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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggtttttattgtctagttatagtagtttaaagatctaaagagttctcctttcgattgagtttgagcttaaatttgatcacatactgctttgtttaaagttgtttgcttttgattctatagGCTGATGGATGGAAAGTAGAGAAGATTAGTTTACTGGCAAATCCAAATCAAGTTCATCCGACTAGGTTCTGGGGTGTTTATACAAAGCTTAAGATCTTTA

Basic information

species Arabidopsis thaliana
transcript AT5G18480.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G18480.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G37000.1 (Glycine max), 3'ss of exon 1
-----------------------------------------------------------------gtttggtttttattgtctagttatagtagtttaaagatctaaagagttctcctttcgattgagtttgagct-taaatttgatcacatactgctttgtt----taaagttgtttgcttttgattct---atagGCTGATGGATGGAAAGTAGAGAAGATTAGTTTACTGGCAAATCCAAATCAAGTTCATCCGACTAGGTTCTGGGGTGTTTATACAAAGCTTAAGATCTTTA
                                                                   ||   ||| ||  |   |||  | | |     |   |||||   |  |  ||   | | | ||| ||   ||   ||||| | | ||  | | | |    |||||   |||    ||| || |    ||||||||||| |||| ||| |||||||||||||||||||||||||| |||||||| | ||| |  || || |||||||| ||||||||||| || || ||||
gtactcttttcctttgccaattgtattattgcggaacgagaaatgaaaaatttctgatcactttatattaaatttgatattaatgtttcatttgacatgaatcctaaattttgttagttataacttattttaagtgatattgttgattatagacctcgtgggtagggtaaagggttttatgattgctttttgtgtagGCTGATGGGTGGATAGTTGAGAAGATTAGTTTACTGGCAAATCCTAATCAAGTACGTCCAAAGAGATTTTGGGGTGTCTATACAAAGCTCAAAATATTTA

upper sequence: AT5G18480.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G30700.1 (Glycine max), 3'ss of exon 1
---------------------------------------------------------------------gtttggtttttattgtctagttata-gtagtttaaagatctaaagagttctc-ctttcgattgagtttgagcttaaatttgatcacatactgctttgtttaaagttgtt-tgcttt-tgattctatagGCTGATGGATGGAAAGTAGAGAAGATTAGTTTACTGGCAAATCCAAATCAAGTTCATCCGACTAGGTTCTGGGGTGTTTATACAAAGCTTAAGATCTTTA
                                                                       ||   | | | ||| |  || ||  |   |   |||| |    |||| |  |||   ||| |||   |   |  |||  |  ||     | |  | | || | | || || ||  |  || | ||||||||||| |||| ||| ||||||||||||||| |||| ||||| |||||||| | ||| |  || || ||||||                         
gtactcttttcctttgcgaaatgtattaacgcggaaccagaaatgaaattttgtgatcactttatattaaatttaatatcagtgtttcattttatatgaatcctagattttgttagttataacttattattaagtgatactgttgattatagaactcgtggatagggtaaagggttttatgattggtttttttgtagGCTGATGGGTGGATAGTTGAGAAGATTAGTTTATTGGCGAATCCTAATCAAGTACGTCCAAAGAGATTTTGGGGT-------------------------

upper sequence: AT5G18480.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G43630.1 (Glycine max), 3'ss of exon 1
---------gtttggtttttattgtctagttatagtagtttaaagatctaaa---gagttctcctttcgat-tgagtttg-----agcttaaatttg-atcacatactgctttg--tttaaagttgtttgcttttgattc--------tatagGCTGATGGATGGAAAGTAGAGAAGATTAGTTTACTGGCAAATCCAAATCAAGTTCATCCGACTAGGTTCTGGGGTGTTTATACAAAGCTTAAGATCTTTA
          | |  | |||| ||  |  |  |   | ||| ||  | | ||    |  | ||  || ||  ||| | ||     | || |  ||||  |    |     |||   | || | ||| | | ||||  |||        |  |||||||||| |||| ||| |||| ||||||||||||||| ||||| |||| ||| | ||| |  || || |||||||| || |||||||| || || ||||
gtaataatcatcttctctttaatgggtcttcgtcaaaatttgaaattttgaactttaactttctgtttgacatgaatctgttgacacctgagttttgtgtagtttgtaattttaactctatatttggtggatttttgttcgaattttgtgaagGCTGATGGGTGGATAGTGGAGATGATTAGTTTACTGGCTAATCCTAATCGAGTGCGTCCAAAGAGATTTTGGGGTGTCTACACAAAGCTCAAAATATTTA

upper sequence: AT5G18480.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G40980.1 (Glycine max), 3'ss of exon 1
--------------------gtttggtttttattgt-ctagttatagtagtttaaagatctaaagagttctcctttcgattgagtttgagcttaaatttgatcacatactgctttgtttaaagttgtttgcttttgattctat--agGCTGATGGATGGAAAGTAGAGAAGATTAGTTTACTGGCAAATCCAAATCAAGTTCATCCGACTAGGTTCTGGGGTGTTTATACAAAGCTTAAGATCTTTA
                      | ||| ||  |     | |  ||   |  |  | | |  | |    |||  |  |   |||||||    |    | ||||   | ||| |||| |||   |   ||   |||  ||| | |  |||||||||| |||| ||| |||| |||||||||||| || ||||| |||| ||| | ||| |  ||||| |||||||| || |||||||| || || ||||
gtattcatcatcttctttttaatgggtcttcctcaaatttgaaatttgaactctatgtttgacatgaatctgttgacacctgagttttgtgtagtttgtgatttta-act-ctttatttggtggatttgtgtttgaattttgtgaagGCTGATGGGTGGATAGTGGAGATGATTAGTTTACTTGCTAATCCTAATCGAGTGCGTCCAAAGAGGTTTTGGGGTGTCTACACAAAGCTCAAAATATTTA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|125039397|gb|EL111666.1|EL111666
EST:     TACTCTAAGAAGTTACTCAAG                         GCTGATGGTATGGAAAGTAGAGAAGATTAGTTTACTGGCAAATCCAAATCA
genomic: TACTCTAAGAAGTTACTCAAGgtttggtttt ... gattctatagGCTGATGG-ATGGAAAGTAGAGAAGATTAGTTTACTGGCAAATCCAAATCA
EST: gi|86066475|gb|DR362232.1|DR362232
EST:     TCGCTTTGGTTTCTGATGGTGTCTCAGACTACTCTAAGAAGTTACTCAAG                         GCTGATGGATGGAAAGTAGAGAAGATTAGTTTACTGGCAAATCCAAATCAA
genomic: TCGCTTTGGTTTCTGATGGTGTCTCAGACTACTCTAAGAAGTTACTCAAGgtttggtttt ... gattctatagGCTGATGGATGGAAAGTAGAGAAGATTAGTTTACTGGCAAATCCAAATCAA
EST: gi|124891296|gb|EH970198.1|EH970198
EST:     CGCTTTGGTTTCTGATGGTGTCTCAGACTACTCTAAGAAAGTTACTCAAG                         GCTGATGGATGGAAAGT
genomic: CGCTTTGGTTTCTGATGGTGTCTCAGACTACTCTAAGAA-GTTACTCAAGgtttggtttt ... gattctatagGCTGATGGATGGAAAGT
EST: gi|19878999|gb|AU239830.1|AU239830
EST:     TCGCTTTGGTTTCTGATGGTGTCTCAGACTACTCTAAGAAGTTACTCAAG                         GCTGATGGATGGAAAGTAGAGAAGATTAGTTTACTGGCAAATCCAAATCAA
genomic: TCGCTTTGGTTTCTGATGGTGTCTCAGACTACTCTAAGAAGTTACTCAAGgtttggtttt ... gattctatagGCTGATGGATGGAAAGTAGAGAAGATTAGTTTACTGGCAAATCCAAATCAA
EST: gi|124918990|gb|EH992779.1|EH992779
EST:     CTCTAAGAAGTTACTCAAG                         GCTGATGGATGGAAAGTAGAGAAGATTAGTTTACTGGCAAATCCAAATCAA
genomic: CTCTAAGAAGTTACTCAAGgtttggtttt ... gattctatagGCTGATGGATGGAAAGTAGAGAAGATTAGTTTACTGGCAAATCCAAATCAA
EST: gi|124879399|gb|EH958836.1|EH958836
EST:     TCGCTTTGGTTTCTGATGGTGTCTCAGACTACTCTAAGAAGTTACTCAAG                         GCTGATGGATGGAAAGTAGAGAAGATTAGTTTAC
genomic: TCGCTTTGGTTTCTGATGGTGTCTCAGACTACTCTAAGAAGTTACTCAAGgtttggtttt ... gattctatagGCTGATGGATGGAAAGTAGAGAAGATTAGTTTAC
EST: gi|125244107|gb|EL258192.1|EL258192
EST:     TACTCTAAGAAGTTACTCAAG                         GCTGATGGATGGAAAGTAGAGAAGATTAGTTTACTGGCAAATCCAAATCAA
genomic: TACTCTAAGAAGTTACTCAAGgtttggtttt ... gattctatagGCTGATGGATGGAAAGTAGAGAAGATTAGTTTACTGGCAAATCCAAATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaaatttgatcacatactgctttgtttaaagttgtttgcttttgattctatagGCTGATGGATGGAAAGTAGAGAAGATTAGTTTACTGGCAAATCCAAATCAAGTTCATCCGACTAGGTTCTGGGGTGTTTATACAAAGCTTAAGATCTTTA
                                         ttttgat  putative branch site (score: 4)
                      tttgtttaaa  TA-rich tract