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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaattattacccctctgataatgatttttgttctcattcaactgagtcttagagtttcaaactttctcctgtagGTTGAGTTGGAAGACCCGGTTGAGAACATTGGCGCTAAGCTTGTGAGGCAAGCGGCTGCCAAAACCAATGACTTGGCTGGTGACGGTACAACAACATCTG

Basic information

species Arabidopsis thaliana
transcript AT1G55490.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 2
-------------------gtatggaatt--attacccctctgat--aatgatttttgttctcattcaactgagtcttagagtttcaaactttctcctgtagGTTGAGTTGGAAGACCCGGTTGAGAACATTGGCGCTAAGCTTGTGAGGCAAGCGGCTGCCAAAACCAATGACTTGGCTGGTGACGGTACAACAACATCTG
                   | || | |||  |||     | || |  | ||  |||| |     ||    |   |  |     || ||  |   |   | ||||||||||||| || ||||||||||| |||||||| ||| | ||||| ||||| |||||||| || || |||||||||||||| || || || || || |
tgtttgaatttgtttatgtggataggatttcatttgaattttgtttaagtgggttttttgggtgtttgttttgatgctttg--ttgaatttgatttgggaagGTTGAGTTGGAGGATCCGGTTGAGAATATTGGCGCCAAGTTGGTGAGACAAGCAGCTGCCAAGACAAACGACTTGGCTGGTGATGGAACCACGACTTCGG

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 2
-----------------gtatggaatt--attacccctctgataatgatttttgttctcattcaactgagtcttagagtt-tcaaactttctcctgta-gGTTGAGTTGGAAGACCCGGTTGAGAACATTGGCGCTAAGCTTGTGAGGCAAGCGGCTGCCAAAACCAATGACTTGGCTGGTGACGGTACAACAACATCTG
                 | || | |||  |||     | || | | |    |||||    |     ||  |    |  || |  || ||  |   ||| |||||||||||| || || |||||||| ||||| || ||| | ||||| |||||||||||||| || || |||||||||||||| || || || || || |
tttgaatttgtttacgtggataggatttcatttgaattgtgtttaagtggattgtttgtttgtgtttgtattgatgttttgttgaatttggtttggtaagGTTGAGTTGGAGGATCCCGTTGAGAATATTGGTGCCAAGTTGGTGAGACAAGCGGCTGCCAAGACAAACGACTTGGCTGGTGATGGAACCACGACCTCGG

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 3
---------------gtatggaattattacc-cctctgataatgatttttgttctcattcaactgagt----cttagagtt-tcaaactttctcctgtagGTTGAGTTGGAAGACCCGGTTGAGAACATTGGCGCTAAGCTTGTGAGGCAAGCGGCTGCCAAAACCAATGACTTGGCTGGTGACGGTACAACAACATCTG
                  ||   ||   |    |||   |||  || |     |  |||   | | |     ||||  | | |     | || ||| |||||||||||||| || || |||||||| ||||| |||||  | ||||| ||||| |||||||| ||||| ||||||||||| || || |||||||||||||
atgcctaccatctgtccttgacgttgagattgtctccagtaaatatctcaacacaaatttgtccgtgaggcacttattgatgttttgttatcacctatagGTTGAGTTGGAGGATCCTGTTGAGAATATTGGTGCTAAATTAGTGAGACAAGCAGCTGCCAAGACCAACGACTTGGCTGGGGATGGGACAACAACATCTG

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S14_298V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------------------------------------------------------------gtatggaattattacccctctgat--aatgatttttgttctca----ttcaactgagtcttagagtttcaaactttctcctgtagGTTGAGTTGGAAGACCCGGTTGAGAACATTGGCGCTAAGCTTGTGAGGCAAGCGGCTGCCAAAACCAATGACTTGGCTGGTGACGGTACAACAACATCTG
                                                                                                              || ||  |  ||    ||   ||   |||    |   | | |    ||||| | |  |   || | ||  |  |    |   |||||||| | || || || || |||||||| || || ||| | |||||||||||||| ||||| || ||||||||||||||||||||||| || || ||||
gttagggcttgcatcctctctatgagcccggatttattatgttgtttacttggtttttttggataagcgcgattttttttttgaggggggcggggtgtagaatcttgggataaggtttcgttctttcttgaattagatgcgcatgagtttgagcttttcaattaacgcgctgaatctcggaact----caacagGTTGAGCTTGAGGATCCAGTCGAGAACATCGGTGCCAAGTTGGTGAGGCAAGCGGCAGCCAAGACGAATGACTTGGCTGGTGACGGTACCACCACCTCTG

