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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctcacaattttgcaatccagctgccttcctttttagctacttcttgtatgtatctttttcaaaaataataataataaggtttgtgtatgagttatcagGGAACTGCTGGTGTTGCACTGGCTGGACTATTGGGAACTGTAAGAGCTCAAGGTCGGCCGATATCCGACTTTGTGAACCAAAAGATTGTTGTGGTGGGAG

Basic information

species Arabidopsis thaliana
transcript AT4G00570.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G00570.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA07G08110.1 (Glycine max), 3'ss of exon 8
----------------gtatgctcacaattttgcaat--ccagctgccttccttttta-gctacttcttgtatgtatctttttcaaaaataataataataaggtttgtgtatgagttatcagGGAACTGCTGGTGTTGCACTGGCTGGACTATTGGGAACTGTAAGAGCTCAAGGTCGGCCGATATCCGACTTTGTGAACCAAAAGATTGTTGTGGTGGGAG
                  ||  |   ||| | | ||        ||  ||   |   |  || | |  |  | ||| ||  |  ||   | | | |   ||  ||  |  |||   ||| |||| ||||| ||||||||||| |||||||||||||||||||||||||| ||||| |||||  |  | || ||||||||||||||||| |||||||| ||||
gtgagaatgtgagattaaatattgttaatgtagaaaatgttgaatgtgttatctaacacactgcattattgaagtaactactgaaagtctgaaagtt-caattttacttcatgtcctat-agGGCACTGCAGGTGTTGCACTTGCTGGACTATTGGGAACTGTAAGAGCCCAAGGCCGGCCATTGACTGATTTTGTGAACCAAAAGATAGTTGTGGTTGGAG

upper sequence: AT4G00570.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA03G01680.1 (Glycine max), 3'ss of exon 9
------------gtatgctcacaattttgcaatcca-gctgccttcctttttagctacttcttgtatgtatctttttcaaaaataataataataaggtttgtgtatgagttatcagGGAACTGCTGGTGTTGCACTGGCTGGACTATTGGGAACTGTAAGAGCTCAAGGTCGGCCGATATCCGACTTTGTGAACCAAAAGATTGTTGTGGTGGGAG
            |  |    |   ||||| |    | | ||  |   || |     ||| |||  ||| |     | |  |||    |||  ||   ||  |||   |      |||| ||||||||||||||||| |||||| ||||||||||||||||||| ||||| || ||  |  | || ||||||||||||||||| |||||||| ||||
gtgagaaagtgagattaaatattgttttgtagaaaatgttgaatgtgttatctaacactgctttaatgaagtaactactgaaacttcaattttac--ttcatgtccta-----tagGGCACTGCTGGTGTTGCACTTGCTGGAATATTGGGAACTGTAAGAGCCCAAGGCCGACCATTGACTGATTTTGTGAACCAAAAGATAGTTGTGGTTGGAG

upper sequence: AT4G00570.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA09G39870.1 (Glycine max), 3'ss of exon 8
-------------------gtatgctcacaattttgcaatccagctgccttcctttttagctacttcttgtatgtatctttttcaaaaataataataataaggtttgtgtatgagttatcagGGAACTGCTGGTGTTGCACTGGCTGGACTATTGGGAACTGTAAGAGCTCAAGGTCGGCCGATATCCGACTTTGTGAACCAAAAGATTGTTGTGGTGGGAG
                    | |||| ||| ||      | ||| ||  ||   | |   ||   |  |  | ||  ||| |    ||| |  |||  |      | |  ||     |  |||| || |||||||||||||| |||||||||||||||||||||||  | |||||||| ||  | || || ||| |||| |||||||| |||||||| ||||
gtgagaaagtgatattatattttgctgacatttaaaatcttcag-tgtgttaagtatgcactgtgttcttgaagtgacttct----aaacatcaattgtctttcatttccattgtccaatagGGCACAGCTGGTGTTGCACTTGCTGGACTATTGGGAACTGTAAGGTCCCAAGGTCGACCATTGTCTGATTTTTTGAAGCAAAAGATAGTTGTGGTTGGAG

upper sequence: AT4G00570.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA18G46340.1 (Glycine max), 3'ss of exon 8
----------------gtatgctcacaattttgcaatccagctgccttcctttttagctacttcttgtatgtatctttttcaaaaataataataataaggtttgtgtatgagttatcagGGAACTGCTGGTGTTGCACTGGCTGGACTATTGGGAACTGTAAGAGCTCAAGGTCGGCCGATATCCGACTTTGTGAACCAAAAGATTGTTGTGGTGGGAG
                 |||  |   ||  ||  ||  |  | |  |      | |   |||   |   || |     ||| ||| ||  |||  |      |    ||     |  |||| || |||||||||||||| |||||||||||||||||||| ||| |||||||||  ||  | || || ||| |||| |||||||| || ||||| ||||
gtgagaaagtgatactatattttgctaacatttaaaatcttcagtgtgttaagtaatgcactgtgttcttgaagtgacttctaaa-tatcaattttccttcattgccattgtccaatagGGCACGGCTGGTGTTGCACTTGCTGGACTATTGGGAACTGTTAGATCTCAAGGTCAACCATTGTCTGATTTTTTGAAACAAAAGATAGTCGTGGTTGGAG

upper sequence: AT4G00570.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv15s0046g03670.t01 (Vitis vinifera), 3'ss of exon 8
gtatgctcacaattttgcaatccagctgccttcctttttagctact-tcttgtatgtatctttttcaaaaataataataataaggtttgtgtatgagttatcagGGAACTGCTGGTGTTGCACTGGCTGGACTATTGGGAACTGTAAGAGCTCAAGGTCGGCCGATATCCGACTTTGTGAACCAAAAGATTGTTGTGGTGGGAG
      | |  |||| |   |  | ||||  |  | | | | ||   |   | || |    |  |  | | |  |  |  |    | | |  |||  |||| ||||||||||||||||||| ||||| ||||| || |||||||| ||||| |||||||| ||| |  | |||||||| ||||||||||| ||||| || ||||
-----gttagtatttagt--tggatctgctattttatatggatatagtaaagcatatgatgtgatgcagagttctgtttgtgct-tatattcatgtcttat-agGGAACTGCTGGTGTTGCTCTGGCGGGACTTTTAGGAACTGTTAGAGCACAAGGTCGACCGTTGACTGACTTTGTCAACCAAAAGATAGTTGTAGTTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtatgtatctttttcaaaaataataataataaggtttgtgtatgagttatcagGGAACTGCTGGTGTTGCACTGGCTGGACTATTGGGAACTGTAAGAGCTCAAGGTCGGCCGATATCCGACTTTGTGAACCAAAAGATTGTTGTGGTGGGAG
     tgtatctttttcaaaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctcacaattttgcaatccagctgccttcctttttagctacttcttgtatgtatctttttcaaaaataataataataaggtttgtgtatgagttatcagGGAACTGCTGGTGTTGCACTGGCTGGACTATTGGGAACTGTAAGAGCTCAAGGTCGGCCGATATCCGACTTTGTGAACCAAAAGATTGTTGTGGTGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG