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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgaaatagtagttttatactctctctttctcatctgcacaaaagtattcacttcagaacttggtaaaaagtcttatcccttacctatgtagCTCCTTTGGGTCAATCTTATAATGGATACTCTTGGGGCTCTTGCTTTAGCCACTGAGCCACCAACCGATCACTTAATGGATCGAGCGCCTGTTGGCAGAA

Basic information

species Arabidopsis thaliana
transcript AT4G29900.1
intron # 28
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 28
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 26
gttcgaaatagtagttttatactctctctttctcatctgcacaaaagtattcacttcagaa----cttggtaaaaagtcttatcccttacctatgtagCTCCTTTGGGTCAATCTTATAATGGATACTCTTGGGGCTCTTGCTTTAGCCACTGAGCCACCAACCGATCACTTAATGGATCGAGCGCCTGTTGGCAGAA
          || |  ||    | | |||||||    |   |  | ||||| | |   ||     | || |   ||    | |  |||  || | ||||| |||||||| |||||||| ||||||||||| || || || ||  | || ||||| |||||||| |||||| | ||||||||| | || || ||  |||
----------gttgactttctttttttctttctaggttatgctcatgtattaagtcaggatgagccatgatgctaaaatctgttgctt-tctctatagCTTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCAACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAA

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 28
lower sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 26
gttcgaaatagtagttttatactctctctttctcatctgcacaaaagtattcacttcagaa----cttggtaaaaagtcttatcccttacctatgtagCTCCTTTGGGTCAATCTTATAATGGATACTCTTGGGGCTCTTGCTTTAGCCACTGAGCCACCAACCGATCACTTAATGGATCGAGCGCCTGTTGGCAGAA
          || |  ||    | |||||||||    |   |  | ||||| | |   ||     | ||  |  ||    | |  |||  || | ||||| |||||||| |||||||| ||||||||||| || || || ||  | || ||||| |||||||| |||||| | ||||||||| | || || ||  |||
----------gttgactttctttttctctttctaggttatgctcacgtattaagtcaggatgagtcatgacattaaaatctgttgctt-tctctatagCTTCTTTGGGTAAATCTTATCATGGATACTCTGGGAGCACTAGCCCTGGCAACTGAACCACCAACTGATCACCTCATGGATCGATCCCCAGTGGGTCGAA

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 28
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 29
gttcgaaatagtagttttatactctctctttctcatctgcacaaaagtatt-cacttcagaacttggtaaaaa--gtcttatcccttacctatgtagCTCCTTTGGGTCAATCTTATAATGGATACTCTTGGGGCTCTTGCTTTAGCCACTGAGCCACCAACCGATCACTTAATGGATCGAGCGCCTGTTGGCAGAA
        | || |        |  ||   |||    |  |||    ||||          | ||| | ||    || || ||   |     |  ||||||| ||||| |||||||| |||||||||||||| || ||||| || |||||||| |||||||| |||||| | ||| |  |  | || |||||  |||
------gttggtggcccacccattgctgcctcttgagttgacagttctattatgtcgtctcatttgtttaactctgtgttgtctactttgcttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAA

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 28
lower sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 23
gttcgaaatagtagttttatactctctctttctcatctgcacaaaagtattcacttcagaacttggtaaaaagtcttatcccttaccta-tgtagCTCCTTTGGGTCAATCTTATAATGGATACTCTTGGGGCTCTTGCTTTAGCCACTGAGCCACCAACCGATCACTTAATGGATCGAGCGCCTGTTGGCAGAA
                                             |||  | |  ||     |            ||||   |    |  |  |||| |||||||| |||||||| ||||||||| | || || || |||||||||||||| ||||| || ||  ||||||||||| |  |||| || ||  | |
------------------------------------------gtgagtcgttatctctcgtttcatctgttcagtttataagtcgttttctacagCTGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCA

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 28
lower sequence: EFJ25508 (Selaginella moellendorffii), 3'ss of exon 24
gttcgaaatagtagttttatactctctctttctcatctgcacaaaagtattcacttcagaacttggtaaaaagtcttatcccttacctatgtagCTCCTTTGGGTCAATCTTATAATGGATACTCTTGGGGCTCTTGCTTTAGCCACTGAGCCACCAACCGATCACTTAATGGATCGAGCGCCTGTTGGCAGAA
                                   |  |  |   |    ||  ||||    |  ||  |   | | |  | ||  |||   |||| |||||||| |||||||| ||||||||| | || || || |||||||||||||||||||| || ||  ||||||||||| |  |||| || ||  | |
----------------------------------gtgagt-cggtatctctcgtttca----tctgttcagtttataagtcgttttctac--agCTGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAGCCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacaaaagtattcacttcagaacttggtaaaaagtcttatcccttacctatgtagCTCCTTTGGGTCAATCTTATAATGGATACTCTTGGGGCTCTTGCTTTAGCCACTGAGCCACCAACCGATCACTTAATGGATCGAGCGCCTGTTGGCAGAA
                                        cccttac  putative branch site (score: 3)
                                  tcttatcccttacct  CT-rich tract
                           taaaaagt  TA-rich tract