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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggctctttttgtgtccattgtaatttatgagtgttttcttttatgcctaatgaggtgggtggattatggcagGAACCCTCAAGTTGACTTGCAAGCTCAGGATCGTGCACATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTCCGGTTCTGCACCGAG

Basic information

species Arabidopsis thaliana
transcript AT5G18620.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 11
gtaaggctctttttgtgtccattgtaatttatgagtgttttcttttatgcctaatgaggtgggtggat--tatggcagGAACCCTCAAGTTGACTTGCAAGCTCAGGATCGTGCACATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTCCGGTTCTGCACCGAG
||| | |  |||        | | |  | |     |    | | | | |   || |   ||| |   |  | |  |||||| |||||||| ||  ||||||| || |||||||||||||| ||||||||||| |||||||||||||| || || |||||||| |||
gtatgtccttttcaaatcgtaattttttctcattctacaatttgtgaagttaaaggttatggttatttggtttcacagGAATCCTCAAGTGGATCTGCAAGCGCAAGATCGTGCACATAGAATTGGTCAAAAGAAAGAAGTTCAAGTTTTTCGTTTCTGCACTGAG

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 11
-------gtaaggctctttttgtgtccattg--taatttatgagtgttttcttttatgcctaatgaggtgggtggattatggcagGAACCCTCAAGTTGACTTGCAAGCTCAGGATCGTGCACATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTCCGGTTCTGCACCGAG
          | |||    |||  ||  |||  ||   || || ||  |    | ||||||  ||   |   ||        |||||| || |||| |||  ||||||||||||| |||||||||||||| |||||||| |||||||||||||||||||| || ||||| |||
gtatgagactatgctaaacttgattctgttgcttaccctaagaatgaatc---taatgcctc-tgttatttctgtgcctc--cagGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 11
-------------------gtaaggctctttttgtgtccattgtaat-ttatgagtgttttctt--ttatgcctaatga-ggtgggtggattatggcagGAACCCTCAAGTTGACTTGCAAGCTCAGGATCGTGCACATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTCCGGTTCTGCACCGAG
                   || ||   | || |         || ||   || |||   |   |  || |   |  |||   | ||||| ||||  ||||||||||||||||||| ||||||||||||||||||| ||||||||||||||||| |||||||||||||| ||||| || ||||| |||
gttagtattcttgttgattgtcagcagccttcta-acttgcagtgatgccataagttcatgactaattgtttttgttgataattggtgg-ttataacagGAACCCTCAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 11
----------gtaa-ggctctttttgtgtccattgtaatttatgagtgttttcttttatgcctaatga-ggtgggtggatt-atggcagGAACCCTCAAGTTGACTTGCAAGCTCAGGATCGTGCACATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTCCGGTTCTGCACCGAG
           ||   | | |        |||| || ||||||   |||   |   |     |  ||| ||| ||||  || |   ||||||||| |||||||||||||| |||||||||||||| ||||||||||||||||| |||||||||||||| ||||| || || || |||
gtcagtatttctagtagttttgaacacagccat-gttatttatatctgtacccaaattattttgttgatggttggtgcttttacaacagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGTTTTTGTACTGAG

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 11
--------gtaaggctctttttgtgtccattgt--aatttatgagtgttttcttttatgcctaatga-ggtgggtggatt-atggcagGAACCCTCAAGTTGACTTGCAAGCTCAGGATCGTGCACATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTCCGGTTCTGCACCGAG
         | | |   || | |  ||     |   ||||||   |||       |     |  ||| ||| ||||  || |   ||||||||| |||||||||||||| |||||||||||||| ||||||||||||||||| |||||||||||||| ||||| || || || |||
gtcagtatttcaagtagttatggactcagccatctgatttatatctgtaccaaaattattttgttgatggttggtgcttttacaacagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAG

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 11
-----------------------gtaaggctctt-tttgtgtccat--tgtaa-tttatgagtgttttcttttatgcctaatgaggtgggtggattatggcagGAACCCTCAAGTTGACTTGCAAGCTCAGGATCGTGCACATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTCCGGTTCTGCACCGAG
                       | |    |||   |||   |  |    ||| || |||| |  ||  |||| |   | || |  | ||||| ||||  ||||||||| ||||||||| ||||||||||||||||||| ||||||||||||||||| |||||||||||||| ||||| || ||||| |||
gcaagtattcatattgattgtcagcagccttctaacttgcagcggtgccataagttcatgactaattctttttgt---tgataa--ttggtgg-ttataacagGAACCCACAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 11
------------gtaaggctctttttgtgtccattgtaatttatgag---tgttttcttttatgcctaatgaggtgggtggattatggca-----gGAACCCTCAAGTTGACTTGCAAGCTCAGGATCGTGCACATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTCCGGTTCTGCACCGAG
              |    | ||| | | ||  ||  |||    | |   |||| | || | | || |    | ||      |||| |||     ||||||| |||||||| |||||||| || |||||||| ||| ||||||||||||| ||||||||||||||||| || |||||||| |||
gtgagcatttctccatttttttttctttttcttttagaatgctagggaattgttatattatttaccaatctggttgatctctttattgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 11
gtaaggctctttttgtgtccattgtaatttatgagtgttttcttttatgcctaatgaggtgggtggattatg--gcagGAACCCTCAAGTTGACTTGCAAGCTCAGGATCGTGCACATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTCCGGTTCTGCACCGAG
                       |||||  |  | || ||| || |  |    |||   |  |   ||||||  ||||||| |||||||| || |||||||| || ||||| |||||| ||||||| || ||||||||||||||||| ||||| || |||||  ||
-----------------------gtaat--aataatgatttgttctgagtggcatgtttttag-aaattatgctgcagGAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACAGAAAAAAGAAGTTCAAGTTTTCCGATTTTGCACGCAG

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 11
gtaaggctctttttgtgtccattgtaatttatgagtgttttcttttatgcctaatgaggtgggtggattatggcagGAACCCTCAAGTTGACTTGCAAGCTCAGGATCGTGCACATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTCCGGTTCTGCACCGAG
                       |||||  |  | || ||| || |  |    |||   | |      |   ||||||| |||||||| || |||||||| || ||||| |||||| ||||||| || ||||||||||||||||| ||||| || |||||  ||
-----------------------gtaat--agtaatgatttgttctgagtggcatgttttagaaattatgctgcagGAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACAGAAAAAAGAAGTTCAAGTTTTCCGATTTTGCACGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtaatttatgagtgttttcttttatgcctaatgaggtgggtggattatggcagGAACCCTCAAGTTGACTTGCAAGCTCAGGATCGTGCACATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTCCGGTTCTGCACCGAG
                           gcctaat  putative branch site (score: 3)
                ttttcttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggctctttttgtgtccattgtaatttatgagtgttttcttttatgcctaatgaggtgggtggattatggcagGAACCCTCAAGTTGACTTGCAAGCTCAGGATCGTGCACATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTCCGGTTCTGCACCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT