Skip to another splice site:
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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGGTAGAGAACGGTGTGCAGCTCACATTGACCTCCACTGTCAAGACCAATGGCAAGATAAGAATCAATGGAGAAGTGCTAAACGGATCACACCTCAAAgtattcttttatcttataattgcacctcgtttgtttcatctttgtgactgtctacctgagaaaacgaagaacacctcgattgatttctgtctttgtgtgtgttcag

Basic information

species Oryza sativa
transcript LOC_Os01g12810.1
intron # 2
splice site 5'
intron type U2

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|29628279|gb|CB633290.1|CB633290
EST:     ATGGCAAGATAAGAATCAATGGAGAAGTGCTAAACGGATCACACCTCAAA                         GAGAAGCACGAAGCTGGCAGCAATGGCGCCCTGCACCCATCAAACGGGCAA
genomic: ATGGCAAGATAAGAATCAATGGAGAAGTGCTAAACGGATCACACCTCAAAgtattctttt ... gtgtgttcagGAGAAGCACGAAGCTGGCAGCAATGGCGCCCTGCACCCATCAAACGGGCAA
EST: gi|58669267|gb|CK057953.1|CK057953
EST:     ATGGCAAGATAAGAATCAATGGAGAAGTGCTAAACGGATCACACCTCAAA                         GAGAAGCACGAAGCTGGCAGCAATGGCGCCCTGCACCCATCAAACGGGCAA
genomic: ATGGCAAGATAAGAATCAATGGAGAAGTGCTAAACGGATCACACCTCAAAgtattctttt ... gtgtgttcagGAGAAGCACGAAGCTGGCAGCAATGGCGCCCTGCACCCATCAAACGGGCAA
EST: gi|88294370|gb|CI667344.1|CI667344
EST:     ATGGCAAGATAAGAATCAATGGAGAAGTGCTAGACGGATCACACCTCAAA                         GAGAAGCACGAAGCTGGCAGCAATGGCGCCCTGCACCCATCAAACGGGCAA
genomic: ATGGCAAGATAAGAATCAATGGAGAAGTGCTAAACGGATCACACCTCAAAgtattctttt ... gtgtgttcagGAGAAGCACGAAGCTGGCAGCAATGGCGCCCTGCACCCATCAAACGGGCAA
EST: gi|88569665|gb|CI660840.1|CI660840
EST:     ATGGCAAGATAAGAATCAATGGAGAAGTGCTAAACGGATCACACCTCAAA                         GAGAAGCACGAGGCTGGCAGCAATGGCGCCCTGCACCCATCAAACGGGCAA
genomic: ATGGCAAGATAAGAATCAATGGAGAAGTGCTAAACGGATCACACCTCAAAgtattctttt ... gtgtgttcagGAGAAGCACGAAGCTGGCAGCAATGGCGCCCTGCACCCATCAAACGGGCAA
EST: gi|87010971|gb|CI286046.1|CI286046
EST:     ATGGCAAGATAAGAATCAATGGAGAAGTGCTAAACGGATCACACCTCAAA                         GAGAAGCACGAAGCTGGCAGCAATGGCGCCCTGCACCCATCAAACGGGCAA
genomic: ATGGCAAGATAAGAATCAATGGAGAAGTGCTAAACGGATCACACCTCAAAgtattctttt ... gtgtgttcagGAGAAGCACGAAGCTGGCAGCAATGGCGCCCTGCACCCATCAAACGGGCAA
EST: gi|88288639|gb|CI663428.1|CI663428
EST:     ATGGCAAGATAAGAATCAATGGAGAAGTGCTAGACGGATCACACCTCAAA                         GAGAAGCACGAAGCTGGCAGCAATGGCGCCCTGCACCCATCAAACGGGCAA
genomic: ATGGCAAGATAAGAATCAATGGAGAAGTGCTAAACGGATCACACCTCAAAgtattctttt ... gtgtgttcagGAGAAGCACGAAGCTGGCAGCAATGGCGCCCTGCACCCATCAAACGGGCAA
EST: gi|58664404|gb|CK053090.1|CK053090
EST:     ATGGCAAGATAAGAATCAATGGAGAAGTGCTAAACGGATCACACCTCAAA                         GAGAAGCACGAAGCTGGCAGCAATGGCGCCCTGCACCCATCAAACGGGCAA
genomic: ATGGCAAGATAAGAATCAATGGAGAAGTGCTAAACGGATCACACCTCAAAgtattctttt ... gtgtgttcagGAGAAGCACGAAGCTGGCAGCAATGGCGCCCTGCACCCATCAAACGGGCAA
EST: gi|88356454|gb|CI652891.1|CI652891
EST:     ATGGCAAGATAAGAATCAATGGAGAAGTGCTAAACGGATCACACCTCAAA                         GAGAAGCACGAAGCTGGCAGCAATGGCGCCCTGCACCCATCAAAC
genomic: ATGGCAAGATAAGAATCAATGGAGAAGTGCTAAACGGATCACACCTCAAAgtattctttt ... gtgtgttcagGAGAAGCACGAAGCTGGCAGCAATGGCGCCCTGCACCCATCAAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGGTAGAGAACGGTGTGCAGCTCACATTGACCTCCACTGTCAAGACCAATGGCAAGATAAGAATCAATGGAGAAGTGCTAAACGGATCACACCTCAAAgtattcttttatcttataattgcacctcgtttgtttcatctttgtgactgtctacctgagaaaacgaagaacacctcgattgatttctgtctttgtgtgtgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT