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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttgttgtgtttacagtgatgaaagaaggcttatagattttgaaaggcacacaaagacaccacacaaagacaccacattctaaccaatttttaagtatgcagATTAGACATGGTGAAGCTGTTGGGGTGATTGGTCCTTCTGGAACTGGAAAATCAACAATTTTAAAGATTATGGCTGGTCTTCTTGCTCCAGACAAG

Basic information

species Arabidopsis thaliana
transcript AT1G65410.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g46740.1 (Oryza sativa), 3'ss of exon 3
-gtattttgttgtgtttacagtgatgaaagaaggcttatagattttgaaaggcacacaaagacaccacacaaagacaccacattctaaccaatttttaagtatgcagATTAGACATGGTGAAGCTGTTGGGGTGATTGGTCCTTCTGGAACTGGAAAATCAACAATTTTAAAGATTATGGCTGGTCTTCTTGCTCCAGACAAG
 ||   | |   |  ||||   | |||        |||||   |||      ||   |     | |   ||        |   |  ||   ||| |||    || |||||||||| || ||||| |||||  | ||||||||||| ||||| ||||| |||||  |||| ||| |||||||||| || || ||||||||||||
agtcactaggaatcattacttagttgattat---tttataatcttttggtttcatttatttttagcctgcagttcagttatggttcaaattattatta----tgtagATTAGACACGGAGAAGCCGTTGGAATAATTGGTCCTTCGGGAACAGGAAAGTCAACTGTTTTGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAG

upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G868168_T01 (Zea mays), 3'ss of exon 3
gtattttgttgtgtttacagtgatgaaagaaggcttatagattttgaaaggcacacaaagacaccacacaaagacaccacattctaaccaatttttaagtatgcagATTAGACATGGTGAAGCTGTTGGGGTGATTGGTCCTTCTGGAACTGGAAAATCAACAATTTTAAAGATTATGGCTGGTCTTCTTGCTCCAGACAAG
        || |||| || || ||      | | ||  |    |    |||        |           |  ||  | | | | |   | ||||     || ||||||||||||||||||| |||||| | ||||| ||||| || || ||||||||||| || || ||| |||||||||| || |||||||| ||||||
actacgcattctgttcactgttatattttgatgttttcatgactcagtaggtttggtttgttgtagttatgattcaaaataatgttat--acttttg----tgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG

upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G868168_T03 (Zea mays), 3'ss of exon 3
gtattttgttgtgtttacagtgatgaaagaaggcttatagattttgaaaggcacacaaagacaccacacaaagacaccacattctaaccaatttttaagtatgcagATTAGACATGGTGAAGCTGTTGGGGTGATTGGTCCTTCTGGAACTGGAAAATCAACAATTTTAAAGATTATGGCTGGTCTTCTTGCTCCAGACAAG
        || |||| || || ||      | | ||  |    |    |||        |           |  ||  | | | | |   | ||||     || ||||||||||||||||||| |||||| | ||||| ||||| || || ||||||||||| || || ||| |||||||||| || |||||||| ||||||
-----gcattctgttcactgttatattttgatgttttcatgactcagtaggtttggtttgttgtagttatgattcaaaataatgttat--acttttg----tgtagattagACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG

upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G38730.1 (Glycine max), 3'ss of exon 2
gtattttgttgtgtttacagtgatgaaagaaggcttatagattttgaaaggcacacaaagacaccacacaaagacaccacattctaaccaatttttaagtatgcagATTAGACATGGTGAAGCTGTTGGGGTGATTGGTCCTTCTGGAACTGGAAAATCAACAATTTTAAAGATTATGGCTGGTCTTCTTGCTCCAGACAAG
     || || || | |      | |   | | |||   ||||  | ||        ||  |      |            ||||      |     | |    |||||||||||||||||||||||||  | |||||||||||||| || || ||||| ||| |||| |||||||| ||||| ||||||||||| ||||| 
--ccattattttgataaattcatttaggcaggtcttgctgattcagcaat---tgttaaatctttttgctgttttttttt-ttcttttttctgacataatgaatagATTAGACATGGTGAAGCTGTTGGAATAATTGGTCCTTCTGGGACCGGCAAATCTACAGTTTTGAAGATTATTGCTGGACTTCTTGCTCCGGACAAA

upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G47600.1 (Glycine max), 3'ss of exon 2
--gtattttgttgtgtttacagtgatgaaagaaggcttatagattttgaaaggcacacaaagacaccacacaaagacaccacattctaaccaatttttaagtatgcagATTAGACATGGTGAAGCTGTTGGGGTGATTGGTCCTTCTGGAACTGGAAAATCAACAATTTTAAAGATTATGGCTGGTCTTCTTGCTCCAGACAAG
    || |      |||   ||||  |   || | |||  |||||  |||   |   | ||  |      |   |      | ||||      |     | |    |||| |  |||||||||||||||||  | |||||||| ||||| ||||| ||||| ||| |||| |||||||| || || ||||||||||| ||||| 
ttaaatgtaaactagttgtaagtg--gggggaggtcttgcagattcagaa---cttgctaaatctttttgct--gttttttctttcttctttttgacataatgaataGATCAAGCATGGTGAAGCTGTTGGAATAATTGGTCCCTCTGGGACTGGCAAATCTACAGTTTTGAAGATTATTGCAGGACTTCTTGCTCCGGACAA-

upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv04s0023g00290.t01 (Vitis vinifera), 3'ss of exon 2
----gtattttgttgtgtttacagtgatgaaagaaggcttatagattttgaaaggcacacaaagacaccacacaaagacaccacattctaaccaatttttaagtatgcagATTAGACATGGTGAAGCTGTTGGGGTGATTGGTCCTTCTGGAACTGGAAAATCAACAATTTTAAAGATTATGGCTGGTCTTCTTGCTCCAGACAAG
    | ||||| |||| | |    | ||         |   |  ||||||           |  |  |       |    |   | | ||||| |||        |  ||||||||||||| |||||||||||| | ||||| |||||||| ||||| ||||||||| || | |||||||| || || ||||||||||||||||||
gagtggatttttttgtctctcttttcatatttagtttcccttgaattttggtta-tgttttatcattctctgtttattttct-tactttaacccatt--------tatagATTAGACATGGGGAAGCTGTTGGGATTATTGGGCCTTCTGGCACTGGGAAATCAACAGTTCTGAAGATTATTGCGGGACTTCTTGCTCCAGACAAG

upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ22908 (Selaginella moellendorffii), 3'ss of exon 1
gtattttgttgtgtttacagtgatgaaagaaggcttatagattttgaaaggcacacaaagacaccacacaaagac-accacattctaa-ccaatttttaagtatgcagATTAGACATGGTGAAGCTGTTGGGGTGATTGGTCCTTCTGGAACTGGAAAATCAACAATTTTAAAGATTATGGCTGGTCTTCTTGCTCCAGACAAG
                                                  |     |  ||  |  || || |||   |||  |||||  |  ||| |   | ||||| |  | |||||||| ||||| ||  | ||||| ||||||||||| ||||| || || ||||| |||||||||||||| ||||||| ||| ||||||
--------------------------------------------------gtgtggattga-gcagcataacgactgtcactctctaaatccttttctttttgtgcagGTCCGCCATGGTGAGGCTGTGGGAATTATTGGACCTTCTGGAACAGGAAAGTCCACGATTTTGAAGATTATGGCTGGACTTCTTGTTCCTGACAAG

upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ30431 (Selaginella moellendorffii), 3'ss of exon 1
gtattttgttgtgtttacagtgatgaaagaaggcttatagattttgaaaggcacacaaagacaccacacaaagac-accacattctaa-ccaatttttaagtatgcagATTAGACATGGTGAAGCTGTTGGGGTGATTGGTCCTTCTGGAACTGGAAAATCAACAATTTTAAAGATTATGGCTGGTCTTCTTGCTCCAGACAAG
                                                  |     |  ||  |  || |  ||    |||  |||||  |  ||| |   | ||||| |  | |||||||| ||||| ||  | ||||| ||||||||||| ||||| || || ||||| |||||||||||||| ||||||| ||| ||||||
--------------------------------------------------gtgtggattga-gcagcatagcgattgtcactctctaaatccttttctttttgtgcagGTCCGCCATGGTGAGGCTGTGGGAATTATTGGACCTTCTGGAACAGGAAAGTCCACGATTTTGAAGATTATGGCTGGACTTCTTGTTCCTGACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacacaaagacaccacacaaagacaccacattctaaccaatttttaagtatgcagATTAGACATGGTGAAGCTGTTGGGGTGATTGGTCCTTCTGGAACTGGAAAATCAACAATTTTAAAGATTATGGCTGGTCTTCTTGCTCCAGACAAG
                              ttctaac  putative branch site (score: 1)
                                      aatttttaagtat  TA-rich tract