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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctatagtcagtttctttcagcgtatatgtttataaagggtttttgattttagactaccaatatgaatagttgtttggtttattcttttggtcgtggatagGGGGGCGTAGAGAAGATGATTGGATCTGCCCAAGTTGTGGCAATGTCAACTTTTCATTCAGGACAACTTGCAATATGCGTAATTGCACTCAGCCTAGACC

Basic information

species Arabidopsis thaliana
transcript AT1G67325.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G67325.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G36990.3 (Glycine max), 3'ss of exon 2
ctatagtcagtttctttcagcgtatatgtttataaagggtttttgattttagactacc-aatatgaatagttgtttggtttattcttttggtcgtggatagGGGGGCGTAGAGAAGATGATTGGATCTGCCCAAGTTGTGGCAATGTCAACTTTTCATTCAGGACAACTTGCAATATGCGTAATTGCACTCAGCCTAGACC
| | | |||   || |    | | | |  | ||  |  ||| | |||  |    |    ||  | ||     ||    ||||||   ||  | ||   ||||  | ||||| |||||||||||||  ||||| || |||||||||||||| || || |||||||||||||| || ||||||||||||||||| || || ||
ccacactcaccatcgtgttactttttttgtaattcaatgttgtggatgatgtggtgttgaacctaaactcaggtgcattttatttggttt-ttgtttgtagGTAGTCGTAGGGAAGATGATTGGACATGCCCCAGCTGTGGCAATGTCAATTTCTCTTTCAGGACAACTTGTAACATGCGTAATTGCACTCAACCAAGGCC

upper sequence: AT1G67325.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G00920.2 (Glycine max), 3'ss of exon 2
ctatagtcagtttctttcagcgtatatgtttataaagggtttttgattttagactaccaatatgaatagttgtttggtttattcttttggtcgtggatagGGGGGCGTAGAGAAGATGATTGGATCTGCCCAAGTTGTGGCAATGTCAACTTTTCATTCAGGACAACTTGCAATATGCGTAATTGCACTCAGCCTAGACC----------------
                                                        | ||  | |   |   |||  ||  || ||      ||   ||||  | ||||| |||||||||||||  ||||| || ||||| ||||| || || || |||||||||||||| || ||||||||||||||||| || || ||                
-------------------------------------------------------cctaaagttagatgcattttaattggttttt------gtctgtaggtagtcgtagggaagatgattggacatgccccagctgtggtaatgttaatttctctttcagGACAACTTGTAACATGCGTAATTGCACTCAACCAAGGCCGGCTGATCATAATTCT

upper sequence: AT1G67325.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G00920.1 (Glycine max), 3'ss of exon 2
ctatagtcagtttctttcagcgtatatgtttataaagggtttttg----attttagactaccaatatgaatagttgtttggtttattcttttggtcgtggatagGGGGGCGTAGAGAAGATGATTGGATCTGCCCAAGTTGTGGCAATGTCAACTTTTCATTCAGGACAACTTGCAATATGCGTAATTGCACTCAGCCTAGACC
 ||| |  | |   ||  |    | ||  |||    | |||| ||    || |     |     ||    ||| ||  |  || |||  |||  | ||   ||||  | ||||| |||||||||||||  ||||| || ||||| ||||| || || || |||||||||||||| || ||||||||||||||||| || || ||
ttat-gctactaatttgtaattcaaattcttacttggtgtttgtggatgatctggagttgaacctaaagttagatgcatt-ttaattggttt--ttgtctgtagGTAGTCGTAGGGAAGATGATTGGACATGCCCCAGCTGTGGTAATGTTAATTTCTCTTTCAGGACAACTTGTAACATGCGTAATTGCACTCAACCAAGGCC

upper sequence: AT1G67325.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0010g03700.t01 (Vitis vinifera), 3'ss of exon 2
-------ctatagtcagtttctttcagcgtatatgtttataaagggtttttgattttagactaccaatatgaatagttgtttggtttattcttttggtcgtggatagGGGGGCGTAGAGAAGATGATTGGATCTGCCCAAGTTGTGGCAATGTCAACTTTTCATTCAGGACAACTTGCAATATGCGTAATTGCACTCAGCCTAGACC
            |||    | |        ||   ||| |      ||||   | |||   |  ||| |||   | |  || | ||||| ||| |   ||| | |||  ||    |||||||||||||||| ||| || || ||||||||||| || ||||| || ||||| |||||||||||||| ||||| || || || |||||
tgacatttggctgtccacatgtgattttacattcctttgttgcttattttctttgttatcatctcaagatgcccaatcatt-gatttatgcttat--ccgtagGTAGCAGG----AGAGAAGATGATTGGACCTGTCCTAGCTGTGGCAATGTTAATTTTTCTTTTAGGACGACTTGCAATATGCGCAATTGTACCCAACCCAGACC

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|116475626|gb|EG518218.1|EG518218
EST:     GTAGACAACAGAAATTCATCAGCAGCCAAGCGTGCTAGAACTGACG                         GGGGGCGTAGAGAAGATGATTGGATCTGCCCAAGTTGTGGCAATGTCAACT
genomic: GTAGACAACAGAAATTCATCAGCAGCCAAGCGTGCTAGAACTGACGgtatgacatt ... tcgtggatagGGGGGCGTAGAGAAGATGATTGGATCTGCCCAAGTTGTGGCAATGTCAACT
EST: gi|116475625|gb|EG518217.1|EG518217
EST:     GTAGACAACAGAAATTCATCAGCAGCCAAGCGTGCTAGAACTGACG                         GGGGGCGTAGAGAAGATGATTGGATCTGCCCAAGTTGTGGCAATGTCAACT
genomic: GTAGACAACAGAAATTCATCAGCAGCCAAGCGTGCTAGAACTGACGgtatgacatt ... tcgtggatagGGGGGCGTAGAGAAGATGATTGGATCTGCCCAAGTTGTGGCAATGTCAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttagactaccaatatgaatagttgtttggtttattcttttggtcgtggatagGGGGGCGTAGAGAAGATGATTGGATCTGCCCAAGTTGTGGCAATGTCAACTTTTCATTCAGGACAACTTGCAATATGCGTAATTGCACTCAGCCTAGACC
 ttttgat  putative branch site (score: 4)
                                tttattctttt  TA-rich tract