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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagacttgaaatagaaattttgttatgtgcttatgcccctcaaaatgcgtatgcacattataaaaattttgatagttcctatggtgcatatctttctcagAAGTTCTCCGCCATCTTCTTATGGCCATGATCTGGTCTCAAGCAGAGGATCATACAGCGACGAGTGGCATGCAGATTTGCTTGGTTGCTGTTCAGAGCCA

Basic information

species Oryza sativa
transcript LOC_Os03g06120.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g06120.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G027821_T01 (Zea mays), 3'ss of exon 3
----tagacttgaaatagaaattttgttatgtgcttatgcccctcaaaatgcgtatgcacattataaaaattttgatagttcctatggtgcatatctttctcagAAGTTCTCCGCCATCTTCTTATGGCCATGATCTGGTCTCAAGCAGAGGATCATACAGCGACGAGTGGCATGCAGATTTGCTTGGTTGCTGTTCAGAGCCA
    || | | | ||   | | ||   | |||||  |  || | ||   |||  || |  |  ||||||  | |  ||||||  ||| || || ||     |||| | ||| | | |  | | ||||| |||||||| |||||||| |||||||| |||||||| || |||||||||||||| ||||| ||||||||||| || 
gaagtaaaatgggaaagaacagttcactctgtgc--acaccacgcagc-tgctaatacgtac-ataaaacatctagtagttctgatgatgtatgtccgatgcagATGCTCTTCACAAGTTCCATATGGTCATGATCTTGTCTCAAGTAGAGGATCGTACAGCGATGAATGGCATGCAGATTTACTTGGCTGCTGTTCAGAACCG
















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|87021652|gb|CI276051.1|CI276051
EST:     TCATGATGACTCTCCAAAGAAGCAAAAGGATGCCTGCACTGCACCACG                         AAGTTCTCCGCCATCTTCTTATGGCCATGATCTGGTCTCAAGCAGAGGATC
genomic: TCATGATGACTCTCCAAAGAAGCAAAAGGATGCCTGCACTGCACCACGgttagtaagt ... tctttctcagAAGTTCTCCGCCATCTTCTTATGGCCATGATCTGGTCTCAAGCAGAGGATC
EST: gi|58681562|gb|CK070249.1|CK070249
EST:     TATCATGATGACTCTCCAAAGAAGCAAAAGGATGCCTGCACTGCACCACG                         AAGTTCTCCGCCATCTTCTTATGGCCATGATCTGGTCTCAAGCAGAGGATC
genomic: TATCATGATGACTCTCCAAAGAAGCAAAAGGATGCCTGCACTGCACCACGgttagtaagt ... tctttctcagAAGTTCTCCGCCATCTTCTTATGGCCATGATCTGGTCTCAAGCAGAGGATC
EST: gi|58673353|gb|CK062039.1|CK062039
EST:     TATCATGATGACTCTCCAAAGAAGCAAAAGGATGCCTGCACTGCACCACG                         AAGTTCTCCGCCATCTTCTTATGGCCATGATCTGGTCTCAAGCAGAGGATC
genomic: TATCATGATGACTCTCCAAAGAAGCAAAAGGATGCCTGCACTGCACCACGgttagtaagt ... tctttctcagAAGTTCTCCGCCATCTTCTTATGGCCATGATCTGGTCTCAAGCAGAGGATC
EST: gi|29637808|gb|CB642817.1|CB642817
EST:     TATCATGATGACTCTCCAAAGAAGCAAAAGGATGCCTGCACTGCACCACG                         AAGTTCTCCGCCATCTTCTTATGGCCATGATCTGGTCTCAAGCAGAGGATC
genomic: TATCATGATGACTCTCCAAAGAAGCAAAAGGATGCCTGCACTGCACCACGgttagtaagt ... tctttctcagAAGTTCTCCGCCATCTTCTTATGGCCATGATCTGGTCTCAAGCAGAGGATC
EST: gi|33803494|gb|CF327622.1|CF327622
EST:     TATCATGATGACTCTCCAAAGAAGCAAAAGGATGCCTGCACAGCACCACG                         AAGTTCTCCGCCATCTTCTTATGGCCATGATCTGGTCTCAAGCAGAGGATC
genomic: TATCATGATGACTCTCCAAAGAAGCAAAAGGATGCCTGCACTGCACCACGgttagtaagt ... tctttctcagAAGTTCTCCGCCATCTTCTTATGGCCATGATCTGGTCTCAAGCAGAGGATC
EST: gi|27554129|gb|CA998029.1|CA998029
EST:     TATCATGATGACTCTCCAAAGAAGCAAAAGGATGCCTGCACTGCACCACG                         AAGTTCTCCGCCATCTTCTTATGGCCATGATCTGGTCTCATGCAGATGATC
genomic: TATCATGATGACTCTCCAAAGAAGCAAAAGGATGCCTGCACTGCACCACGgttagtaagt ... tctttctcagAAGTTCTCCGCCATCTTCTTATGGCCATGATCTGGTCTCAAGCAGAGGATC
EST: gi|27548516|gb|CA766467.2|CA766467
EST:     TATCATGATGACTCTCCAAAGAAGCAAAAGGATGCCTGCACTGCACCACG                         AAGTTCTCCGCCATCTTCTTATGGCCATGATCTGGTCTCAAGCAGAGGATC
genomic: TATCATGATGACTCTCCAAAGAAGCAAAAGGATGCCTGCACTGCACCACGgttagtaagt ... tctttctcagAAGTTCTCCGCCATCTTCTTATGGCCATGATCTGGTCTCAAGCAGAGGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcgtatgcacattataaaaattttgatagttcctatggtgcatatctttctcagAAGTTCTCCGCCATCTTCTTATGGCCATGATCTGGTCTCAAGCAGAGGATCATACAGCGACGAGTGGCATGCAGATTTGCTTGGTTGCTGTTCAGAGCCA
                     ttttgat  putative branch site (score: 4)
                                           tatctttctc  putative PPT
         acattataaaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagacttgaaatagaaattttgttatgtgcttatgcccctcaaaatgcgtatgcacattataaaaattttgatagttcctatggtgcatatctttctcagAAGTTCTCCGCCATCTTCTTATGGCCATGATCTGGTCTCAAGCAGAGGATCATACAGCGACGAGTGGCATGCAGATTTGCTTGGTTGCTGTTCAGAGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT