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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtaaatgtatgtgatgtactgtaaggagtgctaaccgtattgtgcattgtaagcatttgagttacagcaattaaaatgtggccattctgatgtgtgcagGGAAAACAAAAAGTGAGATATGGAAAAGTTGGTTTTCCTGACAATGAAATCACTGCCAGAAATATCATTATTGCAACGGGGTCTGTTCCTTTTGTCCCCA

Basic information

species Oryza sativa
transcript LOC_Os01g23610.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 3
--agtaaatgtatgtgatgtactgtaaggagtgctaaccgtattgtgcattgtaagcatttgagttacagcaattaaaatgtggccattctgatgtgtgcagGGAAAACAAAAAGTGAGATATGGAAAAGTTGGTTTTCCTGACAATGAAATCACTGCCAGAAATATCATTATTGCAACGGGGTCTGTTCCTTTTGTCCCCA
    ||||  | || | ||  || |      |    |   | |      ||||  |  | | | ||  ||  |||||| | |     ||||||| | || |||| || ||||||||||||||||| ||||||||||| || ||||||||||||||||| ||||| ||||| ||||| || || |||||||||||||||||||
catataaacat-tgagttgagctatgtctgctatatagtctttcaaatgttgtctgagtatcatttgtagtgattaaa-tattctgtttctgatatctgtagGGGAAGCAAAAAGTGAGATATGGGAAAGTTGGTTTCCCAGACAATGAAATCACTGCTAGAAACATCATAATTGCCACTGGATCTGTTCCTTTTGTCCCCA

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------------------------------------------------agtaaatg---tatgtga-tgtactgtaaggagtgctaaccgtattgtgcattgtaagcatttgagttacagcaattaa-aatgtggccattct--gatgtgtgcagGGAAAACAAAAAGTGAGATATGGAAAAGTTGGTTTTCCTGACAATGAAATCACTGCCAGAAATATCATTATTGCAACGGGGTCTGTTCCTTTTGTCCCCA
                                                                                      | |  |||   ||  |||   |    || |   |  |||||    |     ||  ||   |   | | | |   ||||  |||     ||||     || | | |||||    ||||| |||| ||||||||| ||||| ||  |||| |||| ||| ||||| | |||||| || ||||| || || ||||||||||||||||| |
gtaagttgtccatgctgacaaagacaagatctttcaagcaattcaaattaaagcctggtttatgacagttttgaacttcatggaaaaatggatggtttacttgagcctgtcctatgctttaataaccaatctcatggttacaaaagtcctaatgatatttattatcaataatttcatttatgaatttattcagGGCCCTCAAAAGGTGAAATATGGAAAGGTTGGCTTCTCTGAGAATGTAATAACTGCAAAAAATATAATCATTGCTACTGGTTCTGTTCCTTTTGTCCCAA
















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|58675783|gb|CK064470.1|CK064470
EST:     CGATGAAAGCTTTGGGTGTGGATATATTGACTGGTTTTGGCACCATTGTG                         GGAAAACAAAAAGTGAGATATGGAAAAGTTGGTTTTCCTGACAATGAAATC
genomic: CGATGAAAGCTTTGGGTGTGGATATATTGACTGGTTTTGGCACCATTGTGgtaggtcatc ... atgtgtgcagGGAAAACAAAAAGTGAGATATGGAAAAGTTGGTTTTCCTGACAATGAAATC
EST: gi|58670429|gb|CK059115.1|CK059115
EST:     CGATGAAAGCTTTGGGTGTGGATATATTGACTGGTTTTGGCACCATTGTG                         GGAAAACACACAGTGAGATATGGAAAAGTTGGTTTTCCTGACAA
genomic: CGATGAAAGCTTTGGGTGTGGATATATTGACTGGTTTTGGCACCATTGTGgtaggtcatc ... atgtgtgcagGGAAAACAAAAAGTGAGATATGGAAAAGTTGGTTTTCCTGACAA
EST: gi|58684178|gb|CK072865.1|CK072865
EST:     CGATGAAAGCTTTGGGTGTGGATATATTGACTGGTTTTGGCACCATTGTG                         GGAAAACAAAAAGTGAGATATGGAAAAGTTGGTTTTCCTGACAATGAAATC
genomic: CGATGAAAGCTTTGGGTGTGGATATATTGACTGGTTTTGGCACCATTGTGgtaggtcatc ... atgtgtgcagGGAAAACAAAAAGTGAGATATGGAAAAGTTGGTTTTCCTGACAATGAAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgtaagcatttgagttacagcaattaaaatgtggccattctgatgtgtgcagGGAAAACAAAAAGTGAGATATGGAAAAGTTGGTTTTCCTGACAATGAAATCACTGCCAGAAATATCATTATTGCAACGGGGTCTGTTCCTTTTGTCCCCA
                                        ttctgat  putative branch site (score: 3)
                        aattaaaatgt  TA-rich tract