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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagagttttatttagagaagaatgaatgtcaataagcaagtttcgtcttgttaacagtatgtctattttttgtttcagAAATTTAATCTCCATTTGATGCTTAATGCGGATAAAGAATTTCTTGCTCAAAAAAGTGCACCACATCGTGATTTTTATAACGTTAGGAAAGTCGACACTC

Basic information

species Arabidopsis thaliana
transcript AT2G38280.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G38280.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os05g28180.2 (Oryza sativa), 3'ss of exon 3
gcaagagttttatttagagaagaatga-------atgtcaataagcaagtttcgtcttgttaa--cagtatgtcta-----ttttttgtttc-agAAATTTAATCTCCATTTGATGCTTAATGCGGATAAAGAATTTCTTGCTCAAAAAAGTGCACCACATCGTGATTTTTATAACGTTAGGAAAGTCGACACTC-----------------------------------
| ||   | || |  |   |   |          |  |   | |  ||  ||         ||  | |||||| |      |||||  |||| ||||||| ||  | ||||||||| | || |||||||  || |||||||| || || | ||||||||||||||||||||| || || ||||| || || ||||                                   
gtaatcatattgtcaaatcattgaccccttgcttaccttggtgaataaacttgactcctaaaattctgtatgtgtgaatgttttttcatttctagaaattcaaatttcatttgatgttaaacgcggatagGGAGTTTCTTGCCCAGAAGACTGCACCACATCGTGATTTTTACAATGTCAGGAAGGTTGATACTCATGTACACCACTCAGCGTGCATGAATCAAAAACAC

upper sequence: AT2G38280.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os05g28180.1 (Oryza sativa), 3'ss of exon 3
gcaagagttttatttagagaagaatga-------atgtcaataagcaagtttcgtcttgttaa--cagtatgtcta-----ttttttgtttc-agAAATTTAATCTCCATTTGATGCTTAATGCGGATAAAGAATTTCTTGCTCAAAAAAGTGCACCACATCGTGATTTTTATAACGTTAGGAAAGTCGACACTC
| ||   | || |  |   |   |          |  |   | |  ||  ||         ||  | |||||| |      |||||  |||| ||||||| ||  | ||||||||| | || |||||||  || |||||||| || || | ||||||||||||||||||||| || || ||||| || || ||||
gtaatcatattgtcaaatcattgaccccttgcttaccttggtgaataaacttgactcctaaaattctgtatgtgtgaatgttttttcatttctagAAATTCAAATTTCATTTGATGTTAAACGCGGATAGGGAGTTTCTTGCCCAGAAGACTGCACCACATCGTGATTTTTACAATGTCAGGAAGGTTGATACTC

upper sequence: AT2G38280.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G416667_T03 (Zea mays), 3'ss of exon 7
---------------------gcaagagttttattta----gagaagaatgaatgtcaataagcaagtttcgtcttgttaacagtatgtctattttttgtttcagAAATTTAATCTCCATTTGATGCTTAATGCGGATAAAGAATTTCTTGCTCAAAAAAGTGCACCACATCGTGATTTTTATAACGTTAGGAAAGTCGACACTC
                       |     ||  ||||    || |    ||||||        ||| | |     ||| |   | || ||| | |||  |||||||| |||||  ||||| ||||| | ||||||||||  ||||||||||| || || | ||| ||||||||||||||||| || || ||||| || |||||||
gtaatcatgttgtaaaattgtttacctccttcgtttacgatgaaatagttgaatgctctcctacaattctttggatgtgat--gcatttct-tatttcctttcagAAGTTTAAATTCCATCTGATGTTAAATGCGGATAGGGAATTTCTTGCCCAGAAGACTGCCCCACATCGTGATTTTTACAATGTCAGGAAGGTTGACACTC

