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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcttatggatatctgtcttcttcttcacagaaagttaattttatgaatcattgaggtactgatgcgtttcaattttgttgcagAAACTAAAGCTTGGGAGGTGGATACATTGCGAGGTCATATGAATAACGTTTCATCCGTTATGTTCCATGCAAAACAGGACATTATCGTGTCAAACTCTGA

Basic information

species Arabidopsis thaliana
transcript AT2G21390.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g50350.1 (Oryza sativa), 3'ss of exon 2
-------gtatttcttatgga-tatctgtcttcttcttcac-agaaagttaattttatgaatcat---tgaggtactgatgcgtttcaattttgttgcagAAACTAAAGCTTGGGAGGTGGATACATTGCGAGGTCATATGAATAACGTTTCATCCGTTATGTTCCATGCAAAACAGGACATTATCGTGTCAAACTCTGA
        | |    | ||||  ||     | |    |||| |     ||| ||  | | || ||   ||| | | |       | |  |||| |  |||| || || |||||||| || ||||| ||||| || || ||||||||||| || |  || |||||||||||||| || ||||| || ||||| ||||| ||
gcaaactttgtggggtgtggaacattcacttccactatcaccattgcattatttaaagggataataggtgatgcaatctaaatgtgctgttttttgacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAACGTGTCCTGTGTGATGTTCCATGCAAAGCAAGACATCATAGTGTCCAACTCAGA

upper sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os09g04110.1 (Oryza sativa), 3'ss of exon 2
gtatttcttatggatatctgtcttcttcttcacagaaagttaattttatga-atcattgaggtac------tgatgcgtttcaattttgttg--------cagAAACTAAAGCTTGGGAGGTGGATACATTGCGAGGTCATATGAATAACGTTTCATCCGTTATGTTCCATGCAAAACAGGACATTATCGTGTCAAACTCTGA
 |||| ||  || | ||  ||   ||    || |     |||  |  ||   |  |||||||||       ||||||  |  || | || |         |||| || || |||||||| || ||||| ||||| || || |||||||| || || | ||| |||||||||||||| || ||||| || ||||| ||||| ||
-tatt-ctactgcacattggtagactggc-caaacgctattatatgcataccactattgaggtatttgaaatgatgcaatctaagtgtgctatttttggacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAATGTGTCCTGCGTGATGTTCCATGCAAAGCAAGACATCATTGTGTCCAACTCAGA

upper sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g50340.1 (Oryza sativa), 3'ss of exon 2
--------gtatttcttatggatatctgtcttcttcttca-cagaaagttaat----tttatgaatcattgaggtactgatgcgtttcaattttgttgcagAAACTAAAGCTTGGGAGGTGGATACATTGCGAGGTCATATGAATAACGTTTCATCCGTTATGTTCCATGCAAAACAGGACATTATCGTGTCAAACTCTGA
              |  |   | | || | | | | | || || |  | || |    | | ||||| | ||   |    ||| | |    |||||   |||| || || |||||||| || ||||| ||||| || || |||||||| || |||| ||| ||||||||||| || || ||||| || ||||| ||||| ||
attgctagactggccaaacacaaaactatatgcatatgcagcaaaccgctattgaggtatttgaattaatgtaatctaaatgtgctatttttttgg-acagACACGAAGGCTTGGGAAGTTGATACTTTGCGGGGACACATGAATAATGTGTCATGCGTGATGTTCCATGCTAAGCAAGACATCATTGTGTCCAACTCAGA

upper sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G04290.1 (Glycine max), 3'ss of exon 2
----------gtattt-cttatggatatctgtcttcttcttcacagaaagttaattttatgaatcatt---gaggtactgatgcgtttcaattttgttgcagAAACTAAAGCTTGGGAGGTGGATACATTGCGAGGTCATATGAATAACGTTTCATCCGTTATGTTCCATGCAAAACAGGACATTATCGTGTCAAACTCTGA
          | |||  ||| |   ||| |            | ||     || ||||    | | |     ||   || ||   |||     || |  |||| || || || ||||| ||||||||  || |||| || |||||||| |||||||  |||||||||||||| ||||||||||| || |||||||| |||||
ctttttgcatgcattaactttttagtatttagtaaaccaaataaagtttagtatttttggtgaccttctcaaagtccctaatatattttcccgtttt--cagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA

upper sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G12080.1 (Glycine max), 3'ss of exon 2
----gtatttcttatggatatc-tgtcttcttcttcacagaaagttaa----ttttatgaatcatt---gaggtactgatgcgtttcaattttgttgcagAAACTAAAGCTTGGGAGGTGGATACATTGCGAGGTCATATGAATAACGTTTCATCCGTTATGTTCCATGCAAAACAGGACATTATCGTGTCAAACTCTGA
    | ||   |||    | |  | | |  |    || | || |||      ||||||  | | |     ||   || ||   |||     |  || |||| || || || ||||| ||||||||  || |||| || |||||||| |||||||  |||||||||||||| ||||||||||| || |||||||| |||||
gcttgcatgcattaactttttagtatttagtaaaccaaaaaatgtttggtttttttattgaccttctcaaagtccctaatattttttcccctgttttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA

upper sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G33270.1 (Glycine max), 3'ss of exon 2
gtatttcttatggatatctgtcttcttcttcaca-----gaaagtta----attttatgaatcattga----ggtactgatgcgtttcaattttgttg-cagAAACTAAAGCTTGGGAGGTGGATACATTGCGAGGTCATATGAATAACGTTTCATCCGTTATGTTCCATGCAAAACAGGACATTATCGTGTCAAACTCTGA
 ||  |||||  ||| | |  | | || ||   |      ||| ||      ||| | |   |||||     | |  | |||  ||     | | ||| |||| || || || ||||| ||||| || ||| |||| || |||||||| |||||||  |||||||||||||| |||||||| || || |||||||| |||||
-taaatctta-agatgtataccatgttttttggatgcgttaaacttgtagtgtttgaggtggcattgtttttgctgttaatgatttatttctctattgtcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGATATCATTGTGTCAAATTCTGA

upper sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G34310.1 (Glycine max), 3'ss of exon 2
----gtatttcttatggatatc-tgtcttcttcttcacagaaagttaat--tttatgaa----tcattgaggtactgatgcgtttcaattttgttg-cagAAACTAAAGCTTGGGAGGTGGATACATTGCGAGGTCATATGAATAACGTTTCATCCGTTATGTTCCATGCAAAACAGGACATTATCGTGTCAAACTCTGA
    | |||   |||  ||||  ||   | |     | |  ||| |  |  | | |||     |  ||  | |  | |||  ||  |  | | ||  |||| || || || ||||| ||||| || ||| |||| || |||||||| |||||||  |||||||||||||| || ||||| || || |||||||| || ||
ggatgcattaaatataaatattgtgggatgtggcgaataataagcttgtagtgtttgaggtgctgcttatgctgttaatgatttgtatctctattttcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAGCAGGATATCATTGTGTCAAATTCCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaagttaattttatgaatcattgaggtactgatgcgtttcaattttgttgcagAAACTAAAGCTTGGGAGGTGGATACATTGCGAGGTCATATGAATAACGTTTCATCCGTTATGTTCCATGCAAAACAGGACATTATCGTGTCAAACTCTGA
                            tactgat  putative branch site (score: 2)
                                            ttttgtt  putative PPT
      ttaattttatgaatca  TA-rich tract