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S276_75V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------------------------------gtatggaattattacccct-ctgataatgatttttgttctcattcaactgagtcttagagtttcaaactttctcctgtagGTTGAGTTGGAAGACCCGGTTGAGAACATTGGCGCTAAGCTTGTGAGGCAAGCGGCTGCCAAAACCAATGACTTGGCTGGTGACGGTACAACAACATCTG
                                                                               | |   || || | | | | || || |||   || |  ||  || || |||    ||  |     ||||      ||||||| ||| | |||||||| || ||||| ||||| || ||| | || ||||||||  ||||||| ||||| || ||||||||||| ||||| || || ||||
gttagtggtgtctccccttacgtgagggtcgaggttcatgtgtttctgctccttggaaatctcctgagaaccacgtggcgaactcaagtaatgcacttgcttatgatgggattag--ctagttgaattga---ctatggcgctgaactcaa---tgtagGTCGAGCTCGAAGACCCAGTCGAGAATATTGGAGCCAAGTTGGTTAGGCAAGCTTCTGCCAAGACCAACGATTTGGCTGGTGATGGTACCACCACCTCTG

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ32217 (Selaginella moellendorffii), 3'ss of exon 2
gtatggaattattacccctctgataatgatttttgttctcattca-actgagtcttagagtttcaaactttctcctgtagGTTGAGTTGGAAGACCCGGTTGAGAACATTGGCGCTAAGCTTGTGAGGCAAGCGGCTGCCAAAACCAATGACTTGGCTGGTGACGGTACAACAACATCTG
                      ||     || |  ||||  || |  ||| |  ||   | |  |||   | |  | ||| |||| |||||||||||||||||||||||||| |  || || ||||||||||| ||| | |||||||| || |||||||| || || || || || ||  
--------------------gtatgtgccttgtctttcttgttgatgctgtggtttgctgatggaaa---tgtattttagATTGAATTGGAAGACCCGGTTGAGAACATTGGTGTGAAACTCGTGAGGCAAGCTGCTTCTAAAACCAACGATTTGGCTGGGGATGGAACGACGACTTCCT

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ16507 (Selaginella moellendorffii), 3'ss of exon 2
gtatggaattattacccctctgataatgatttttgttctcattca-actgagtcttagagtttcaaactttctcctgtagGTTGAGTTGGAAGACCCGGTTGAGAACATTGGCGCTAAGCTTGTGAGGCAAGCGGCTGCCAAAACCAATGACTTGGCTGGTGACGGTACAACAACATCTG
                      ||     || |  ||||  || |  ||| |  ||   | |  |||   | |  | ||| |||| |||||||||||||||||||||||||| |  || || ||||||||||| ||| | |||||||| || |||||||| || || || || || ||  
--------------------gtatgtgtcttgtctttcttgttgatgctgtggtttgctgatggaaa---tgtattttagATTGAATTGGAAGACCCGGTTGAGAACATTGGTGTGAAACTCGTGAGGCAAGCTGCTTCTAAAACCAACGATTTGGCTGGGGATGGGACGACGACTTCCT

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|47830371|gb|CK120055.1|CK120055
EST:     AGTATGGATCACCACGAATTGTTAATGATGGTGTGACTGTTGCAAGAGAG                         GTTGAGTTGGAAGACCCGGTTGAGAACATTGGCGCTAAGCTTGTGAGGCAA
genomic: AGTATGGATCACCACGAATTGTTAATGATGGTGTGACTGTTGCAAGAGAGgtatggaatt ... tctcctgtagGTTGAGTTGGAAGACCCGGTTGAGAACATTGGCGCTAAGCTTGTGAGGCAA
EST: gi|164016063|gb|ES176456.1|ES176456
EST:     GATGGTGTGACTGTTGCAAGAGAG                         GTTGAGTTGGAAGACCCGGTTGAGAACATTGGCGCTAAGCTTGTGAGGCAA
genomic: GATGGTGTGACTGTTGCAAGAGAGgtatggaatt ... tctcctgtagGTTGAGTTGGAAGACCCGGTTGAGAACATTGGCGCTAAGCTTGTGAGGCAA
EST: gi|125265165|gb|EL279250.1|EL279250
EST:     TCACCACGAATTGTTAATGATGGTGTGACTGTTGCAAGAGAG                         GTTGAGTTGGAAGACCCGGTTGAGAACATT
genomic: TCACCACGAATTGTTAATGATGGTGTGACTGTTGCAAGAGAGgtatggaatt ... tctcctgtagGTTGAGTTGGAAGACCCGGTTGAGAACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgatttttgttctcattcaactgagtcttagagtttcaaactttctcctgtagGTTGAGTTGGAAGACCCGGTTGAGAACATTGGCGCTAAGCTTGTGAGGCAAGCGGCTGCCAAAACCAATGACTTGGCTGGTGACGGTACAACAACATCTG
                                          ctttctcctgt  CT-rich tract
     tttttgtt  TA-rich tract