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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAATTGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTGgtatgggctgtttgtactgaactgaaacttatattttctggcagaaatcttattactttttttcaccattcttccattaaagccattacttagtagagca...

Basic information

species Oryza sativa
transcript LOC_Os02g02530.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g02530.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA14G21190.1 (Glycine max), 5'ss of exon 2
GGAATTGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTGgtatgggctgtttgtactgaactgaaacttatattttctggcagaaatcttattactttt-tttcaccattcttccattaaagccattacttagtagagca-----
|||||||| ||||| || ||||| || ||||| ||||||||||||||||||||| |   | ||| | ||  | | |   ||||  |   |     ||  ||| ||  |||   || || ||    | |   ||    |  || | ||   ||     
GGAATTGAAATGCTCTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTGgtaagtatttttttttctttaattatggttatggtgctt----aaagcctttttgttttaactttacgatagagcgac--aatttttctctcattaccccaatgaa

upper sequence: LOC_Os02g02530.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA06G08620.2 (Glycine max), 5'ss of exon 7
GGAATTGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTGgtatgggctgtttgtactgaactgaaacttatattttctggcagaaatcttattactttttttcaccat-tcttccattaaagccattacttag--tagagca--
|||||||| ||||| || ||||| || ||||| ||||||||||||||||||||| | | | ||  | ||    | |    ||  |  |   ||  ||| ||| ||  |||     | ||| | | ||| |||  |  |  || |   || | ||  
GGAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTGgtaggtgtttttctttctatctttag---taattaatggtgctcaaagcttctt--tttaagaaaacatatataccaataatcctttggctgaagataaaccata

upper sequence: LOC_Os02g02530.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA04G08510.1 (Glycine max), 5'ss of exon 7
GGAATTGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTGgtatgggctgtttgtactgaactga--aacttatattttctg--gcagaaatcttattactttttttcaccattcttccattaaagccattacttagtagagca
|||||||| ||||| || ||||| || ||||| ||||||||||||||||||||| | | | ||  | ||    | |  || | ||  |       ||     | | |  |    | |  |||| |  ||| ||      |  | | |  |||   
GGAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTGgtaggtgtttttctttctttttttagtaattaatggtgctcaaagcttcgttttaagaaaacatgtataccaataatcctttggc-tgaagattaaccaga---

upper sequence: LOC_Os02g02530.3 (Oryza sativa), 5'ss of exon 6
lower sequence: AT2G03120.1 (Arabidopsis thaliana), 5'ss of exon 6
GGAATTGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTGgtatgggctgtttgtactgaact---------gaaacttatat---tttctggcagaaatcttattactttttttcaccattcttccattaaagccattacttagtagagca----
|||||||||||||| || || ||||||||||| |||||||| || || |||||| |  |||  | |  ||||            |||||| | |    |||| |  ||||    | | | |||    |  | ||   ||||       |    |  | ||       
GGAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTGgtaagaactgcatcttttgaatgctattcttgaaaacttgtttggacttctagatgaaaagaaaattcgtttgaaaatgactcaatcattcggtgtttgttatgcttgacttgcag

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|58684751|gb|CK073438.1|CK073438
EST:     GAATTGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTG                         GCTGGCCTCTTTTTCTATGATATTTTCTGGGTTTTCTTCACTCCTGTTATG
genomic: GAATTGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTGgtatgggctg ... tttgattcagGCTGGCCTCTTTTTCTATGATATTTTCTGGGTTTTCTTCACTCCTGTTATG




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAATTGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTGgtatgggctgtttgtactgaactgaaacttatattttctggcagaaatcttattactttttttcaccattcttccattaaagccattacttagtagagca

- - - GAGATG