Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttagatttttttttatgcagtcatgctctgctatcggttcatgttttaacttggccacacttaaatttggcaagctatgactccttgcagttttagtgtgtggttaacatctgttattatttagttgctccttcattgtgcatttcactagttgctgatctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTATCATGCAACGTCAAAGACAAAGACAG

Basic information

species Oryza sativa
transcript LOC_Os02g36740.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g36740.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G156734_T01 (Zea mays), 3'ss of exon 5
gtaagttagatttttttttatgcagtcatgctctgctatcggttcatgttttaacttggccacacttaaatttggcaagctatgactccttgcagttttagtgtgtggttaacatctgttattatttagttgctccttcat---tgtgcatttcactagtt--gctgatctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTATCATGCAACGTCAAAGACAAAGACAG
                                                                                                    ||  ||| |||| |  |  |||   |    || |  ||  |   |||  | || |||   |  | || | ||| |||| | ||||||||||| || |||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||
----------------------------------------------------------------------------------------------------gttagtgattaatacattgtatatctcctgtgtttttttgtcgatgtaaagttaactgactctgttggtatttgacagCTATTTCTTTTGAGAGCGGCTGGATTTTTGCTGCCATGCTATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG

upper sequence: LOC_Os02g36740.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G118957_T05 (Zea mays), 3'ss of exon 2
gtaagttagatttttttttatgcagtcatgctctgctatcggttcatgttttaacttggccacacttaaatttggcaagctatgactccttgcagttttagtgtgtggttaacatctgttattatttagttgctccttcattgtgcatttcactagtt--gctgatctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTATCATGCAACGTCAAAGACAAAGACAG
                                                                                                 |||| |   | |  |   |   | |  | |  ||  |    |  |||  | || | |   |  |||| |||||  ||| | ||||||||||| || |||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||
------------------------------------------------------------------------------------------------gttagcgatcgatacattgcatatctcctgtgttttttttggcgatgtaaagttaattgactctgctggtctttggcagCTATTTCTTTTGAGAGCCGCTGGATTTTTGCTGCCATGCTATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG

upper sequence: LOC_Os02g36740.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G02960.2 (Arabidopsis thaliana), 3'ss of exon 6
gtaagttagatttttttttatgcagtcatgctctgctatcggttcatgttttaacttggccacacttaaatttggc-aagctatgactccttgcagttttagtgtgtggttaacatctgttattatttagttgctccttcattgtgcatttcactagttgctgatctttaac--agTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTATCATGCAACGTCAAAGACAAAGACAG
                                                                  |||  |     |||||    |   ||    ||||  | | |  ||    || |||    || |||||   |  ||      |   ||  | |  |||||  |||    || |  | ||  |  | |||||||||||| | || ||||||||||||||||||||||| || |||||  | || || | |||||| ||||||
-----------------------------------------------------------------gtaagctcattgaagcttcttccttttttctttttcttttattttttgtctcagttgcatttaagttgtaacaccaa-----accacaaaattgtctgattcttattttagCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAG

upper sequence: LOC_Os02g36740.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G62460.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagttagatttttttttatgcagtcatgctctgctatcggttcatgttttaacttggccacacttaaatttggcaagctatgactccttgcagttttagtgtgtggttaacatctg-ttattatttagttgctccttcattgtgcatttcactagttgctgatctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTATCATGCAACGTCAAAGACAAAGACAG
                                                                          | | | ||   |||  |  | |   |||  ||     |  |||  || ||  ||  ||| |    |||| | | |||  ||  |  ||  | |     || | ||  |  |  | || ||||| ||| | || || || || |||||||||||||||||||||||  | ||||||| |||||||||||||
--------------------------------------------------------------------------gtacg-tacatctctct-tactcacagttcgttacagaattctcctttttgctttcttgttataacatttttcgtttt-cttttgtcttctttcggttagCTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCTTGGGCTATTAGTATATTACAACGTCGAAGACAAAGACAG

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|218486849|gb|FG957899.1|FG957899
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGC-
EST: gi|29663450|gb|CB659725.1|CB659725
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|58602522|gb|CK013050.1|CK013050
EST:     TAACCATTACTAGTAGTGATGATGAAGATAACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|29677125|gb|CB673400.1|CB673400
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|33793334|gb|CF322548.1|CF322548
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|86869793|gb|CI316521.1|CI316521
EST:     AACCACTACTACTACTGATGATGAAGATGACGCATC-GCCTATTTTCTCC                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: AACCATTACTAGTAGTGATGATGAAGATGACGCATCTG-CTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|5803574|gb|AI978544.1|AI978544
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|29686718|gb|CB682993.1|CB682993
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|27576199|gb|CA998893.1|CA998893
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|88841916|gb|CI081172.1|CI081172
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|27578072|gb|CB000767.1|CB000767
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|29686717|gb|CB682992.1|CB682992
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|27554462|gb|CA998362.1|CA998362
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|86887217|gb|CI326032.1|CI326032
EST:     GCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: GCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|88243846|gb|CI242968.1|CI242968
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|58695300|gb|CK083987.1|CK083987
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTTGAGGGCTGCTGGATTTTTTGCTGCCATGCTATATCATGG
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTT-GAGGGCTGCTGGATTTTT-GCTGCCATGCTATATCATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattatttagttgctccttcattgtgcatttcactagttgctgatctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTATCATGCAACGTCAAAGACAAAGACAG
                                       tgctgat  putative branch site (score: 3)
                                             tcttt  CT-rich tract
     atttagtt  TA-rich tract