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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttagtctctctttttagattcttttcaacaaaatgtggttactgccttgctaaaagaagaacatctctcgtgaatggcagAGAAGCTATGGTCTGGACTTGAGAACTTTGTTTTTGATTGGCTAATCAACGCTGACAG

Basic information

species Arabidopsis thaliana
transcript AT5G15680.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G15680.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G06550.1 (Glycine max), 3'ss of exon 4
-------------------gtttgtta--gtctctctttttag---attcttttcaacaaa-atgtggttactgccttgctaaaagaagaacatctc----tcgtgaatggcagAGAAGCTATGGTCTGGACTTGAGAACTTTGTTTTTGATTGGCTAATCAACGCTGACAG
                    | |||||  || | | ||||||    ||| | | ||   |   | || | | |   |   |  |   | ||| | |     |  |   | ||||||||||| |||||||| ||||| || ||||||||||| ||| |||| || || |||||
gtttgtacattgtttgtagctatgttattgtgtttgtttttaatatattatgtgcatttattgtctgatgagtttttatttttacttataacctttgcacgtttttcgttgcagAGAAGCTGTGGTCTGGGCTTGAAAATTTTGTTTTTGACTGGTTAATAAATGCAGACAG

upper sequence: AT5G15680.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv14s0083g00750.t01 (Vitis vinifera), 3'ss of exon 4
gtttgttagtctctctttttagatt--cttttcaacaaaatgtggttactgccttgctaaaagaagaacatctctcgtgaatggcagAGAAGCTATGGTCTGGACTTGAGAACTTTGTTTTTGATTGGCTAATCAACGCTGACAG
||||| |    | |  | ||   ||  | |||||||    | |  ||      | | ||||   | |    ||       || ||||| ||||| |||||||| ||||| || ||||| ||||||||||||||||| ||||||||
gtttggttaattgttatattgcctttgcatttcaacttg-tatttttttgttttaggtaaactgaaatgggcttaacctcattgcagAAAAGCTTTGGTCTGGGCTTGAAAATTTTGTCTTTGATTGGCTAATCAATGCTGACAG
















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|164029099|gb|ES152237.1|ES152237
EST:     CTCAGCTTGCATTCGCTTTGTGGAGTGTTGCCCGCAGGAAGGGCTCACTG                         AGAAGCTATGGTCTGGACTTGAGAACT
genomic: CTCAGCTTGCATTCGCTTTGTGGAGTGTTGCCCGCAGGAAGGGCTCACTGgtttgttagt ... tgaatggcagAGAAGCTATGGTCTGGACTTGAGAACT
EST: gi|116437673|gb|EG480265.1|EG480265
EST:     CTCAGCTTGCATTCGCTTTGTGGAGTGTTGCCCGCAGGAAGGGCTCACTG                         AGAAGTTATGGTCTGGACTTGAGAACTTTGTTTTTGATTGGCTAATCAACG
genomic: CTCAGCTTGCATTCGCTTTGTGGAGTGTTGCCCGCAGGAAGGGCTCACTGgtttgttagt ... tgaatggcagAGAAGCTATGGTCTGGACTTGAGAACTTTGTTTTTGATTGGCTAATCAACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacaaaatgtggttactgccttgctaaaagaagaacatctctcgtgaatggcagAGAAGCTATGGTCTGGACTTGAGAACTTTGTTTTTGATTGGCTAATCAACGCTGACAG
                      tgctaaa  putative branch site (score: 2)
                                      tctctcgt  putative PPT
                         taaaagaa  TA-rich tract