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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttctttttctagtttgatgatatttgtggtcacaactttcttttttgcttttgtggttgaaaatgaaaacttgctgttttgattaagtacttgagcttgtaactatgtttttgtttcagcagGTTTCTTCTTTCAGAGAAAGCAAGTCTGATGATAGAAAGTTCTATATATTCACAGCAACAAAGACCCTTCATTTGAGGACTGATTCTATAACTGATAGAG

Basic information

species Arabidopsis thaliana
transcript AT4G22540.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G22540.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G14820.1 (Glycine max), 3'ss of exon 1
gtaagttttctttttctagtttgatgatatttgtggtcacaactttcttttttgcttttgtggttgaaaatgaaaacttgctgttttgattaagtacttgagcttgtaactatgtttttgtttcagcagGTTTCTTCTTTCAGAGAAAGCAAGTCTGATGATAGAAAGTTCTATATATTCACAGCAACAAAGACCCTTCATTTGAGGACTGATTCTATAACTGATAGAG
                   ||| | | |  |    || | || |||  | | |  |||| |  | |||  |      ||      | |||||| || | ||  | |||  ||| |  |||||  ||||| | || || |||||||| |||||||| || ||||||  ||||||||||||||| || |||||||| || ||| |||| |||||||| |  |  ||  | |
------------------atttcaggttcct----gttataaattttgtctatatttttttaatagaattttt---tttatataatagattaaataatgga--tggtacttat-tcattgtta-agcagATCTCGTCGTTCAGAGAGAGCAAGTCAGACGATAGACGGTTCTATATATTCACGGCCACAAAGACTCTCCATCTGAGAACTGATTCGAGGAAGGACCGTG

upper sequence: AT4G22540.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G04340.2 (Glycine max), 3'ss of exon 1
gtaagttttctttttctagtttgatgatatttgtggtcacaactttcttttttgcttttgtggttgaaaatgaaaacttgctgttttgattaagtacttgagcttgtaactatgtttttgtttcagcagGTTTCTTCTTTCAGAGAAAGCAAGTCTGATGATAGAAAGTTCTATATATTCACAGCAACAAAGACCCTTCATTTGAGGACTGATTCTATAACTGATAGAG
                || | | |   ||| | ||     || ||| |||||| |       || |||||| |||         || |||| | ||  |||      |    | ||  |  || ||||| | || || ||||| || |||||||| || ||||||  |||||||||||||||| |||||||||| || ||| |||| || ||||| |  |  ||  | |
--------------gataatataaaattatatatgccattaaatttttttttttc------agtagaaaataaaa---------ttggatttaatagatgaataatgatacttattcattgttaagcagATCTCGTCATTCAGGGAGAGCAAGTCAGACGATAGACGGTTCTATATATTCACATCAACAAAGACTCTCCATCTGAGAACCGATTCGAGGAAGGACCGTG

upper sequence: AT4G22540.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G04340.1 (Glycine max), 3'ss of exon 2
gtaagttttctttttctagtttgatgatatttgtggtcacaactttcttttttgcttttgtggttgaaaatgaaaacttgctgttttgattaagtacttgagcttgtaactatgtttttgtttcagcagGTTTCTTCTTTCAGAGAAAGCAAGTCTGATGATAGAAAGTTCTATATATTCACAGCAACAAAGACCCTTCATTTGAGGACTGATTCTATAACTGATAGAG--------------
                          |||| ||   | | || ||| ||||||         || |||||| |||         || |||| | ||  |||      |    | ||  |  || ||||| | || || ||||| || |||||||| || ||||||  |||||||||||||||| |||||||||| || ||| |||| || ||||| |  |  ||  | |              
--------------------------atatatgccatta-aattttttttttt-------cagtagaaaataaaa---------ttggatttaatagatgaataatgatacttattcattgttaagcagatctcgtcattcagGGAGAGCAAGTCAGACGATAGACGGTTCTATATATTCACATCAACAAAGACTCTCCATCTGAGAACCGATTCGAGGAAGGACCGTGTGGCGTGGATACAA

upper sequence: AT4G22540.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G41940.1 (Glycine max), 3'ss of exon 1
gtaagttttctttttctagtttgatgatatttgtggtcacaactttcttttttgcttttgtggttgaaaatgaaaacttgctgttttgattaagtacttgagcttgtaactatgtttttgtttcagcagGTTTCTTCTTTCAGAGAAAGCAAGTCTGATGATAGAAAGTTCTATATATTCACAGCAACAAAGACCCTTCATTTGAGGACTGATTCTATAACTGATAGAG
                        || |  || |  | |   |||| |               |||   |     | || ||   |  ||| |  | ||||  ||  |  |  ||   ||||| ||||| |||| || || ||||| |||||||| |||||| |    ||||||||||| |||||||| |||||||| ||| |||| |||||||| |  |  ||| | |
------------------------tgttccttttaattatt-ctttttcaacgaaaaacaaacttggttagagtgagtttcttcgtgcattga--aattgaagttaca-ttgcgtgaatgttt-agcagATTTCGTCGTTTAGAGAGAGCAAGTCAGATGATCGGCGTTTCTATATATTTACAGCAACGAAGACCCTCCATCTGAGAACTGATTCAAGGAAAGATCGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacttgctgttttgattaagtacttgagcttgtaactatgtttttgtttcagcagGTTTCTTCTTTCAGAGAAAGCAAGTCTGATGATAGAAAGTTCTATATATTCACAGCAACAAAGACCCTTCATTTGAGGACTGATTCTATAACTGATAGAG
                             ttgtaac  putative branch site (score: 2)
                                        tttttgtttc  putative PPT
         ttttgattaa  TA-rich tract