Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatcttatagtcttatagtacttaagcttgaaactaagagagaaaactatctggtcactacgtaattttactcatatgttaccgtcatcatcctctgcagCAATTCCCACCAGAGTACGAGTCAGAATTGCAGCTCAATGCAACTTTCACTCCTGCAGCTTTTTCACCGAGACGGAAAGGTGAGCATCCGTATCGTGGCG

Basic information

species Oryza sativa
transcript LOC_Os01g38229.2
intron # 11
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|88839274|gb|CI000746.1|CI000746
EST:     TCCTGATGGTTCCTCAAGAGACCCGGACGCAATGCAGACGAGGCTTTGAG                         CAATTCCCACCAGAGTACGAGTCAGAATTGCAGCTCAATGCAACTTTCACT
genomic: TCCTGATGGTTCCTCAAGAGACCCGGACGCAATGCAG-CGAGGCTTTGAGgtagtactgt ... tcctctgcagCAATTCCCACCAGAGTACGAGTCAGAATTGCAGCTCAATGCAACTTTCACT
EST: gi|3761203|gb|C98451.1|C98451
EST:     TTCCTACAAGAGACCCGGACGCAATGCAGCGAGGCTTTGAG                         CAATTCCCANCAGAGTACGAGTCAGAATTGCAGCTCAATGCAACTTTCACT
genomic: TTCCT-CAAGAGACCCGGACGCAATGCAGCGAGGCTTTGAGgtagtactgt ... tcctctgcagCAATTCCCACCAGAGTACGAGTCAGAATTGCAGCTCAATGCAACTTTCACT
EST: gi|88845684|gb|CI008681.1|CI008681
EST:     TTCCTGATGGTTCCTCAAGAGACCCGGACGCAATGCAGCGAGGCTTTGAG                         CAATTCCCACCAGAGTACGAGTCAGAATTGCAGCTCAATGCAACTTTCACT
genomic: TTCCTGATGGTTCCTCAAGAGACCCGGACGCAATGCAGCGAGGCTTTGAGgtagtactgt ... tcctctgcagCAATTCCCACCAGAGTACGAGTCAGAATTGCAGCTCAATGCAACTTTCACT
EST: gi|29632145|gb|CB637154.1|CB637154
EST:     TTCCTGATGGTTCCTCAAGAGACCCGGACGCAATGCAGCGAGGCTTTGAG                         CAATTCCCACCAGAGTACGAGTCAGAATTGCAGCTCAATGCAACTTTCACT
genomic: TTCCTGATGGTTCCTCAAGAGACCCGGACGCAATGCAGCGAGGCTTTGAGgtagtactgt ... tcctctgcagCAATTCCCACCAGAGTACGAGTCAGAATTGCAGCTCAATGCAACTTTCACT
EST: gi|55827806|gb|AU056044.2|AU056044
EST:     TNCCTGATGGTTCCTCAAGAGACCCGGACGCAATGCAGCGAGGCTTTGAG                         CAATTCCCACCAGAGTACGAGTCAGAATTGCAGCTCAATGCAACTTTCACT
genomic: TTCCTGATGGTTCCTCAAGAGACCCGGACGCAATGCAGCGAGGCTTTGAGgtagtactgt ... tcctctgcagCAATTCCCACCAGAGTACGAGTCAGAATTGCAGCTCAATGCAACTTTCACT
EST: gi|86899779|gb|CI327577.1|CI327577
EST:     CAATGCAGCGAGGCTTTGAG                         CAATTCCCACCAGAGTACGAGTCAGAATTGCAGCTCAATGCAACTTTCACT
genomic: CAATGCAGCGAGGCTTTGAGgtagtactgt ... tcctctgcagCAATTCCCACCAGAGTACGAGTCAGAATTGCAGCTCAATGCAACTTTCACT
EST: gi|86490225|gb|CI132858.1|CI132858
EST:     CGGACGCAATGCAGCGAGGCTTTGAG                         CAATTCCCACCAGAGTACGAGTCAGAATTGCAGCTCAATGCAACTTTCACT
genomic: CGGACGCAATGCAGCGAGGCTTTGAGgtagtactgt ... tcctctgcagCAATTCCCACCAGAGTACGAGTCAGAATTGCAGCTCAATGCAACTTTCACT
EST: gi|29656736|gb|CB653011.1|CB653011
EST:     TTCCTGATGGTTCCTCAAGAGACCCGGACGCAATGCAGCGAGGCTTTGAG                         CAATTCCCACCAGAGTACGAGTCAGAATTGCAGCTCAATGCAACTTTCACT
genomic: TTCCTGATGGTTCCTCAAGAGACCCGGACGCAATGCAGCGAGGCTTTGAGgtagtactgt ... tcctctgcagCAATTCCCACCAGAGTACGAGTCAGAATTGCAGCTCAATGCAACTTTCACT
EST: gi|88974555|gb|CI022096.1|CI022096
EST:     TTCCTGATGGTTCCTCAAGAGACCCGGACGCAATGCAGCGAGGCTTTGAG                         CAATTCCCACCAGAGTACGAGTCAGAATTGCAGCTCAATGCAACTTTCACT
genomic: TTCCTGATGGTTCCTCAAGAGACCCGGACGCAATGCAGCGAGGCTTTGAGgtagtactgt ... tcctctgcagCAATTCCCACCAGAGTACGAGTCAGAATTGCAGCTCAATGCAACTTTCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actatctggtcactacgtaattttactcatatgttaccgtcatcatcctctgcagCAATTCCCACCAGAGTACGAGTCAGAATTGCAGCTCAATGCAACTTTCACTCCTGCAGCTTTTTCACCGAGACGGAAAGGTGAGCATCCGTATCGTGGCG
                                          tcatcctct  CT-rich tract
                 taattttactcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatcttatagtcttatagtacttaagcttgaaactaagagagaaaactatctggtcactacgtaattttactcatatgttaccgtcatcatcctctgcagCAATTCCCACCAGAGTACGAGTCAGAATTGCAGCTCAATGCAACTTTCACTCCTGCAGCTTTTTCACCGAGACGGAAAGGTGAGCATCCGTATCGTGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - -gcttgaa
- - - - - - - - - - - - - - - - - - - agagaaaa