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'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatctgtatccagtcatatacataatctttggtgttagattgaaggttgctagcacttttgctcactatttttccatcgcttttgaatcttcaactcagGGAAAGATGAGTTCTAGACCTTTTCGTCCTCCAAAACCTGAAGATGTTGCCACTATTTGTTACACTAGTGGCACAACCGGCACACCAAAG

Basic information

species Oryza sativa
transcript LOC_Os11g04980.2
intron # 9
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|29679209|gb|CB675484.1|CB675484
EST:     CAACATCTACTGGAGTGGAAATTATAATTTACTCCAGACTACTCAACCAG                         GGAAAGATGAGTTCTAGACCTTTTCGTCCTCCAAAACCTGAAGATGTTGCC
genomic: CAACATCTACTGGAGTGGAAATTATAATTTACTCCAGACTACTCAACCAGgtgaatttgc ... ttcaactcagGGAAAGATGAGTTCTAGACCTTTTCGTCCTCCAAAACCTGAAGATGTTGCC
EST: gi|29679207|gb|CB675482.1|CB675482
EST:     CAACATCTACTGGAGTGGAAATTATAATTTACTCCAGACTACTCAACCAG                         GGAAAGATGAGTTCTAGACCTTTTCGTCCTCCAAAACCTGAAGATGTTGCC
genomic: CAACATCTACTGGAGTGGAAATTATAATTTACTCCAGACTACTCAACCAGgtgaatttgc ... ttcaactcagGGAAAGATGAGTTCTAGACCTTTTCGTCCTCCAAAACCTGAAGATGTTGCC
EST: gi|33676001|gb|CF304240.1|CF304240
EST:     CAACATCTACTGGAGTGGAAATTATAATTTACTCCAGACTACTCAACCAG                         GGAAAGATGAGTTCTAGACCTTTTCGTCCTCCAAAACCTGAAGATGTTGCC
genomic: CAACATCTACTGGAGTGGAAATTATAATTTACTCCAGACTACTCAACCAGgtgaatttgc ... ttcaactcagGGAAAGATGAGTTCTAGACCTTTTCGTCCTCCAAAACCTGAAGATGTTGCC
EST: gi|58696224|gb|CK084911.1|CK084911
EST:     CAACATCTACTGGAGTGGAAATTATAATTTACTCCAGACTACTCAACCAG                         GGAAAGATGAGTTCTAGACCTTTTCGTCCTCCAAAACCTGAAGATGTTGCC
genomic: CAACATCTACTGGAGTGGAAATTATAATTTACTCCAGACTACTCAACCAGgtgaatttgc ... ttcaactcagGGAAAGATGAGTTCTAGACCTTTTCGTCCTCCAAAACCTGAAGATGTTGCC
EST: gi|29671403|gb|CB667678.1|CB667678
EST:     CAACATCTACTGGAGTGGAAATTATAATTTACTCCAGACTACTCAACCAG                         GGAAAGATGAGTTCTAGACCTTTTCGTCCTCCAAAACCTGAAGATGTTGCC
genomic: CAACATCTACTGGAGTGGAAATTATAATTTACTCCAGACTACTCAACCAGgtgaatttgc ... ttcaactcagGGAAAGATGAGTTCTAGACCTTTTCGTCCTCCAAAACCTGAAGATGTTGCC
EST: gi|58663800|gb|CK052486.1|CK052486
EST:     CAACATCTACTGGAGTGGAAATTATAATTTACTCCAGACTACTCAACCAG                         GGAAAGATGAGTTCTAGACCTTTTCGTCCTCCAAAACCTGAAGATGTTGCC
genomic: CAACATCTACTGGAGTGGAAATTATAATTTACTCCAGACTACTCAACCAGgtgaatttgc ... ttcaactcagGGAAAGATGAGTTCTAGACCTTTTCGTCCTCCAAAACCTGAAGATGTTGCC
EST: gi|33675052|gb|CF303291.1|CF303291
EST:     CAACATCTACTGGAGTGGAAATTATAATTTACTCCAGACTACTCAACCAG                         GGAAAGATGAGTTCTAGACCTTTTCGTCCTCCAAAACCTGAAGATGTTGCC
genomic: CAACATCTACTGGAGTGGAAATTATAATTTACTCCAGACTACTCAACCAGgtgaatttgc ... ttcaactcagGGAAAGATGAGTTCTAGACCTTTTCGTCCTCCAAAACCTGAAGATGTTGCC
EST: gi|29670550|gb|CB666825.1|CB666825
EST:     CAACATCTACTGGAGTGGAAATTATAATTTACTCCAGACTACTCAACCAG                         GGAAAGATGAGTTCTAGACCTTTTCGTCCTCCAAAACCTGAAGATGTTGCC
genomic: CAACATCTACTGGAGTGGAAATTATAATTTACTCCAGACTACTCAACCAGgtgaatttgc ... ttcaactcagGGAAAGATGAGTTCTAGACCTTTTCGTCCTCCAAAACCTGAAGATGTTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttgctagcacttttgctcactatttttccatcgcttttgaatcttcaactcagGGAAAGATGAGTTCTAGACCTTTTCGTCCTCCAAAACCTGAAGATGTTGCCACTATTTGTTACACTAGTGGCACAACCGGCACACCAAAG
               tgctcac  putative branch site (score: 2)
                                           tcttc  putative PPT
                    actattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatctgtatccagtcatatacataatctttggtgttagattgaaggttgctagcacttttgctcactatttttccatcgcttttgaatcttcaactcagGGAAAGATGAGTTCTAGACCTTTTCGTCCTCCAAAACCTGAAGATGTTGCCACTATTTGTTACACTAGTGGCACAACCGGCACACCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG