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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagatttgatccgatgtttaaccaaaataaagtatggttcaaaagcatagaagttgtaccgtatccattttctaaacatgtgttctgctctgtactcagGAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGCTTTTTGGATTCGATGGCAACACTAAATTTGCCTGCTTGGGGATATGGTC

Basic information

species Oryza sativa
transcript LOC_Os01g63270.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 2
-----ttagatttgatccgatgtttaaccaaaataaagtatggttcaaaagcatagaagttgtaccgtatccattttctaaacatgtgttctgc--tctgtactcagGAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGCTTTTTGGATTCGATGGCAACACTAAATTTGCCTGCTTGGGGATATGGTC
      |  ||   ||| ||  ||||      |    | ||  |||| ||   |        ||   |  | ||  |  |||    | ||   |  | | | | |||||||||||||||||||| || ||||| |||||||||||||| |||||||||||||||||||| ||||||||| | ||||||||||||||||| ||||| |
caaggattcatggcatctgagttttactttccaattgggat--ttcataaattt-----ccataattttccaatgatgcaaattaatatttaacgattttttcacagGAAAAAGATGCAGCTCTAGGGAATGGCGGCTTGGGTAGGCTTGCATCTTGCTTTTTGGATTCAATGGCAACATTGAATTTGCCTGCTTGGGGCTATGGCC

upper sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G45210.1 (Glycine max), 3'ss of exon 3
----ttagatttgatccgatgtttaaccaaaataaagtatggttcaaaagcatagaagttgtaccgtatccattttctaaacatgtgttctgctctgtactcagGAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGCTTTTTGGATTCGATGGCAACACTAAATTTGCCTGCTTGGGGATATGGTC
    ||       |  |    |||   || |   | |  |||||  ||    |||    |  | |  ||    |     |  |    | |  || ||    ||||| || |||||||| || |||||||||||  | |||||||| || ||||||||| ||||||| ||||||||||| ||||||||| ||||||| |||||| 
agcattttcgaaaagtctgcatttcttcatatgtatgattggttttaatatctagtgtctaaaactcatttgctgaaccattacacatgcaactttg----cagGAGAAGGATGCAGCACTAGGAAATGGTGGTCTTGGTAGGCTTGCTTCTTGCTTTCTGGATTCCATGGCAACACTTAATTTGCCTTCTTGGGGGTATGGTT

upper sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA18G07480.1 (Glycine max), 3'ss of exon 2
-----ttagatttgatccgatgtttaaccaaaataaagtatggttcaaaagcatagaagttgtaccgtatccattttctaaacatgtgttctgctctgtactcagGAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGCTTTTTGGATTCGATGGCAACACTAAATTTGCCTGCTTGGGGATATGGTC
     ||       |  |    |||   || |   | |  |||||  ||    |||    ||||    |  ||||| ||  ||   |   |       |   ||||| || |||||||| || |||||||||||  | |||||||| || ||||||||| ||||||| ||||||||||| ||||||||| ||||||| |||||| 
aagcattttccaaaagtctgcatttcttcatatgtatggttggttttaatatctag----tgtataaaactcatttgctggaccattaaacgtgcaactttgcaGGAGAAGGATGCAGCACTAGGAAATGGTGGTCTTGGTAGGCTTGCTTCTTGCTTTCTGGATTCCATGGCAACACTTAATTTGCCTTCTTGGGGGTATGGT-

upper sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G46970.1 (Arabidopsis thaliana), 3'ss of exon 3
ttagatttgatccgatgtttaaccaaaataaagtatggttcaaaagcatagaagttgtaccgtatccattttctaaacatgtgttctgctctgtactcagGAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGCTTTTTGGATTCGATGGCAACACTAAATTTGCCTGCTTGGGGATATGGTC
              |  ||| |    |  |   |    ||  ||  | | | |  |  |    |   ||||| | | |   | | |   | ||     |||| |||||||||||||| ||||||||||| || || || || || || || || |||||||||||||| || |||||| ||||||||||||| |||||| 
------------gtacattttaagttaccatttttctctttgaagacttgggacctaaat--aaattattttttgatc---tctccatgtttgcttgtagGAGAAAGATGCAGCTCTAGGAAATGGTGGGTTAGGGAGACTTGCCTCGTGTTTCTTGGATTCGATGGCCACCCTAAATCTGCCTGCTTGGGGTTATGGTT

upper sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv06s0004g06020.t01 (Vitis vinifera), 3'ss of exon 2
-----ttagatttgatccgatgtttaaccaaaataaagtatggttcaaaagcatagaagttgtaccgtatccattttctaaacatgtgttctgctctgtactcagGAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGCTTTTTGGATTCGATGGCAACACTAAATTTGCCTGCTTGGGGATATGGTC
       |   ||     |  |||||    |||||| | ||   ||    || |      |  ||  |     |||  | |  ||  |   || | | |    ||||||||||||| || || |||||||||||  |||| ||||| || || |||||| | || || ||||||||| ||||||||||||| |||||||||||| 
agtctgcattcttcgattgtagtttatttgaaataatg-atatctct---gcgtttggtctcaacttttgaactttgatgattataagaaatgatatct-tatagGAAAAAGATGCGGCACTAGGAAATGGTGGACTGGGAAGGCTTGCTTCATGCTTTCTTGACTCCATGGCAACATTAAATTTGCCTGCGTGGGGATATGGTT

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|29625767|gb|CB630778.1|CB630778
EST:     CGGAGGCCGTGAAGAAGTTCGGGTACGAGCTCGAGGCCCTCGTCGGGCAG                         GAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGC
genomic: CGGAGGCCGTGAAGAAGTTCGGGTACGAGCTCGAGGCCCTCGTCGGGCAGgtgagctccc ... ctgtactcagGAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGC
EST: gi|29625892|gb|CB630903.1|CB630903
EST:     CGGAGGCCGTGAAGAAGTTCGGGTACGAGCTCGAGGCCCTCGTCGGGCAG                         GAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGC
genomic: CGGAGGCCGTGAAGAAGTTCGGGTACGAGCTCGAGGCCCTCGTCGGGCAGgtgagctccc ... ctgtactcagGAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatagaagttgtaccgtatccattttctaaacatgtgttctgctctgtactcagGAAAAAGATGCAGCTCTGGGAAATGGTGGCTTGGGTAGGCTCGCATCTTGCTTTTTGGATTCGATGGCAACACTAAATTTGCCTGCTTGGGGATATGGTC
                         ttctaaa  putative branch site (score: 2)
                                      ttctgctct  putative PPT
                      attttctaaa  TA-rich tract