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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattgaatgtgttttacctcatcagttgtgatttaactgtgtaggtttttggttttgctaatgcggttttggtttgtgtttgccagCCAATCAAGGAAGGTGCTTTGGGAAACATTCCAACTATTGCCTTCTGTGACACGGATTCTCCAATGGGATTTGTCGACATTGGTATTCCTGCTAACAACA

Basic information

species Arabidopsis thaliana
transcript AT3G04770.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G04770.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g42450.1 (Oryza sativa), 3'ss of exon 2
gtata--ttgaatgtgttttacctcatcagttgtgatttaactgtgtaggtttttggttttgctaatgcggttttggtttgtgtttgccagCCAATCAAGGAAGGTGCTTTGGGAAACATTCCAACTATTGCCTTCTGTGACACGGATTCTCCAATGGGATTTGTCGACATTGGTATTCCTGCTAACAACA
|||    || | | ||||| |     ||  | || |||| |   ||    ||    |   |   ||  | |  |    |  ||| | | ||||||| |||||   |||  | ||||||||||| || ||||||||||||||||| || ||||||||| | | ||| || ||||||||||||||||||||||
gtaagatttcagtatgtttgattgtttct-tggtaatttgatc-tgccaattgagtgcactctcaagcctgcctgttgtaatgtgtac-agCCAATTAAGGAGTCTGCACTTGGAAACATTCCTACCATTGCCTTCTGTGACACTGACTCTCCAATGCGCTATGTTGATATTGGTATTCCTGCTAACAACA

upper sequence: AT3G04770.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g28410.1 (Oryza sativa), 3'ss of exon 2
gtatattgaatgtgttttacc--tcatcagttgtgatttaact-gtgtaggtttttggttttgctaatgcggttttggtttgtgtttgccagCCAATCAAGGAAGGTGCTTTGGGAAACATTCCAACTATTGCCTTCTGTGACACGGATTCTCCAATGGGATTTGTCGACATTGGTATTCCTGCTAACAACA
     ||  || ||||  |       ||  |||  ||  |  | |  || || |||     ||  |||   |||||| |  || ||   ||||||||||||||   |||| | |||||||| || |||||||| ||||||||||| |||||||| ||| | | |||||||||||                  
----gttatatttgttccatgagcactcttttgcaatggagtttgcatatgtgtttatagctgtcaatt--gttttgat--gttttgtgcagCCAATCAAGGAGTCTGCTCTTGGAAACATCCCCACTATTGCTTTCTGTGACACTGATTCTCCCATGCGCTATGTCGACATTG------------------

upper sequence: AT3G04770.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g08440.1 (Oryza sativa), 3'ss of exon 2
gtatattgaatgtgttttacctcatcagt-tgtgatttaactgtgtaggtttttggtt-ttgctaatgcggttttggtttgtgtttgccagCCAATCAAGGAAGGTGCTTTGGGAAACATTCCAACTATTGCCTTCTGTGACACGGATTCTCCAATGGGATTTGTCGACATTGGTATTCCTGCTAACAACA
||  |    ||      |  | |   |||  ||   | || || |||   | ||| ||  || |  ||   |  ||  || ||| ||| |||||||||||||   |||| |||||||||| || || ||||||||||||||||| ||||| |||||| | | |||||| || || || || || |||||||
gtgaaaatgat-caccatgtcacggtagtgcgttggtgaattgggtacagtattgtttactgatcgtgttatcctgaattatgtctgc-agCCAATCAAGGAGTCTGCTCTGGGAAACATCCCGACCATTGCCTTCTGTGACACCGATTCCCCAATGCGGTATGTCGATATCGGCATCCCGGCCAACAACA

upper sequence: AT3G04770.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G092719_T01 (Zea mays), 3'ss of exon 2
------gtatattgaatgt-gttttacctcatcagttg-tgatttaactgtgtaggtttttggttttgctaatgcggttttggtttgtgtttgccagCCAATCAAGGAAGGTGCTTTGGGAAACATTCCAACTATTGCCTTCTGTGACACGGATTCTCCAATGGGATTTGTCGACATTGGTATTCCTGCTAACAACA
       ||  || | | |     | |   |  | ||  ||| |  ||  || ||  |  ||||      | ||   |  ||||    |||||| |||||||||||||   |||| |||| ||||| ||||| ||||||||||||||||| || ||||| ||| | |  ||||| || || || || || |||||||
gtgacaatagtttcagtttcaaagttctgaagtacttactgagtggaccctgcagtgtgatggtgaactaattgttatgctggtaatcgtttgc-agCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGACACTGACTCTCCCATGCGGTACGTCGATATCGGCATCCCAGCGAACAACA

