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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTCCCCTGAAGTGCATGCCAATGCTGCCGAAATTCTTTGTGCCGTGACTCGATGTGCTCCTCCATCTCTTGCTGCAAAGATATGCAGCCCAAGgtttccattttataaccttgttacaaagtcacagtttaatccttatcttgtgatttcgggaaacctttttaaaatgaactttgtgcatggatattttttt...

Basic information

species Oryza sativa
transcript LOC_Os01g40340.3
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g40340.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G470292_T01 (Zea mays), 5'ss of exon 9
GACTCCCCTGAAGTGCATGCCAATGCTGCCGAAATTCTTTGTGCCGTGACTCGATGTGCTCCTCCATCTCTTGCTGCAAAGATATGCAGCCCAAGgt-ttccattttataaccttgttacaaagtcacagtttaatcctt--atcttgtgatt-tcgggaaacctttttaaaatgaactttgt-gcatggatattttttt
|| || ||||||||||||||||||||||| |||||||| ||||| || ||||| ||||| ||||||||||||||||||||||||||||| ||||||| ||| |  || |||| |  ||  |  || |||  ||| || ||   | || |  ||  |  |||||  | || | ||   || | | | |  || |       
GATTCTCCTGAAGTGCATGCCAATGCTGCGGAAATTCTATGTGCAGTTACTCGGTGTGCGCCTCCATCTCTTGCTGCAAAGATATGCAGTCCAAGgtattctaacttctaacttcattctactgttacaagttactcatttggtattttttttgccaagaaacaatgttcatatcttctgtattgtactgaaaag-----
















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|2310353|gb|C26508.1|C26508
EST:     GTGACTCGATGTGCTCCTCCATCTCTTGCTGCAAAGATATNCAGCCCAAG                         TTTTGTTGGGAGGCTATTTCGTCATGCACTTGAAGAATCAAGGCCCAAATC
genomic: GTGACTCGATGTGCTCCTCCATCTCTTGCTGCAAAGATATGCAGCCCAAGgtttccattt ... gaaatttcagTTTTGTTGGGAGGCTATTTCGTCATGCACTTGAAGAATCAAGGCCCAAATC
EST: gi|58605044|gb|CK033077.1|CK033077
EST:     GTGACTCGATGTGCTCCTCCATCTCTTGCTGCAAAGATATGCAGCCCAAG                         TTTNGTCGGGAGGCTATTTCGTCATGCACTTGAAGAATCAAGGCCCAAATC
genomic: GTGACTCGATGTGCTCCTCCATCTCTTGCTGCAAAGATATGCAGCCCAAGgtttccattt ... gaaatttcagTTTTGTTGGGAGGCTATTTCGTCATGCACTTGAAGAATCAAGGCCCAAATC
EST: gi|58672704|gb|CK061390.1|CK061390
EST:     GTGACTCGATGTGCTCCTCCATCTCTTGCTGCAAAGATATGCAGCCCAAG                         -TTTGTTGGGAGGCTATTTCGTCATGCACTTGAAGAATCAAGGCCCAAATC
genomic: GTGACTCGATGTGCTCCTCCATCTCTTGCTGCAAAGATATGCAGCCCAAGgtttccattt ... gaaatttcagTTTTGTTGGGAGGCTATTTCGTCATGCACTTGAAGAATCAAGGCCCAAATC
EST: gi|29669991|gb|CB666266.1|CB666266
EST:     GTGACTCGATGTGCTCCTCCATCTCTTGCTGCAAAGATATGCAGCCCAAG                         TTTTGTTGGGAGGCTATTTCGTCATGCACTTGAAGAATCAAGGCCCAAATC
genomic: GTGACTCGATGTGCTCCTCCATCTCTTGCTGCAAAGATATGCAGCCCAAGgtttccattt ... gaaatttcagTTTTGTTGGGAGGCTATTTCGTCATGCACTTGAAGAATCAAGGCCCAAATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTCCCCTGAAGTGCATGCCAATGCTGCCGAAATTCTTTGTGCCGTGACTCGATGTGCTCCTCCATCTCTTGCTGCAAAGATATGCAGCCCAAGgtttccattttataaccttgttacaaagtcacagtttaatccttatcttgtgatttcgggaaacctttttaaaatgaactttgtgcatggatattttttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG