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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgagtaaggtcatttcactttatgtaaattatatgtttttagtgaggcttttcaaaaaaaaacatttctggtgttcatgctgataagttattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT

Basic information

species Oryza sativa
transcript LOC_Os02g07760.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07760.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G128114_T03 (Zea mays), 3'ss of exon 9
-----agtgagtaaggtcat---ttcactttatgtaaattatatgtttttagt--gaggcttttcaaaaaaaaacatttctggtgttcatgctgataagttattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT
       |||  |  ||| |   || |   | ||||   | | |  ||| |||  ||| | ||| ||  |          || || |||     |  | |||||||  |||| |||||||| |||||||| ||||||||||||||||||||||||||||||||||||||||||||  |||||||||||
atttttttgaacatagtcttgttttgaaggtttgtatgctctgtcatttcagtctgagaccttttaatga----------tgatgctcacaaaaaataattattttttagGTCTCTTTGGAACTTGGTGGGAATGCACCTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCTGTTAAAGGCAGT

upper sequence: LOC_Os02g07760.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G119482_T01 (Zea mays), 3'ss of exon 10
-agtgagtaaggtcatttcactttatgtaaattatatgtttttagtgaggcttttcaaaaaaaaacatttctggtgttcatgctgata-agttattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT
   |    ||  |  | |   |||       ||  ||| | |        |  |   | |   |    |  || |   ||     | | | | || ||  |||| || ||||| |||||||| |||||||||||||||||||| |||||||| ||||||||||||||  |||||||||||
gttttttgaacatggtcttgttttg-aaggtttgcatgctct-gtcatttcagtctgagacctagtgatgatgctcaccaaaaaaaaacaataatgttgtagGTCTCCTTGGAACTTGGTGGGAATGCACCTTGCATTGTTTTCGATGATGCGGACATTGATGTTGCTGTTAAAGGCAGT

upper sequence: LOC_Os02g07760.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA15G41690.1 (Glycine max), 3'ss of exon 10
agtgagtaaggtcatttcactttatgtaaattatatgtttttagtgaggcttttcaaaaaaaaacatttctggtgttcatgctgataagttattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT
     ||| | | |  |   ||  ||| ||||   | ||   |   ||| | |  | |     |  ||     | |  ||||   |   | |  || ||||| ||| | || || || ||||||||||||||||| |||||||||||||| ||| | ||||||||  | ||||| | |
-----gtatgcttagat--attgttgtgaatt---tcttcaaatacaggatctatacatcttgatcttatatatatatatgccttt---tgaacttccagGTATCTCTTGAACTCGGCGGCAATGCACCTTGCATAGTTTTTGATGATGCTGACCTGGATGTTGCAGTAAAAGGAACT

upper sequence: LOC_Os02g07760.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA08G17450.1 (Glycine max), 3'ss of exon 10
agtgagtaaggtcatttcactttatgtaaattatatgtttttagtgaggcttttcaaaaaaaaacatttctggtgttcatgctgataagttattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT
     ||| | | |  |    | |||  ||||      ||  | |      ||  ||  |      || |   | |  ||  ||     | |  || ||||| ||| | || || |||||||||||||||||||| |||||||||||||| ||| | ||||||||  | ||||| | |
-----gtatgcttagatattgtcatg--aatttc----ttcaaatacaagattagaaggattttttttaccattatatata-tgccttttgaacttccagGTATCTCTTGAACTCGGTGGCAATGCACCTTGCATAGTTTTTGATGATGCTGACCTGGATGTTGCAGTAAAAGGAACT

upper sequence: LOC_Os02g07760.1 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S6_180V6.1 (Physcomitrella patens), 3'ss of exon 9
agtgagtaaggtcatttcactttatgtaaattat----atgttttta-gtgaggct---tttcaaaaaaaaacatttctggtgttcatgctgataagttattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT-
    |  |   | | || ||| |||| |  || |     |||||||   || | ||     |   |  | || |||     ||   | | || || |        |||||||| || ||||||||||| || ||||| ||||| ||||||||||||||  |  | || |||||  ||||||| ||| 
--ctacgagatttacttaactgtatggattttttccgggtgtttttgcatgtgactgaacctgcgaccagaatattctccttgacaaagatggtatgc------gcagGTTTCCTTAGAGCTTGGTGGTAACGCACCGTGCATCGTTTTTGATGATGCTAATTTGGACGTTGCTGTTAAAGG-AGTG

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|163925517|gb|EG715386.1|EG715386
EST:     CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
genomic: CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
EST: gi|218498176|gb|FG949780.1|FG949780
EST:     CAGCTGTTGGC-AAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
genomic: CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
EST: gi|218492832|gb|FG951181.1|FG951181
EST:     AGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACCTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAA
genomic: AGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATAC-TGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAA
EST: gi|88288968|gb|CI520298.1|CI520298
EST:     CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
genomic: CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
EST: gi|218482143|gb|FG968613.1|FG968613
EST:     CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
genomic: CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
EST: gi|218492318|gb|FG946726.1|FG946726
EST:     CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
genomic: CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
EST: gi|88519470|gb|CI447124.1|CI447124
EST:     CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
genomic: CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
EST: gi|218490731|gb|FG966180.1|FG966180
EST:     CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
genomic: CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
EST: gi|66918914|gb|CX105762.1|CX105762
EST:     CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         G-TTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
genomic: CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
EST: gi|218488132|gb|FG951352.1|FG951352
EST:     CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAATGCACCTTG
genomic: CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTG
EST: gi|58694576|gb|CK083263.1|CK083263
EST:     AGCTGTTGGCNNNNNNNCTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
genomic: AGCTGTTGGC-AAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA
EST: gi|218491346|gb|FG955033.1|FG955033
EST:     CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAG                         GTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTGTGATGATGCA
genomic: CAGCTGTTGGCAAAAAACTGATGGCTGGATCAGCAAATACTGTGAAGAAGgtataaccga ... tattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggcttttcaaaaaaaaacatttctggtgttcatgctgataagttattttacagGTTTCTTTGGAGCTTGGTGGCAATGCACCTTGCATTGTTTTTGATGATGCAGACATTGATGTTGCCATTAAAGGCAGT
                                  tgctgat  putative branch site (score: 3)
                                            ttatttt  putative PPT
     ttttcaaaaaaaaaca  TA-rich tract