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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttagatttttttttatgcagtcatgctctgctatcggttcatgttttaacttggccacacttaaatttggcaagctatgactccttgcagttttagtgtgtggttaacatctgttattatttagttgctccttcattgtgcatttcactagttgctgatctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTATCATGCAACGTCAAAGACAAAGACAG

Basic information

species Oryza sativa
transcript LOC_Os02g36740.8
intron # 6
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|58602522|gb|CK013050.1|CK013050
EST:     TAACCATTACTAGTAGTGATGATGAAGATAACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|5803574|gb|AI978544.1|AI978544
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|27576199|gb|CA998893.1|CA998893
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|58695300|gb|CK083987.1|CK083987
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTTGAGGGCTGCTGGATTTTTTGCTGCCATGCTATATCATGG
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTT-GAGGGCTGCTGGATTTTT-GCTGCCATGCTATATCATGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 65 (upstream exon), 72 (downstream exon)
Score: 17

CTAATGGCTCTTCTACTCTTAAGGCATACACTAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTATCATGCAACGTCAAAGACAAAGACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattatttagttgctccttcattgtgcatttcactagttgctgatctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTATCATGCAACGTCAAAGACAAAGACAG
                                       tgctgat  putative branch site (score: 17)
                                             tcttt  CT-rich tract
     atttagtt  TA-rich tract