTCTGTGGATATTGGCTTGGTTCTTCATGTCGTTCCACTGGCCACCGAGACAAACgtaagaagag ... tttctatcagCGCCAATCTCAAAGGCTGCCATAATTGGTGTTGCTGTGGGTGGACTTGTTATCCTCCTGATGATCTTAGTAGCTGTATGCAGGCCACACCATCCACCTGC


Block sizes: 42 (upstream exon), 8 (downstream exon)
Score: 1

CTTTTTAGGTAATCCTGGACTCTGTGGATATTGGCTTGGTTCTTCATGTCGTTCCACTGGCCACCGAGACAAACgtaagaagag ... tttctatcagCGCCAATCTCAAAGGCTGCCATAATTGGTGTTGCTGTGGGTGGACTTGTTATCCTCCTGATGATCTTAGTAGCTGTATGCAGGCCACACCATCCACCTGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 129

CTTTTTAGGTAATCCTGGACTCTGTGGATATTGGCTTGGTTCTTCATGTCGTTCCACTGGCCACCGAGACAAACgtaagaagag ... tttctatcagCGCCAATCTCAAAGGCTGCCATAATTGGTGTTGCTGTGGGTGGACTTGTTATCCTCCTGATGATCTTAGTAGCTGTATGCAGGCCACACCATCCACCTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttgtcaatacattataaaccaagatcttttcttctggattttctatcagCGCCAATCTCAAAGGCTGCCATAATTGGTGTTGCTGTGGGTGGACTTGTTATCCTCCTGATGATCTTAGTAGCTGTATGCAGGCCACACCATCCACCTGC
                                            ttttctatc  CT-rich tract
         tcaatacattataaa  TA-rich tract