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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttttcgggtcttactttctcaaggttcttcgtcttttccttatctaaattttttcttcttaaacttaagctagAAGGATGATCTCAAGACTGTGGTATCTTACCTGAGAAACAGCAATCAAGTATCCCGTATTGGACTTTGGGGACGATCTATGGGTGCAGTTACCAG

Basic information

species Arabidopsis thaliana
transcript AT4G17150.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 5
---------------------------------------------------------------------------------------------gtgtgttttcgggtct-tactttctcaaggttcttcgtcttttccttatctaaattttttcttcttaaa-----cttaagctagAAGGATGATCTCAAGACTGTGGTATCTTACCTGAGAAACAGCAATCAAGTATCCCGTATTGGACTTTGGGGACGATCTATGGGTGCAGTTACCAG
                                                                                               |      |   ||| ||   |  || | || || || |  |  |  |  ||  ||| ||   || ||     | |  |  |||| |||||||||||||  ||||| ||  |  | |||| || ||| |||||||| ||||| ||||||||||||||||| |||||||| ||||| ||
gtaagctacccctttttgcatgtatttatttctttaatcagtttccacaattgcatcttttatgcatctaactaaagtttctgtatgaaattaacgatgcagcacatctataaagttgcatgcttttttgtgtaattttcctgcaatgtttctcaagtttaatgtttcctgtgacagAAAGATGATCTCAAGATGGTGGTGTCACATTTAAGAAGCAACAAACAAGTATCTCGTATAGGACTTTGGGGACGATCAATGGGTGCTGTTACAAG

upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G00770.1 (Glycine max), 3'ss of exon 5
-----------------------------------gtgtgttttcgggtcttacttt----ctcaaggttcttcgtcttttccttatcta---aattttttcttcttaaacttaagctagAAGGATGATCTCAAGACTGTGGTATCTTACCTGAGAAACAGCAATCAAGTATCCCGTATTGGACTTTGGGGACGATCTATGGGTGCAGTTACCAG
                                    |   |||  || | |||  ||     ||    |  | | |||||||   | |||   ||   | ||   |      |  | ||||| |||||||||||||  ||||| || ||  |||| | || ||| ||| |||| ||||| || ||||||||||||||||||||||| ||||| ||
gtaagttatctcattatgcatgtttttatttgtttattaatttctggctattatgttgagtttctgcatattccatcttttctgaaactaccaaaacgtgtccattcctttgtgtggtagAAAGATGATCTCAAGATGGTGGTGTCATATTTGAGGAGCAACAAACAAATATCTCGTATAGGTCTTTGGGGACGATCTATGGGTGCTGTTACTAG

upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G12950.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------------------------------------gtgtgttttcgg-gtcttactttctcaaggttcttcgtcttttc------cttatctaaatt--ttttcttcttaaa-----cttaagctagAAGGATGATCTCAAGACTGTGGTATCTTACCTGAGAAACAGCAATCAAGTATCCCGTATTGGACTTTGGGGACGATCTATGGGTGCAGTTACCAG
                                                                                     ||  ||  |   |    || |    || ||| || |  ||||        ||  ||  | |  || ||   || ||     | |  |  |||| || || |||||||  ||||| ||  |  | | || || ||| | |||||| | |||||| |||||||||||||| |||||||| ||||| ||
gtaagttacctctttttgcatgtatttatttctttaattagtttccaaaattacatcttatatgcatctaacgaaagtttctttatgaattaacaatgcaacacatctataaagttgtttgcttttttgtgtaattttcctgcaatggttatcaagtttaatgtttcctgtgacagAAAGACGACCTCAAGATGGTGGTGTCACATTTAAAAAGCAACAAACTAGTATCTCATATTGGTCTTTGGGGACGATCAATGGGTGCTGTTACTAG

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|19878908|gb|AU239739.1|AU239739
EST:     CGGGGTCAGGCTTATCTGAGGGTGATTATGTAAGCCTTGGCTGGCATGAG                         AAGGATGATCTCAAGACTGTGGTATCTTACCTGAGAAACAGCAATCAAGTA
genomic: CGGGGTCAGGCTTATCTGAGGGTGATTATGTAAGCCTTGGCTGGCATGAGgtgtgttttc ... cttaagctagAAGGATGATCTCAAGACTGTGGTATCTTACCTGAGAAACAGCAATCAAGTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaggttcttcgtcttttccttatctaaattttttcttcttaaacttaagctagAAGGATGATCTCAAGACTGTGGTATCTTACCTGAGAAACAGCAATCAAGTATCCCGTATTGGACTTTGGGGACGATCTATGGGTGCAGTTACCAG
                       atctaaa  putative branch site (score: 3)
                     ttatctaaattttttc  TA-rich tract