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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttttcattattctatcttcttttcactaacagagtttcgtcattaacttcacaagcttgtgatattgcatatctgagaacaaatatgctcactaaattatttttcaacgtttctattagATGACCACAAAACCAAGGGAAGTGGATTGGCTCCATGGCCAGCTCGATTAACCTCTCCTCCTCCTCGGCTAGCTGACTTTGGCTATTCCACTGACATTTT

Basic information

species Arabidopsis thaliana
transcript AT3G23300.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 4
gtgagttttcattattctatcttcttttcactaacagagtttcgtcattaacttcacaagcttgtgatattgcatatctgagaacaaatatgctcactaaattatttttcaacgtttctattagATGACCACAAAACCAAGGGAAGTGGATTGGCTCCATGGCCAGCTCGATTAACCTCTCCTCCTCCTCGGCTAGCTGACTTTGGCTATTCCACTGACATTTT
           |  |  |  || || || | | |   ||||  |  |||  |||     || ||     |   ||||   |  |||      |    ||| || ||| |  |   |  ||| ||||||| ||| | ||||||| |||||||| ||||||||||| ||  |||| ||| ||||||||||| |  ||||||||||||||||||| | ||| || ||
-----------tcttcttggctactgtttattga---agttgtgcaattg-ctttgagtgcatgcagcct---atattccaagacac---cacctgataatttttttgttga---tcttatcagATGACAACAGAGCCAAGGGTAGTGGATTAGCTCCATGGCCTGCAAGATTGACCACTCCTCCTCCTAGATTAGCTGACTTTGGCTATTCAAATGAAATGTT

upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G04370.1 (Glycine max), 3'ss of exon 4
gtgagttttcattattctatcttcttttcactaacagagtttcgtcattaacttcacaagcttgtgatattgcatatctgagaacaaatatgctcactaaattatttttcaacgtttctattagATGACCACAAAACCAAGGGAAGTGGATTGGCTCCATGGCCAGCTCGATTAACCTCTCCTCCTCCTCGGCTAGCTGACTTTGGCTATTCCACTGACATTTT
          || |||  || | | || ||  |    | |   |  ||||  |    |  ||| |   |||  |  |   | |   ||||     || | ||  | ||      | |  |  |||||  |||| | | || |||  ||| |||||||| |||||||||||||| ||| |||| |||||||| || |||||||||  |||||||||||| || ||
----------atgatttcat-tccattccatcat--aattcctggtattatttcttgactcttct---attagaagttgaaaagttaata-----accatatattcttctggtctatgcag-

upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 5
gtgagttttcattattctatcttcttttcactaacagagtttcgtcattaacttcacaagcttgtgatattgcatatctgagaacaaatatgctcactaaattatttttcaacgtttctattagATGACCACAAAACCAAGGGAAGTGGATTGGCTCCATGGCCAGCTCGATTAACCTCTCCTCCTCCTCGGCTAGCTGACTTTGGCTATTCCACTGACATTTT
 | | || | || |   | | || |||| | | |    ||||   ||||                  ||    | || ||   ||||   | | | || |   | ||||    | || ||| ||| ||| ||| | ||||||| |||||||||||||||||||| ||  |||| ||| ||||||||||| |  |||| |||||||||||||| |  || || ||
-taaattatgatgacaat-ttttatttttattga---ggtttaaccatt------------------tacaataaatgtggatacaagactccac-ctgatgaaatttttgctgattttatcagACGACAACAGAGCCAAGGGTAGTGGATTGGCTCCATGGCCTGCAAGATTGACCACTCCTCCTCCTAGATTAGCAGACTTTGGCTATTCAAACGAAATGTT

upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G35120.4 (Glycine max), 3'ss of exon 5
gtgagttttcattattctatcttcttttcactaacagagtttcgtcattaacttcacaagcttgtgatattgcatatctgagaacaaatatgctcactaaattatttttcaacgtttctattagATGACCACAAAACCAAGGGAAGTGGATTGGCTCCATGGCCAGCTCGATTAACCTCTCCTCCTCCTCGGCTAGCTGACTTTGGCTATTCCACTGACATTTT
       ||  ||||| ||| || ||   |  |  | ||    |  | ||| ||    || ||| | |||            |  |||  |    ||| ||   ||| |  |  ||   |  ||||||| ||| | ||||||| |||||||| ||||||||||| ||  |||| ||   |||||||||| |  ||||||||||||||||||| | |||||| ||
-------ttttttattttatgttgttga-atgattaaagaagag--aataatttagagag-ttgcggtat------------atgaaacttaactactgaaacttttgttgattttatcac-agATGACAACAGAGCCAAGGGTAGTGGATTAGCTCCATGGCCTGCAAGATTGACTAGTCCTCCTCCTAGATTAGCTGACTTTGGCTATTCGAGTGACATGTT

upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 5
gtgagttttcattattctatcttcttttcactaacagagtttcgtcattaacttcacaagcttgtgatat-tgcatatctgagaacaaatatgctcactaaattatttttcaacgtttctattagATGACCACAAAACCAAGGGAAGTGGATTGGCTCCATGGCCAGCTCGATTAACCTCTCCTCCTCCTCGGCTAGCTGACTTTGGCTATTCCACTGACATTTT
                 | | || | || | |||   | |   |  | ||| || |  |||| ||| ||| || |  | ||| |   ||       ||| ||   ||| |  || ||   |  ||||||| ||| | ||||||| |||||||| ||||||||||| ||  |||| ||   |||||||||| |  ||||||||||||||||||| | |||||| ||
-----------------tttattttgtttaataattaaataa-gagaataatttaaagagct-gtggtatatgaaagtttgaaacttaac-----tactgaaacttttgttcactttatcac-agATGACAACAGAGCCAAGGGTAGTGGATTAGCTCCATGGCCTGCAAGATTGACTAGTCCTCCTCCTAGATTAGCTGACTTTGGCTATTCAAATGACATGTT

upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G18630.1 (Glycine max), 3'ss of exon 4
gtgagttttcattattctatcttcttttcactaacagagtttcgtcattaacttcacaagcttgtgatattgcatatctgagaacaaatatgctcactaaattatttttcaacgtttctattagATGACCACAAAACCAAGGGAAGTGGATTGGCTCCATGGCCAGCTCGATTAACCTCTCCTCCTCCTCGGCTAGCTGACTTTGGCTATTCCACTGACATTTT
         ||| |||  ||    ||    | | |||| ||  |  ||||  |    |  ||| |   |||  |  |   | |   ||||     || |   ||| ||     | |      |||    |||| | | || |||  ||  |||||||| |||||||||||||| ||  |||| |||||||| || |||||||||  |||||| ||||| || ||
---------catgatttcattccgtt----ccatcagaattctggtattatttcttgactcttct---attagaagttgaaaagtcaata-----acca---tatattctgctggtctatgcagAGATGCACAGAGCAAAAGGAGCTGATTTGGCTCCTTGGCCAGCTCGATTGACTACTCCACCTCCTCGTCTGGCTGACTTTAACTATTCAACTGAAATGTT

upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 5
gtgagttttcattattctatcttcttttcactaacagagtttcgtcattaacttcacaagcttgtgatattgcatatctgagaacaaatatgctcactaaattatttttcaacgtttctattagATGACCACAAAACCAAGGGAAGTGGATTGGCTCCATGGCCAGCTCGATTAACCTCTCCTCCTCCTCGGCTAGCTGACTTTGGCTATTCCACTGACATTTT
           |||  || | |  ||   |  ||    |||| |||||     ||       || || |||| |  |     ||| |  ||||| ||||||  ||| ||    | || ||||||||||||| ||| ||| ||| |||| ||||||||| ||||||||| |    ||| |||| ||||| || |||||||| ||||||||||| |  ||||| ||
-----------ttac-ctttttagttgaaaaaaaataggtttggtcatggttctc-------tg-gaaattgaaggttcttaaacta-catgctaactaaa--attgttgtgtgctt-tattagATGACCATAAATCCAGGGGTAGTGAATTGGCTCCTTGGCCAGCTAGGGCGACCGCTCCACCTCCACGTCTAGCTGATTTTGGCTATTCAAAAGACATATT

upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0005g03630.t01 (Vitis vinifera), 3'ss of exon 4
gtgagttttcattattctatcttcttttcactaacagagtttcgtcattaacttcacaagcttgtgatattgcatatctgagaacaaatatgctcactaaattatttttcaacgtttctattagATGACCACAAAACCAAGGGAAGTGGATTGGCTCCATGGCCAGCTCGATTAACCTCTCCTCCTCCTCGGCTAGCTGACTTTGGCTATTCCACTGACATTTT
              |  |  ||| |  |   |    || | |  ||| || |||||  || ||   | |||| | ||    ||| |||||  |  |||||||| | |     || | | || |||  ||||  |||| |  || |||||||||||||| |||||||||||||||||  ||||||||||||| |||||||| ||||||||| ||| |||||| ||
-------------gtgtttccttgtgctgtattgttgactgttttcacta-cttcatgagatta--acattggaaatt---gaaaaaatacacgaactaaattttgt-----cggtcccatcagAAAACCATCAAACAAGAGGTAGTGGATTGGCTCCTTGGCCAGCTCGATTAACTGCTCCTCCTCCTCGTCTAGCTGATTTTGGCTATACCAGTGACATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcatatctgagaacaaatatgctcactaaattatttttcaacgtttctattagATGACCACAAAACCAAGGGAAGTGGATTGGCTCCATGGCCAGCTCGATTAACCTCTCCTCCTCCTCGGCTAGCTGACTTTGGCTATTCCACTGACATTTT
                         cactaaa  putative branch site (score: 2)
                                             tttctatt  putative PPT
                          actaaattatttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttttcattattctatcttcttttcactaacagagtttcgtcattaacttcacaagcttgtgatattgcatatctgagaacaaatatgctcactaaattatttttcaacgtttctattagATGACCACAAAACCAAGGGAAGTGGATTGGCTCCATGGCCAGCTCGATTAACCTCTCCTCCTCCTCGGCTAGCTGACTTTGGCTATTCCACTGACATTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA