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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacctatgggcttcttctaattatttttcgcgaaatcatgtgtcttcgagaatcgttgtttattgagatgtttgttcttctttcagAGATGTCTCTGTACGGAGAGAAAGAGTGGTACTTCTTCTCACCTAGAGATCGGAAATACCCAAACGGTTCGCGTCCTAACCGGGCAGCAGGAACCGGTTA

Basic information

species Arabidopsis thaliana
transcript AT5G08790.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G08790.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g66120.1 (Oryza sativa), 3'ss of exon 1
gtacacctatgggcttcttctaatt----atttttcgcgaaatcatgtgtcttcgagaatcgtt--gtttattgagat--gtttgttcttctttc--agAGATGTCTCTGTACGGAGAGAAAGAGTGGTACTTCTTCTCACCTAGAGATCGGAAATACCCAAACGGTTCGCGTCCTAACCGGGCAGCAGGAACCGGTTA
||||    ||   | || || |       | |  || | |        | | ||| |||| | |   || |||  | |   ||||||  | ||    || |||| | |||||||||||||| ||||||||||||||||| ||  |||| || || ||||| ||||| ||||| || ||||| || || ||  | || ||
gtacgataatcctcctcctccatcctcccaatcatcaccaccatcaacgccgtcgtgaattgattgattgatttggtttgatttgttggtgttgtgtagGGATGGCGCTGTACGGAGAGAAGGAGTGGTACTTCTTCTCCCCGCGAGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCGGGGTA

upper sequence: AT5G08790.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os05g34830.1 (Oryza sativa), 3'ss of exon 1
gtacacctatgggcttcttctaattatttttcgcgaaatcatgtgtcttcgagaatcgttgtttattgagatgtttgtt-cttctttcagAGATGTCTCTGTACGGAGAGAAAGAGTGGTACTTCTTCTCACCTAGAGATCGGAAATACCCAAACGGTTCGCGTCCTAACCGGGCAGCAGGAACCGGTTA
         |  |  ||||| |  |   |    |  |  ||||     |  | |     |||| || ||   ||   |  || | | |||  ||| | |||||||| ||||| ||||||||||||||||| ||| | || || || ||||| ||||| ||||| || ||||| || || ||  |||| ||
--------gtacgtctcttccatctccctcctcc--atccatgcaaactt-atagctactgttcatcgat-cgtccatgactccatgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA

upper sequence: AT5G08790.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os05g34830.2 (Oryza sativa), 3'ss of exon 1
------------gta-cacctatgggcttcttctaattatttttcgcgaaatcatgtgtcttcgagaatcgttgtttattgagatgtttgtt-cttctttcagAGATGTCTCTGTACGGAGAGAAAGAGTGGTACTTCTTCTCACCTAGAGATCGGAAATACCCAAACGGTTCGCGTCCTAACCGGGCAGCAGGAACCGGTTA
            | | | || | |  | |||  |   | |   ||    |  ||||     |  | |     |||| || ||   ||   |  || | | |||  ||| | |||||||| ||||| ||||||||||||||||| ||| | || || || ||||| ||||| ||||| || ||||| || || ||  |||| ||
gttcgatccatggcatctcccaagtacgtctcttccatctccctcctccatccatgcaaactt-atagctactgttcatcgat-cgtccatgactccatgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA

upper sequence: AT5G08790.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G32850.1 (Glycine max), 3'ss of exon 1
----------------------------------------gtacacctatgggcttcttctaattatttttcgcgaaatcatgtgtcttcgagaatcgttgtttattgagatgtttgttcttct-ttcagAGATGTCTCTGTACGGAGAGAAAGAGTGGTACTTCTTCTCACCTAGAGATCGGAAATACCCAAACGGTTCGCGTCCTAACCGGGCAGCAGGAACCGGTTA
                                         | |   | |    ||| |     | ||  |      |   | | | |      | | |    |  |   || | |||| || | | |||||||| |||| ||||| ||||||||||||||||| ||||| ||| |||| || |||||||||||||||||| | || |||||||| || |||| ||| ||
gtacctttttttcttttctcactctagtctctgtattcttttgccttttttaatttcattagggtcttaattctactacattttttttctctccaccttaaagtcctattatttatgtttttatgtacagAGATGGCTCTTTACGGTGAGAAAGAGTGGTACTTTTTCTCTCCTCGAGACCGAAAATACCCAAACGGTTCGAGACCGAACCGGGCTGCCGGAAGCGGGTA

upper sequence: AT5G08790.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G16440.1 (Glycine max), 3'ss of exon 1
gtacacctatgggcttcttctaa--ttatttttcgcgaaatcatgtgtcttcgagaatcg-ttgtttattgagatgtttgttcttctttcagAGATGTCTCTGTACGGAGAGAAAGAGTGGTACTTCTTCTCACCTAGAGATCGGAAATACCCAAACGGTTCGCGTCCTAACCGGGCAGCAGGAACCGGTTA
|| |   ||     ||||| |    ||   ||| | ||   ||  |   | |     ||  ||| ||  | |   ||| | |  |    |||| ||       ||||| |||||||| ||||||||||| || ||| | |||||||||||||| |||||||| || || ||||| || || |||| ||| ||
gttcgttta---atttcttatggggtttcgttttgtgactgcaactaattgcatagttcaattgattgataatgagttggatgatg---cagAAATTGGCTACTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGATCGGAAATACCCGAACGGTTCACGGCCGAACCGTGCCGCCGGAAGCGGCTA

upper sequence: AT5G08790.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 1
gtacacctatgggcttcttctaattatttttcgcgaaatcatgtgtcttcgagaatcgttgtttattgagatgttt----gttcttcttt-cagAGATGTCTCTGTACGGAGAGAAAGAGTGGTACTTCTTCTCACCTAGAGATCGGAAATACCCAAACGGTTCGCGTCCTAACCGGGCAGCAGGAACCGGTTA
|| |   ||    ||| |     |  ||||  | |||| ||  |    | |       | ||| | |    || ||    |||  ||  | |||| ||   | | ||||| |||||||| ||||||||||| || ||| | || ||||||||||| |||||||| || || ||||| || || |||| ||| ||
gttcgtttagtttcttatgggtttcgttttgtgtgaaaccaattccaattgtatcgtttagttcaattgattgattatgagttggtcaatgcagAAATTGGTTTTTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGACCGGAAATACCCGAACGGTTCACGGCCGAACCGCGCCGCCGGAAGCGGCTA

upper sequence: AT5G08790.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0031g02610.t01 (Vitis vinifera), 3'ss of exon 1
----------gtacacctatgggcttcttctaattatttttcgcgaaatcatgtgtcttcgagaatcg---ttgtttattgagatgtttgttcttctttcagAGATGTCTCTGTACGGAGAGAAAGAGTGGTACTTCTTCTCACCTAGAGATCGGAAATACCCAAACGGTTCGCGTCCTAACCGGGCAGCAGGAACCGGTTA
            | |     |    |||   |||  | | ||             | |||   ||  |   |||  ||||       |||   ||||  |||  ||| |||||||||| || || ||||||||||||||||| || || || || ||||| || ||||||||  | ||||||||||| || ||| |||| ||
aatttttgacaaatatgatcgaaactctgtaaatcgtctctc-tagttcagcaaattttcagaaactgaatttggatatttttggaattgggtttctg-cagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACCGCAAATATCCCAACGGTTCAAGGCCTAACCGGGCGGCCGGATCCGGCTA

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|125266645|gb|EL280730.1|EL280730
EST:     CGCCGAGATTGATCTCTACAAGTTCAATCCTTGGGAGCTTCCAG                         AGATGTCTCTGTACGGAGAGAAAGAGTGGTACTTCTTCTCACCTAGAGATA
genomic: CGCCGAGATTGATCTCTACAAGTTCAATCCTTGGGAGCTTCCAGgtacacctat ... cttctttcagAGATGTCTCTGTACGGAGAGAAAGAGTGGTACTTCTTCTCACCTAGAGAT-
EST: gi|125064709|gb|EL132237.1|EL132237
EST:     TGGGAGCTTCCAG                         AGATGTCTCTGTACGGAGAGAAAGAGTTGGTACTTCTTCTCACCTAGAGAT
genomic: TGGGAGCTTCCAGgtacacctat ... cttctttcagAGATGTCTCTGTACGGAGAGAAAGAG-TGGTACTTCTTCTCACCTAGAGAT
EST: gi|125008758|gb|EL081027.1|EL081027
EST:     GATTGTATCTCTACAAGTTCAATCCTTGGGAGCTTCCAG                         AGNTGTCTCTGTACGGAGAGAAAGAGTGGTACTTCTTCTCACCTAGAGATC
genomic: GATTG-ATCTCTACAAGTTCAATCCTTGGGAGCTTCCAGgtacacctat ... cttctttcagAGATGTCTCTGTACGGAGAGAAAGAGTGGTACTTCTTCTCACCTAGAGATC
EST: gi|116406839|gb|EG449431.1|EG449431
EST:     GGTTATCGCCGAGATTGATCTCTACAAGTTCAATCCTTGGGAGCTTCCAG                         AGATGTCTCTGTACGGAGAGAAAGAGTGGTACTTCTTCTCACCTAGAGATC
genomic: GGTTATCGCCGAGATTGATCTCTACAAGTTCAATCCTTGGGAGCTTCCAGgtacacctat ... cttctttcagAGATGTCTCTGTACGGAGAGAAAGAGTGGTACTTCTTCTCACCTAGAGATC
EST: gi|124715660|gb|EH807062.1|EH807062
EST:     TCCTTGGGAGCTTCCAG                         AGATGTCTCTGTACGGAGAGAAAGAGTGGTACTTCTTCTCACCTAGAGATC
genomic: TCCTTGGGAGCTTCCAGgtacacctat ... cttctttcagAGATGTCTCTGTACGGAGAGAAAGAGTGGTACTTCTTCTCACCTAGAGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatcatgtgtcttcgagaatcgttgtttattgagatgtttgttcttctttcagAGATGTCTCTGTACGGAGAGAAAGAGTGGTACTTCTTCTCACCTAGAGATCGGAAATACCCAAACGGTTCGCGTCCTAACCGGGCAGCAGGAACCGGTTA
                                     tgtttgttcttctttc  CT-rich tract
                        ttgtttatt  TA-rich tract