upper sequence: AT3G04770.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G17000.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------------------------------------------gtatattgaatgt--gttttacctcatcagttgtgatttaactgtgtaggtttttggttttgctaatgcggttt--------tggtttgtgtttgc-cagCCAATCAAGGAAGGTGCTTTGGGAAACATTCCAACTATTGCCTTCTGTGACACGGATTCTCCAATGGGATTTGTCGACATTGGTATTCCTGCTAACAACA
                                                                                     || | ||||  ||  |||| |  |        || | | | || |||   ||| ||  | | ||     | |||        |  ||  | ||||  ||||| ||||||||||||||| | ||||| |||||||||||||| || |||||||| |||||||||||| | | ||| ||  | || || ||||| || || |
gttattacccctttagaagttataaccagagagtattaaaggtgttttcaggagttatattgttcaacttttaaccgtcaaggatgtttgttgagggttggtttgaaatttctgacagtaactgatct-tgtttttttgtgcctgtcctgccatgatttgccttatgttattgatttttgtgcagCCTATCAAGGAAGGTGCTCTTGGAAATATTCCAACTATTGCTTTTTGTGACACTGATTCTCCAATGCGGTATGTTGATGTCGGGATCCCTGCCAATAATA

upper sequence: AT3G04770.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G42150.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------------------------gtatattgaatgtgttttacctcatcagttgtgat-----ttaactgtgtaggtttttg---gttttgct--aatgcggttttggtttgtg-tttgc---cagCCAATCAAGGAAGGTGCTTTGGGAAACATTCCAACTATTGCCTTCTGTGACACGGATTCTCCAATGGGATTTGTCGACATTGGTATTCCTGCTAACAACA
                                                                                 | || ||   || || ||   |    | ||||||      |||||  |||   ||| ||   || ||||   |||  |  ||  |||  || ||||    ||||| |||||||| |||||| | ||||| |||||||||||||| || || ||||| |||||||||||| | | ||| ||  |||| |||||||| || || |
gttattacccctttagaagttagaaccagagagtatttaaggtgttttcaggagttatatagttcaactcttcaccgtcaaggatgtttgttgagtgttggtttgaaatttgtgacagtaattaaccttgttattttgtgtctgtcttgccacaatttgtcttatgttattgatttgtgtgcagCCTATCAAGGAGGGTGCTCTTGGAAATATTCCAACTATTGCTTTTTGCGACACTGATTCTCCAATGCGGTATGTTGATGTTGGGATTCCTGCCAATAATA

upper sequence: AT3G04770.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G01460.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------gtatattgaatgtgttttacct-catcagttgtgatt-taactgtgtaggtt-tttggttttgctaatgcg-gttttggtttgtgtttgc-cagCCAATCAAGGAAGGTGCTTTGGGAAACATTCCAACTATTGCCTTCTGTGACACGGATTCTCCAATGGGATTTGTCGACATTGGTATTCCTGCTAACAACA
                                                               ||  |    || | | |||  |   |   ||| | || |    |||| |  | | | || ||| ||||| | || || ||| || | ||  ||||| || ||||||| |||| | || || ||||| || ||||| ||||||||||| ||||| || ||| | | ||| |||||||| |||||||| |||||||
gtggatacccaaatcagcttcaaatgatatatttgattttagttacttgtgctttgattgattgttgacatgatttatgttatgtatgttgtttgcggttgttgtggtgttgactgtgttgtgttgttaatgtgtgtgtttgttcgtttgtgtgcagCCTATTAAGGAAGCTGCTCTTGGGAATATTCCCACCATTGCTTTCTGTGACACTGATTCGCCTATGAGGTATGTGGACATTGGAATTCCTGCCAACAACA

upper sequence: AT3G04770.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv09s0002g00610.t01 (Vitis vinifera), 3'ss of exon 2
-------gtatattgaatgtgtttt-----acctcatcagtt-gtgatttaa-ctgtgtaggtttttggttttgctaatgcggttttggtttgtgtttgccagCCAATCAAGGAAGGTGCTTTGGGAAACATTCCAACTATTGCCTTCTGTGACACGGATTCTCCAATGGGATTTGTCGACATTGGTATTCCTGCTAACAACA
       ||  ||  ||| | | ||     |    || |||| ||| | | |  | | |||        |||| ||  |    |     |   |||||  ||||| || ||||||| |||  | |||||||||||||||||||| ||||||||||| ||||| |||||| | | ||| ||||||||||| || || || ||||
tattttggttcatctaatttatctttgtatagtgtatgagtttgtgttatgagttatttagtccaggatttttact--tatcatcacaataactgttt-tcagCCTATTAAGGAAGCTGCACTAGGAAACATTCCAACTATTGCTTTCTGTGACACTGATTCCCCAATGCGGTATGTTGACATTGGTATCCCAGCCAATAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaactgtgtaggtttttggttttgctaatgcggttttggtttgtgtttgccagCCAATCAAGGAAGGTGCTTTGGGAAACATTCCAACTATTGCCTTCTGTGACACGGATTCTCCAATGGGATTTGTCGACATTGGTATTCCTGCTAACAACA
                        tgctaat  putative branch site (score: 2)
              ttttt  TA-rich tract