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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtgtgcatttactagtttgctctttagtgctgacagataagattttgccggtggagaaggtcttgcatgatgaattcatatttcatttttctcatgcagCTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCTGTGCTGACTGCAGCGCGCCTGACCCCAAATGGGC

Basic information

species Oryza sativa
transcript LOC_Os02g10480.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10480.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G138349_T02 (Zea mays), 3'ss of exon 2
ggtgtgcatttactagtttgctcttt--agtgctgacagataagattttgccggtggagaaggt---cttgcatgatgaattcatatttcatttttctcatgcagCTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCTGTGCTGACTGCAGCGCGCCTGACCCCAAATGGGC
    | ||   |||||||| |||| |  |||      | || |  | ||   |    || || |   |||  || ||||| ||| ||| ||  |||  | | ||||||||||||| |||||||||||| | ||||| |  ||||||||||  || |||||||||||  | ||  |||| |||||||||||
----tacagccactagttttctctatcaagtatacttatattatgtattaaggtcacagcagcttcgcttatattatgaactcacatt-cacctttgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC
















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|88734623|gb|CI758131.1|CI758131
EST:     AACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAG                         CTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCT
genomic: AACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAGgtacttttac ... tctcatgcagCTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCT
EST: gi|66928181|gb|CX115029.1|CX115029
EST:     AACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAG                         CTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCT
genomic: AACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAGgtacttttac ... tctcatgcagCTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCT
EST: gi|58656726|gb|CK045406.1|CK045406
EST:     AACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAG                         CTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCT
genomic: AACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAGgtacttttac ... tctcatgcagCTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCT
EST: gi|2310113|gb|C26268.1|C26268
EST:     AACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAG                         CTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCT
genomic: AACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAGgtacttttac ... tctcatgcagCTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCT
EST: gi|88732043|gb|CI757220.1|CI757220
EST:     AACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAG                         CTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCT
genomic: AACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAGgtacttttac ... tctcatgcagCTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCT
EST: gi|88388036|gb|CI590312.1|CI590312
EST:     AACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAG                         CTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCT
genomic: AACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAGgtacttttac ... tctcatgcagCTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCT
EST: gi|88735087|gb|CI758595.1|CI758595
EST:     AACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAG                         CTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCT
genomic: AACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAGgtacttttac ... tctcatgcagCTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCT
EST: gi|88727576|gb|CI751231.1|CI751231
EST:     AACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAG                         CTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCT
genomic: AACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAGgtacttttac ... tctcatgcagCTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCT
EST: gi|88305672|gb|CI632039.1|CI632039
EST:     AACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAC                         CTAAGATGGCAGAACTGAAGGAGCTATTGCACAGAAGTGAAAANCGTATCT
genomic: AACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAGgtacttttac ... tctcatgcagCTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCT
EST: gi|88385241|gb|CI630342.1|CI630342
EST:     AACTACGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAG                         CTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCT
genomic: AACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAGgtacttttac ... tctcatgcagCTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCT
EST: gi|88735299|gb|CI758807.1|CI758807
EST:     AACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAG                         CTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCT
genomic: AACTAAGCAGTAAGAAGATCTGAATATGAGTGGAAGACGTGATGATTCAGgtacttttac ... tctcatgcagCTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgccggtggagaaggtcttgcatgatgaattcatatttcatttttctcatgcagCTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCTGTGCTGACTGCAGCGCGCCTGACCCCAAATGGGC
                                  tatttcatttttctc  CT-rich tract
                         atgaattcatatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtgtgcatttactagtttgctctttagtgctgacagataagattttgccggtggagaaggtcttgcatgatgaattcatatttcatttttctcatgcagCTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCTGTGCTGACTGCAGCGCGCCTGACCCCAAATGGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG