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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcagagcagtgttcttgcaacttacttgaacttttctcgttctcgtgtataccactctggttttaattctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAGGTACTAT

Basic information

species Arabidopsis thaliana
transcript AT3G50500.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 4
---gtacgcagagcagtgttcttgcaacttacttgaacttttctcgttctcgtgtataccactctggttttaattctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAGGTACTAT
    | |  |   || || | ||     | |  |||   ||  ||  |     |   | |    |    | || | |     |   |    | | |||||| ||||||| || ||| ||||| |||| |||||| || | |||||||| || || || || |||||||||||||| ||||| ||||| |||       
gtatttcttattacaatgattttct--ttcatctgattgttattctgtactaag-gcatcgtggtaagctgaactatcctactttctccattttcaagCAAGTATGCCACCGTGATTTGAAGTTGGAGAATACACTGCTGGATGGAAGCCCTGCTCCACGCTTGAAAATATGTGACTTTGGCTATTCTAAG-------

upper sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 4
------------------------------------------------gtacgc-agagcagtgttcttgcaacttacttgaacttttctcgt-tctcgtgtataccactctggtttta-attctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAGGTACTAT
                                                 || || |||     ||    ||||  |  |  | |||   |  | | ||   | |         || |||  |    |  |   | | |   ||||| || | || || ||||| |||||| ||||||| || ||||| |||||||| ||||||| || |||||| |||||||||||||| || ||||||       
gtaactgatctctttctccctcactatctaatataaattgtatttaacctatgccagaatgtagtataggcaatgtg-tcaatcttgagtattatgtctgatgtgatgtatgagtcttatgtatcataatatgtctcctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACTTTGTTGGATGGAAGCCCGGCACTTCATTTGAAGATATGTGATTTTGGATACTCCAAG-------

upper sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------gtacgcagagcagtgttcttgcaacttacttgaacttttctcgttctcgtgtataccac-tctggttt-----taattctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAGGTACTAT
                                                                ||  | ||   |     | |||||  || | | | |  | |   |||  || | |  |  |||| | |     |  |  | |  |   | |      ||||||| |||| ||||||||  ||||||||||||| || ||| | ||||||||  ||||||||||||| || ||||| |||||||| || ||||||       
gtaattgaacattttcccctttctgctctgtccaatctaaattgagtttacactgcactgaaatgt-tgtagtatatatgacatgcaatgtattagtattagtattactcttttgaacattatgtctgatgtatcagtcttcttataatatgtctcttcacgaagCAAGTATGTCATCGGGACTTGAAGCTGGAAAACACTTTGCTGGATGGAAGCTCGGCACCTCGTTTAAAGATATGCGATTTTGGGTACTCCAAG-------

upper sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 4
--------------------------------------------------------gtacgcagagcagtgttcttgcaacttacttgaacttttctcgttc----tcgtgtataccactctggttttaattctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAGGTACTAT
                                                          || | |  | |   |  || ||  ||  | |  | ||    ||     |  ||| |         || ||   | | |  |   | |     | |||||| |||| ||||||||  ||||||| ||||| || ||| | |||||||| |||||||||||||| || ||||| |||||||| || ||||||       
gtaattgaacattttccccttttctgttctatccaatctaaattgtgttttacacttcacactgcactgaaatgctgtaatatatgtaatgtattagtattaaacattatgtctgatgtatcagtcttg--tttataatatgtctcttcataaagCAAGTATGTCATCGGGACTTGAAGCTTGAAAACACTTTGCTGGATGGAAGCCCGGCACCTCGTTTAAAGATATGCGATTTTGGGTACTCCAAG-------

upper sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G39020.2 (Glycine max), 3'ss of exon 4
------------------gtacgcagagcagtgttcttgcaactta--cttgaacttt-tctcgttctcgtgtataccactctggtttta-attctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAGGTACTAT
                    ||         | |   |  ||| ||  || |||  |  | | |     ||||  | |  |   || |||       |  |   | | |   ||||| || | || || ||||| |||||| ||||||| || ||||| |||||||| ||||| | || |||||| |||||||||||||| || ||||||       
gtaactgatctctttctcccacattatctgatataaatttaacctacgctagaatgtagtataggcaatgtgtcaatcttttgagtcttatgcatcataatatgtctcctcatgaagGAAGTGTGTCACCGGGACCTGAAGTTGGAAAACACGTTGTTGGATGGAAGCCCGGCGCTTCATTTGAAGATATGTGATTTTGGATACTCCAAG-------

upper sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 4
------------------gtacgcagagcagtgttcttgcaacttacttgaacttttctcgttctcgtgtataccactctggttttaattctgtgtttgattttcctg-tgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAGGTACTAT
                   | |  | |  |    ||||| || ||   |   | ||| |  | ||  |    |  |      || |    || |  |  ||| |  || ||||||||||||| || |||||  ||||| |||||||||| ||||| |||||||| || || || |||||||| |||||||||||||| || ||||||       
gtatttgagcttttcttttttctgaaaaaaaaaatcttgaaaatt-tgtattcctttattctactaattccaattatataatttatctgacttttctatattcttttgatgaagCAAATATGTCACCGGGACTTGAAGTTGGAAAATACTTTGTTGGATGGAAGCCCAGCTCCACGTTTGAAGATATGTGATTTTGGGTACTCCAAG-------

upper sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S240_91V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------gtacgcagagca----gtgttcttgcaactt---acttgaacttttctcgttctcgtgtataccactctggttttaattctgtgtttgattttcctgt-gaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAGGTACTAT
           | ||   ||       ||||| || ||| ||     ||| | ||||   ||| |  |   |    |        | || | |  | ||    | |  | | ||||||| |||||||| ||| ||||  ||||||| || ||||| ||||||||||| || ||| |  ||||||| ||||||||||| ||||| |||       
gtaatgtttctgaaccttgaatcttgtgtgttgtttcaattttgagattggattttttgagttgtgattagttttccctcctgcctgatcccgaatgtgccggttcaattgcagCAAATTTGCCATCGTGATTTGAAATTGGAAAACACTTTGTTGGATGGAAGTCCTGCGCCTAGGCTGAAAATCTGTGATTTTGGGTATTCAAAG-------

upper sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S113_72V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------gtacgcagagcagtgttcttgcaac--ttacttgaacttttctcgttctcgtgtataccactctggttttaattctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAGGTACTAT
                    |          ||| |    | |   ||| || |||||  |   | |    |    | ||||  |    ||||||    || |||||      ||||||| |||||||||||| ||||| ||||||||||  || | || |||||  | || ||| |  ||||||| ||||||||||| ||||| |||       
gtattactctaatccttgaaattttagattatgtccagaaatcggctacctggactttatttagttttcaattcctcgctcttatcaatattctgctcgtggttttctc----agCAAATCTGCCATCGGGATTTGAAGTTGGAAAATACTCTGCTGGACGGAAGCGCCGCTCCTAGGCTGAAAATCTGTGATTTTGGATATTCGAAG-------

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|164035085|gb|ES151173.1|ES151173
EST:     GGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATG                         CAAATATGCCATCGGGATC
genomic: GGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATGgtacgcagag ... tcctgtgaagCAAATATGCCATCGGGATC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgttctcgtgtataccactctggttttaattctgtgtttgattttcctgtgaagCAAATATGCCATCGGGATCTGAAGCTGGAAAATACATTGTTAGATGGAAGTCCGGCACCTCGTTTGAAAATATGTGATTTTGGTTATTCCAAGGTACTAT
                                          ttttcctgt  CT-rich tract
                        ttttaattct  TA-rich tract