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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGGAGTGCATTGACAAGTAACATGATACGATTTTTTAAGACCCAAGATGAATCATGGAGCCATGAGgtatatcaaaggatatttaatatctattcagcatatgtacttgtatatatatatcaatgatacttacagactaaacttactttgcag

Basic information

species Glycine max
transcript GLYMA11G36670.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G36670.1 (Glycine max), 5'ss of exon 5
lower sequence: AT4G14040.1 (Arabidopsis thaliana), 5'ss of exon 4
CTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGGAGTGCATTGACAAGTAACATGATACGATTTTTTAAGACCCAAGATGAATCATGGAGCCATGAGgtatatcaaaggatatttaatatctattcagcatatgtacttgtatatatatatcaatgatacttacagactaaacttactttgcag
||||||||||||| ||||||||||||| | ||| |||||||| ||| | ||||| |||||| | ||||| |||| |   |||||  | ||||||||||||| |  |   | | |  | ||| | | |      | |   ||   || |||   | | |  |  ||  | |||    ||  |||    
CTTGCATGATCCTTCTAAAGATACAGGGTATGTTGGGAGTGCTTTGTCTAGTAATATGATAAGGTTTTTCAAGAACAGTGATGACACGTGGAGCCATGAGgcaagt--gaagtttctaaatctttttcttttgtcttatctcaaatctatgattaacttgtgatt-taaactggtgttgttttag--

upper sequence: GLYMA11G36670.1 (Glycine max), 5'ss of exon 5
lower sequence: AT4G14030.1 (Arabidopsis thaliana), 5'ss of exon 5
CTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGGAGTGCATTGACAAGTAACATGATACGATTTTTTAAGACCCAAGATGAATCATGGAGCCATGAGgtatat-caaaggatatttaatatctattcagcatatgtacttgtatatatatatcaatgat--acttacagactaaacttactt--tgcag
||||||||||||  ||||||||||||| ||||| |||||||| ||| | ||||| |||||| ||||||| |||| |   |||||| |||||||||||||||||  |  |     |  || || |  ||| |     |||  | ||   ||||  || ||||   ||  ||   | | |   ||||  |  ||
CTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCCTTGTCGAGTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGAGCCATGAGgtaagtgtagtttctgattcattttcatt-acttcttgttttggttcttataattctatgactaaccaaccagcaataacaacttgttttag

upper sequence: GLYMA11G36670.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv05s0029g00240.t01 (Vitis vinifera), 5'ss of exon 5
CTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGGAGTGCATTGACAAGTAACATGATACGATTTTTTAAGACCCAAGATGAATCATGGAGCCATGAGgtatatcaaaggatatttaatatctattcagcatatgtacttgtatatatatatcaatgatacttacagactaaactta--ctttgcag--------------------------------------
| ||||||||||| ||||||||||||| ||||| ||  |||| || ||||| |||||| | |||||||| ||||||| |||||  ||||||||||| |||||||      ||||| |   | | | ||||     | |  ||| |    |  ||     ||  |   || ||  | | |  | |  ||                                       
CCTGCATGATCCTTCTAAAGATACAGGGTTTGTAGGTTGTGCCTTAACAAGCAACATGGTGCGATTTTTCAAGACCCCAGATGGGTCATGGAGCCACGAGgtatgc----ggataatatgtgtttcttcaattcctttgtttgaaaccttgcattttgaattgtattagtctctattaaggcatgacaatccacaatatataatcactccctaatttacttatgaag

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|58018645|gb|CX705387.1|CX705387
EST:     CATGGAGCCATGAG                         GTTGCCATATCAGTGAAACCACTGAAAGTGCAAAACTGGATTCTTCCTGAA
genomic: CATGGAGCCATGAGgtatatcaaa ... tactttgcagGTTGCCATATCAGTGAAACCACTGAAAGTGCAAAACTGGATTCTTCCTGAA
EST: gi|18726732|gb|BM523722.1|BM523722
EST:     GTAACATGATACGATTTTTTAAGACCCAAGATGAATCATGGAGCCATGAG                         GTTGCCATATCAGTGAAACCA
genomic: GTAACATGATACGATTTTTTAAGACCCAAGATGAATCATGGAGCCATGAGgtatatcaaa ... tactttgcagGTTGCCATATCAGTGAAACCA
EST: gi|21887640|gb|BQ740853.1|BQ740853
EST:     GTAACATGATACGATTTTTTAAGACCCAAGATGAATCATGGAGCCATGAG                         GTTGCCATATCAGTGAAACCACTGAAAGTGCAAAACTGGATTCTTCCTGAA
genomic: GTAACATGATACGATTTTTTAAGACCCAAGATGAATCATGGAGCCATGAGgtatatcaaa ... tactttgcagGTTGCCATATCAGTGAAACCACTGAAAGTGCAAAACTGGATTCTTCCTGAA
EST: gi|9259532|gb|BE347687.1|BE347687
EST:     CGATTTTTTAAGACCCAAGATGAATCATGGAGCCATGAG                         GTTGCCATATCAGTGAAACCACTGAAAGTGCAAAACTGGATTCTTCCTGAA
genomic: CGATTTTTTAAGACCCAAGATGAATCATGGAGCCATGAGgtatatcaaa ... tactttgcagGTTGCCATATCAGTGAAACCACTGAAAGTGCAAAACTGGATTCTTCCTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGGAGTGCATTGACAAGTAACATGATACGATTTTTTAAGACCCAAGATGAATCATGGAGCCATGAGgtatatcaaaggatatttaatatctattcagcatatgtacttgtatatatatatcaatgatacttacagactaaacttactttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA