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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATTGAGCATGAGCAGGCTAGGAGCTCCTGGAGCAGTTCTTCCCCTTCTTAGGGAATCTCAAACCGAGgtgtgcagctttcctatttctttatgtttccaaacagaatccttgttagaaagactagttgaatgtaggctgtgctatgttaaaagattgtagagctatg...

Basic information

species Oryza sativa
transcript LOC_Os06g09370.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g09370.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G024530_T01 (Zea mays), 5'ss of exon 8
GTATTGAGCATGAGCAGGCTAGGAGCTCCTGGAGCAGTTCTTCCCCTTCTTAGGGAATCTCAAACCGAGgtgtgcagctttcctatttctttatgtttccaaacagaatccttgttagaaagactagttgaatgtaggctgtgc-tatgttaaaagattgtagagctatg---------
|| || |||||||| |||||||||||||| |||||||||||||||||||| |||||||| || |||||| | | ||| ||||| || || || ||| ||||| | | | | || | ||| || | | | || |||| | |
GTGTTAAGCATGAGTAGGCTAGGAGCTCCAGGAGCAGTTCTTCCCCTTCTCGCAGAATCTCAGACTGAGgtgccaaaccttctaatttccttgc-------aaaagtatcgttgttttata-attggt--gacatagacttcccatctttttttcatctgtatgcccaactgcaatgcc

upper sequence: LOC_Os06g09370.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G116785_T01 (Zea mays), 5'ss of exon 6
GTATTGAGCATGAGCAGGCTAGGAGCTCCTGGAGCAGTTCTTCCCCTTCTTAGGGAATCTCAAACCGAGgtgtgcagctttcctatttctttatgtttccaaacagaatccttgttagaaagactagttgaatgtaggctgtgctatgt---taaaagattgtagagctatg
|| ||||||||||| ||| |||||||||| |||||||||||||||||||| | |||||| | || |||||| | | ||| |||| | ||| | ||||||||| | ||| | | | |||| || || | | | ||| | | | ||
GTCTTGAGCATGAGTAGGGTAGGAGCTCCAGGAGCAGTTCTTCCCCTTCTCACAGAATCTAAGACTGAGgtgccaaaccttctaattttgtataacttctat---gaatccttgaaaaaaacattgttgctttgtaactggttgcatacacctcacatattttccatttgtg
















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|87012724|gb|CI295168.1|CI295168
EST:     TAGGAGCTCCTGGAGCAGTTCTTCCCCTTCTTAGGGAATCTCAAACCGAG                         TGCCATAGTAATCCATCTCTAT
genomic: TAGGAGCTCCTGGAGCAGTTCTTCCCCTTCTTAGGGAATCTCAAACCGAGgtgtgcagct ... acttctgcagTGCCATAGTAATCCATCTCTAT
EST: gi|88980643|gb|CI026705.1|CI026705
EST:     TAGGAGCTCCTGGAGCAGTTCTTCCCCTTCTTAGGGAATCTCAAACCGAG                         TGCCATAGTAATCCATCTCTATCAGCTTCAACCATTTCACAAGGGCCACCA
genomic: TAGGAGCTCCTGGAGCAGTTCTTCCCCTTCTTAGGGAATCTCAAACCGAGgtgtgcagct ... acttctgcagTGCCATAGTAATCCATCTCTATCAGCTTCAACCATTTCACAAGGGCCACCA
EST: gi|218483231|gb|FG956163.1|FG956163
EST:     TAGGAGCTCCTGGAGCAGTTCTTCCCCTTCTTAGGGAATCTCAAACCGAG                         TGCCATAGTAATCCATCTCTATCAGCTT
genomic: TAGGAGCTCCTGGAGCAGTTCTTCCCCTTCTTAGGGAATCTCAAACCGAGgtgtgcagct ... acttctgcagTGCCATAGTAATCCATCTCTATCAGCTT
EST: gi|86498321|gb|CI140954.1|CI140954
EST:     TAGGAGCTCCTGGAGCAGTTCTTCCCCTTCTTAGGGAATCTCAAACCGAG                         TGCCATAGTAATCCATCTCTATCAGCTTCAACCATTTCACAAGGGCCACCA
genomic: TAGGAGCTCCTGGAGCAGTTCTTCCCCTTCTTAGGGAATCTCAAACCGAGgtgtgcagct ... acttctgcagTGCCATAGTAATCCATCTCTATCAGCTTCAACCATTTCACAAGGGCCACCA
EST: gi|5039098|gb|AU071208.1|AU071208
EST:     TAGGAGCTCCTGGAGCAGTTCTTCCCCTTCTTAGGGAATCTCAAACCGAG                         TGCCATAGTAATCCATCTCTATCAGCTTCAACCATTTCACAAGGGCCACCA
genomic: TAGGAGCTCCTGGAGCAGTTCTTCCCCTTCTTAGGGAATCTCAAACCGAGgtgtgcagct ... acttctgcagTGCCATAGTAATCCATCTCTATCAGCTTCAACCATTTCACAAGGGCCACCA
EST: gi|218482847|gb|FG953463.1|FG953463
EST:     TAGGAGCTCCTGGAGCAGTTCTTCCCCTTCTTAGGGAATCTCAAACCGAG                         TGCCATAGTAATCCATCTCTATCAG
genomic: TAGGAGCTCCTGGAGCAGTTCTTCCCCTTCTTAGGGAATCTCAAACCGAGgtgtgcagct ... acttctgcagTGCCATAGTAATCCATCTCTATCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATTGAGCATGAGCAGGCTAGGAGCTCCTGGAGCAGTTCTTCCCCTTCTTAGGGAATCTCAAACCGAGgtgtgcagctttcctatttctttatgtttccaaacagaatccttgttagaaagactagttgaatgtaggctgtgctatgttaaaagattgtagagctatg

- - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - GAGCAG