upper sequence: AT2G38280.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA03G07460.1 (Glycine max), 3'ss of exon 6
--------------------gcaagagttttat-ttagag---aagaatgaatgtcaataa---gcaagtttcgtcttgttaacagtatgtctattttttgtttcagAAATTTAATCTCCATTTGATGCTTAATGCGGATAAAGAATTTCTTGCTCAAAAAAGTGCACCACATCGTGATTTTTATAACGTTAGGAAAGTCGACACTC
                      | ||||   |   |  ||   | |  || || | ||| |    ||||  ||   |||||    |    | | | | || ||||||||||| ||||| ||||||||| | |||||||||| ||||||||||||||| |||||||| |||||||| || || ||||| ||||| ||||| |||||||
gtacatatcgaatttactgaatatgagtaacaaactgcagcctatgcttgtattttaattacgtacaagaatcaa-ttgttgtttgacaatttctgtattttttcagAAATTCAATCTTCATTTGATGTTAAATGCGGATAGAGAATTTCTTGCTCAGAAAAGTGCTCCACATCGAGACTTCTATAATGTTAGAAAAGTTGACACTC

upper sequence: AT2G38280.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G29470.1 (Glycine max), 3'ss of exon 7
gcaagagttttatttagagaag--------aatgaatgtcaataagcaagtttcgtcttgttaaca------gtatgtctattttt---tgtttcagAAATTTAATCTCCATTTGATGCTTAATGCGGATAAAGAATTTCTTGCTCAAAAAAGTGCACCACATCGTGATTTTTATAACGTTAGGAAAGTCGACACTC
| |    | | |||||  |||         |    |||    ||    | || | |      | ||      || || | |||| |   | ||||||||||| ||||| ||||||||||| |||||||||| ||||||||||||||| || ||||| |||||||| || || ||||| ||||| ||||| || ||||
gtacatctctaatttactgaaacaaactgcagcctatgcttgtattttaattacatacaagaatcaattgttgtttgacaatttctgtatttttcagAAATTCAATCTTCATTTGATGCTAAATGCGGATAGAGAATTTCTTGCTCAGAAGAGTGCTCCACATCGAGACTTCTATAATGTTAGAAAAGTTGATACTC

upper sequence: AT2G38280.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 6
---------------------------------------------------------------------gcaagagttttatttagagaagaatgaatgtcaataagcaagtttcgtct-tgttaacagtatgtctatttt--ttgtt--tcagAAATTTAATCTCCATTTGATGCTTAATGCGGATAAAGAATTTCTTGCTCAAAAAAGTGCACCACATCGTGATTTTTATAACGTTAGGAAAGTCGACACTC
                                                                           | | | |||         |     |   | | |   ||| ||   ||  ||     ||  | ||||  ||     ||||||||| || || ||| |||||||||||||||||| |||||| ||||| || |||||||||||||||||||| |||||||| || ||||| ||||| || |
gtagatgctacttttctgtatttgattcacatatttgaattttttttttttgatttgtcatttattgaaatgtatgctctttttctttttcttttttctttttttacctctttttgtaaatgacaatctggtggttgttttggttaccaatcagAAATTCAACCTTCATGTGATGCTTAATGCGGATAGAGAATTCCTTGCACAGAAAAGTGCACCACATCGTGACTTTTATAATGTCAGGAAGGTCGATACAC

upper sequence: AT2G38280.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S77_89V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------------------------------------gcaagagttttatttagagaagaatgaatgtcaa----taagcaagtttcgtcttgttaa----cagtatgtctattttttgt------ttcagAAATTTAATCTCCATTTGATGCTTAATGCGGATAAAGAATTTCTTGCTCAAAAAAGTGCACCACATCGTGATTTTTATAACGTTAGGAAAGTCGACACTC
                                                  ||    || ||||| |        |||       | || ||  | |||  ||| ||    |  ||    | ||| ||||      | |||||||| | | | ||  ||||||| ||||||||    || || ||||||||||||||||| || ||||| |||||||||||||| |||||||||||||| |
gtcagtttgcacgatttcccccttgacattgagtcacgcactgctttttggaccactacttagaaacacgctggtgttgtacttttagaaacgtacgtggtgtgaaattactttactgttttttcttgtgagttctgcagAAATTCAGTTTGCACCTGATGCTGAATGCGGACCGTGAGTTCCTTGCTCAAAAAAGTGCGCCTCATCGAGATTTTTATAACGTGAGGAAAGTCGACACAC

