Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcctcactgcctcattacaatgatgattcctgctttgtatgatagagttgatatatcagttattgtgctgtttactcatgttgcttctactcttttccagTGAAGGAGAGTCAGCACCACCCGTAACCT

Basic information

species Oryza sativa
transcript LOC_Os01g24880.1
intron # 3
splice site 3'
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|38469794|gb|CF953925.1|CF953925
EST:     TTCCAATGGTGTCCTATTGGCCGCTTAGCCCAACTTCCATCTGTATTTGA                         TGAAGGAGAGTCAGCACCACCCGTAACCT
genomic: TTCCAATGGTGTCCTATTGGCCGCTTAGCCCAACTTCCATCTGTATTTGAgtatgttcta ... tcttttccagTGAAGGAGAGTCAGCACCACCCGTAACCT
EST: gi|58608025|gb|CK036058.1|CK036058
EST:     TTCCAATGGTGTCCTATNGGCCGCTGAGCCCAACTTCCATCTGTATTTGA                         TGAAGGAGAGTCAGCACCACCCGTAACCT
genomic: TTCCAATGGTGTCCTATTGGCCGCTTAGCCCAACTTCCATCTGTATTTGAgtatgttcta ... tcttttccagTGAAGGAGAGTCAGCACCACCCGTAACCT
EST: gi|29615731|gb|CB620743.1|CB620743
EST:     TTCCAATGGTGTCCTATTGGCCGCTTAGCCCAACTTCCATCTGTATTTGA                         TGAAGGAGAGTCAGCACCACCCGTAACCT
genomic: TTCCAATGGTGTCCTATTGGCCGCTTAGCCCAACTTCCATCTGTATTTGAgtatgttcta ... tcttttccagTGAAGGAGAGTCAGCACCACCCGTAACCT
EST: gi|29656889|gb|CB653164.1|CB653164
EST:     TTCCAATGGTGTCCTATTGGCCGCTTAGCCCAACTTCCATCTGTATTTGA                         TGAAGGAGAGTCAGCACCACCCGTAACCT
genomic: TTCCAATGGTGTCCTATTGGCCGCTTAGCCCAACTTCCATCTGTATTTGAgtatgttcta ... tcttttccagTGAAGGAGAGTCAGCACCACCCGTAACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgatatatcagttattgtgctgtttactcatgttgcttctactcttttccagTGAAGGAGAGTCAGCACCACCCGTAACCT
 agttgat  putative branch site (score: 5)
                                   ttgcttctactctttt  putative PPT
     atatatcagttatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcctcactgcctcattacaatgatgattcctgctttgtatgatagagttgatatatcagttattgtgctgtttactcatgttgcttctactcttttccagTGAAGGAGAGTCAGCACCACCCGTAACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - -actgcct
- - - - - - - - - -atgatga
- - - - - - - - - - - - - - cctgctt
- - - - - - - - - - - - - - - - - -tgtatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgtt