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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcattggtcttgaggtttcttcagtctctaagaatccaactgaatccttactatatattttgtttcctcgtatttcagCTCGAAGCTTGTGCACATCCGTTCTTTGATGAACTCAGAGAACCAAACGCTCGTTTACCAAATGGACGGCCTTTCCCGCCTCTCTTCAACTTCAAACAAG

Basic information

species Arabidopsis thaliana
transcript AT4G18710.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA04G06760.1 (Glycine max), 3'ss of exon 10
-------------------------------------------------------------------gtaagcattggtcttgaggtttcttcag-------------tctcta-agaatccaactgaatccttactatatattttgtttcctcgtatttcagCTCGAAGCTTGTGCACATCCGTTCTTTGATGAACTCAGAGAACCAAACGCTCGTTTACCAAATGGACGGCCTTTCCCGCCTCTCTTCAACTTCAAACAAG
                                                                   |   | |||  || |||  ||  || |              ||| || | || | | |  |    ||      || ||| |||  |  |    ||||| ||||| ||||||||||| ||||||||||||||  | ||||| ||||||||  | |||||||| || || || || ||||| || ||||||||||| |
gtaagtgtggttggctttaccctgctttctgtattcaaactaatttagtattgcattatgtatatcagcctgtatttctcctgaatttgattaaccaatgaatgttgctctttagaaaaactagcacagaaattttagactagtttatttttttatg---cagCTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGTGAACCCAACGCTCGCCTGCCAAATGGTCGCCCATTTCCCCCTCTATTTAACTTCAAACAGG

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G06850.1 (Glycine max), 3'ss of exon 10
-------------------------------------------------------------------gtaagcattggtcttg---aggtttcttcagtctctaagaatccaactgaatccttactatatattttgtttcctcgtatttcagCTCGAAGCTTGTGCACATCCGTTCTTTGATGAACTCAGAGAACCAAACGCTCGTTTACCAAATGGACGGCCTTTCCCGCCTCTCTTCAACTTCAAACAAG
                                                                       | |||  ||  |   | |  | ||     |   | || |   || ||   ||      ||  || ||| |   |    ||||| ||||| ||||||||||| ||||||||||||||  | ||||| || ||||| || |||||||| || || || || ||||| || ||||||||||| |
gtaagtgtggttggctttaccccgctttctgtgttccgactaatttagtattgcattatgtatatcatcctgtatttctcccgccaatggatgttgttctttagaaaaacttgctcaacaattttagactaaattattttcctatg---cagCTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGTGAACCTAATGCTCGCTTGCCAAATGGTCGTCCATTTCCCCCTCTATTTAACTTCAAACAGG

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA15G09090.1 (Glycine max), 3'ss of exon 10
---------------------------------------------------------------gtaagcattggtctt--gaggtttcttcagtctctaagaatccaactgaatccttactatatatttt--------gtttcctcgtattt--cagCTCGAAGCTTGTGCACATCCGTTCTTTGATGAACTCAGAGAACCAAACGCTCGTTTACCAAATGGACGGCCTTTCCCGCCTCTCTTCAACTTCAAACAAG
                                                                ||  |  |  |  |      |||  | | ||  | |   | | |  |||    ||  |   |  ||         | |  | || ||   ||||| ||||| ||||||||||| ||||||||||||||  |||||||  | |||||  | |||||||| || || || || ||||| || ||||||||||| |
gttagtgttttttttttttttttccactttctgtattccaactaatttagtatcagtattttcataccctataattctcctgaatttgattaatcaatgaatgttctatagaaaagctagcacggaaatttgagaagaatctatttgtgttatgcagCTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCTCGCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGG

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G30060.2 (Glycine max), 3'ss of exon 10
---------------------------------------------------------------------gtaagcat-tggtcttg--aggtttcttcagtctctaagaatccaactgaatccttactata-tattttg---------tttcctcgtatttcagCTCGAAGCTTGTGCACATCCGTTCTTTGATGAACTCAGAGAACCAAACGCTCGTTTACCAAATGGACGGCCTTTCCCGCCTCTCTTCAACTTCAAACAAG
                                                                      | | | | || |  |      |||  | | ||  | ||  | | |  |||    ||  | |  | ||||         |||  | ||  | ||||| ||||| ||||||||||| ||||||||||||||  ||||||| || |||||  | |||||||| || || || || ||| | || |||||||| || |
gttagtgtggttgcatttttttttttccactttctgtattccaactaatttagtattacattatttgacatcaccttatgattctcctgaatttaattaatcaatgagtgttctatagaaatactagcacagcaatttgaaaagagtctttttttgttatgcagCTTGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCAATGCTCGCCTGCCAAATGGTCGTCCATTTCCTCCTTTATTTAACTTCAAGCAGG

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA05G29200.1 (Glycine max), 3'ss of exon 9
-------------------------------------------------------------------gtaagca--ttggtcttgaggtttcttcagtctctaagaatccaactgaatccttactata-tattttg--------tttcctcgtatttcagCTCGAAGCTTGTGCACATCCGTTCTTTGATGAACTCAGAGAACCAAACGCTCGTTTACCAAATGGACGGCCTTTCCCGCCTCTCTTCAACTTCAAACAAG
                                                                   |  || |  || ||  |||  | |  |||||   | |   |   |   | |   ||  |||  | ||||        |||| | ||  | ||||| ||||| |||||||| || ||||||||||||||| | ||||| || ||||  || ||| |||| || || || || ||||| |||||||| |||||||
gtgagtgtgattactgcaattttgatttatttgtctgtgtgcaaatcatttaatctttcttcaacgtgccagtatatttgttctgaa-tgttatcagttagtgactgttatatatattaactagcatagcagtttgaggaggattttctttgttatgcagCTAGAAGCATGTGCACACCCATTCTTTGATGAACTCCGTGAACCCAATGCTCACTTGCCAGATGGTCGTCCATTTCCCCCTCTATTCAACTTTAAACAAG

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 3'ss of exon 10
-------------------gtaagcattggtcttgaggtttcttcagtctctaagaatccaactgaatccttactatatattttgtttcctcgt-atttcagCTCGAAGCTTGTGCACATCCGTTCTTTGATGAACTCAGAGAACCAAACGCTCGTTTACCAAATGGACGGCCTTTCCCGCCTCTCTTCAACTTCAAACAAG
                   ||||  ||| ||  |    |||  | |       |   ||||  |  |||||   |   ||   | | |  | || ||| ||||| ||||| ||||||||||| ||||||||||| ||| ||||||| || || ||  | |||||||| || || || || ||||||||||| || || || |
tagtttctttaaatcctaagtaattattagtagtactattt--tgaaatatacattgtccatttccatcctctttgactaagctatatttttgtcattgcagCTAGAAGCATGTGCACATCCTTTCTTTGATGAGCTCCGAGAACCCAATGCCCGCCTGCCAAATGGTCGTCCATTACCACCTCTCTTCAATTTTAAGCAGG

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|125224875|gb|EL238960.1|EL238960
EST:     CAATACTCTCCAAGTCTAAGATGCACAGCG                         CTCGAAGCTTGTGCACATCCGTTCTTTGATGAACTCAGAGAACCAAACGCT
genomic: CAATACTCTCCAAGTCTAAGATGCACAGCGgtaagcattg ... cgtatttcagCTCGAAGCTTGTGCACATCCGTTCTTTGATGAACTCAGAGAACCAAACGCT
EST: gi|116451981|gb|EG494573.1|EG494573
EST:     ATTTTGCATCAAGGCTGCTTCAATACTCTCCAAGTCTAAGATGCACAGCG                         CTCGAAGCTTGTGCACATCCGTTCTTTGATGAACTCAGAGAACCAAACGCT
genomic: ATTTTGCATCAAGGCTGCTTCAATACTCTCCAAGTCTAAGATGCACAGCGgtaagcattg ... cgtatttcagCTCGAAGCTTGTGCACATCCGTTCTTTGATGAACTCAGAGAACCAAACGCT
EST: gi|86056749|gb|DR352506.1|DR352506
EST:     ATTTTGCATCAAGGCTGCTTCAATACTCTCCAAGTCTAAGATGCACAGCG                         CTCGAAGCTTGTGCACATCCGTTCTTTGATGAACTCAGAGAACCAAACGCT
genomic: ATTTTGCATCAAGGCTGCTTCAATACTCTCCAAGTCTAAGATGCACAGCGgtaagcattg ... cgtatttcagCTCGAAGCTTGTGCACATCCGTTCTTTGATGAACTCAGAGAACCAAACGCT
EST: gi|116452048|gb|EG494640.1|EG494640
EST:     ATTTTGCATCAAGGCTGCTTCAATACTCTCCAAGTCTAAGATGCACAGCG                         CTCGAAGCTTGTGCACATCCGTTCTTTGATGAACTCAGAGAACCAAACGCT
genomic: ATTTTGCATCAAGGCTGCTTCAATACTCTCCAAGTCTAAGATGCACAGCGgtaagcattg ... cgtatttcagCTCGAAGCTTGTGCACATCCGTTCTTTGATGAACTCAGAGAACCAAACGCT
EST: gi|86086092|gb|DR381851.1|DR381851
EST:     ATTTTGCMTCAAGGCTGCTTCAATAYTCTCCAAGTCTAAGATGCACAGCG                         CTCGAAGCTTGTGCACATCCGTTCTTTGATGAACTCAGAGAMCCAAACGCT
genomic: ATTTTGCATCAAGGCTGCTTCAATACTCTCCAAGTCTAAGATGCACAGCGgtaagcattg ... cgtatttcagCTCGAAGCTTGTGCACATCCGTTCTTTGATGAACTCAGAGAACCAAACGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctctaagaatccaactgaatccttactatatattttgtttcctcgtatttcagCTCGAAGCTTGTGCACATCCGTTCTTTGATGAACTCAGAGAACCAAACGCTCGTTTACCAAATGGACGGCCTTTCCCGCCTCTCTTCAACTTCAAACAAG
                     tccttac  putative branch site (score: 2)
                                tattttgtttcctc  putative PPT
                        ttactatatattttgt  TA-rich tract