upper sequence: AT2G38280.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S168_82V6.1 (Physcomitrella patens), 3'ss of exon 6
----gcaagagttttatttagag-------aagaatgaatgtcaataagcaagtttcgtcttgttaacagtatgtcta--ttttttgt-------ttcagAAATTTAATCTCCATTTGATGCTTAATGCGGATAAAGAATTTCTTGCTCAAAAAAGTGCACCACATCGTGATTTTTATAACGTTAGGAAAGTCGACACTC
      || |  || || || ||       | | | ||   |    || || | ||  ||||  |   |  |||   |  || |||||       | |||||||| | | | ||  ||||| | || || ||    || ||||| ||||||||||||||||| ||||| ||||| ||||||||| ||||||| ||||| |
cgtgttaatacgttcatctaaagtttgatgacgcaagatctttggcaaacacggttactctttatgcgaaaatgctgaagttctttgtgggttgctacagAAATTCAGTTTGCACCTGATGTTGAACGCAGACCGTGAGTTTCTCGCTCAAAAAAGTGCACCCCATCGAGATTTCTATAACGTTCGGAAAGTTGACACAC

upper sequence: AT2G38280.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ17267 (Selaginella moellendorffii), 3'ss of exon 5
gcaagagttttatttagagaagaatgaatgtcaataagcaagtttcgtcttgttaacagtatgtctattttttgtttcagAAATTTAATCTCCATTTGATGCTTAATGCGGATAAAGAATTTCTTGCTCAAAAAAGTGCACCACATCGTGATTTTTATAACGTTAGGAAAGTCGACACTC
    |  | || | || |   |  |  || | | |    ||||||  |   |||  | | |||              |||||||||| ||| || |||||||||||||| |||   |||||  | |||||||| ||||||||||||||||| ||||| |||||| | || || |||||||
----gtatgttgtataaaagtgctttgatatta-tggttaagttt-attcggttcccgggatg--------------cagAAATTTAGTCTGCACTTGATGCTTAATGCAGATCGGGAATTCTTGGCTCAAAAGAGTGCACCACATCGTGACTTTTACAACGTTCGTAAGGTTGACACTC

upper sequence: AT2G38280.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ30909 (Selaginella moellendorffii), 3'ss of exon 5
gcaagagttttatttagagaagaatgaatgtcaataagcaagtttcgtcttgttaacagtatgtctattttttgtttcagAAATTTAATCTCCATTTGATGCTTAATGCGGATAAAGAATTTCTTGCTCAAAAAAGTGCACCACATCGTGATTTTTATAACGTTAGGAAAGTCGACACTC
                  | |   || ||   | |      || |  |   |||||   |||     |     | | |||||||||| ||| || |||||||||||||| |||   |||||  | |||||||| ||||||||||||||||| ||||| |||||| | || || |||||||
------------------gtatgttgtataaaagtgctttggtattat--ggttaagtttattcggttcccgggatgcagAAATTTAGTCTGCACTTGATGCTTAATGCAGATCGGGAATTCTTGGCTCAAAAGAGTGCACCACATCGTGACTTTTACAACGTTCGTAAGGTTGACACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatgtcaataagcaagtttcgtcttgttaacagtatgtctattttttgtttcagAAATTTAATCTCCATTTGATGCTTAATGCGGATAAAGAATTTCTTGCTCAAAAAAGTGCACCACATCGTGATTTTTATAACGTTAGGAAAGTCGACACTC
                         tgttaac  putative branch site (score: 2)
                                      tctattttttgtttc  putative PPT
                                  tatgtctatttttt  TA-rich tract