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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaaagctaattctcttttgtagaagatcaaatttcgtaaggattgaagcatccgtttaatatgcttaattcatttccttgcag

Basic information

species Zea mays
transcript GRMZM2G421857_T04
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G421857_T04 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 8
GACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaaagctaattctcttttgtagaagatcaaatttcgtaaggattgaagcatccgtttaatatgcttaattcatttccttgcag
|| |||||||||||||||||||||||||| || |||||| ||||||||||||| |||||||| ||   | |     |||||| | |||||| | || || | |||||| ||||||  ||||||| || |      | | |  | |||
GATACAGTGCTAGAATTGGAATTTCAGGGTATCAAAAAGGAATTTACCATGCTCCAGgtaaacaa---gtt--ccatcttttat-gaagataacatgtc-tgaggattaaagcattagtttaatctgttg----tactgcactacag

upper sequence: GRMZM2G421857_T04 (Zea mays), 5'ss of exon 9
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 8
GACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaaagctaattctcttttgtagaagatcaaatttcgtaaggattgaagcatccgtttaata-------tgcttaattcatttccttgcag
||||||||||||||| | || ||||| ||  | |||||| ||||||||||||||||||| |     |   |   | |   ||     | |  ||| |  | | ||    ||||||| | |||||        |  ||| || |  |   | |||
GACACAGTGCTAGAACTTGAGTTTCAAGGTGTCAAAAAGCAATTTACCATGCTTCAGgttattggtatttt--ctatgcattaccttaaagtaaaatctgcatggt---aagcatctgattaatgactcctttttttattttacctttcttcag
















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|51592889|gb|CV072035.1|CV072035
EST:     GGGCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
genomic: GGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
EST: gi|61118945|gb|DN559906.1|DN559906
EST:     TTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
genomic: TTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
EST: gi|6012344|gb|AW061700.1|AW061700
EST:     TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGCCTGTGCGTTCCCCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
EST: gi|211532167|gb|FL123441.1|FL123441
EST:     TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
EST: gi|6636981|gb|AW261253.1|AW261253
EST:     TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAGCTTGCTGCGGAT
EST: gi|211541195|gb|FL123492.1|FL123492
EST:     TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAG                         ACATGGCCTGTGCGTTCACAAAGGCCTGTTGCATCGAAG
genomic: TGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaa ... ttccttgcagACATGGCCTGTGCGTTCACCAAGGCCTGTTGCATCGAAG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACACAGTGCTAGAATTGGAATTTCAGGGCATAAAAAAGAAATTTACCATGCTTCAGgtaaaaaaaaagctaattctcttttgtagaagatcaaatttcgtaaggattgaagcatccgtttaatatgcttaattcatttccttgcag

- - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - AAGAAA