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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagcattttcttgatttagaacaacaacttgtggttttttatctcttcttgaataaccgaagagggacatttcagGCGAGAATAGAGAAGGACCACGAGGTTTTAGAGATAGGATGTGGATGGGGAACTTTGGCCATAGAAGTTGTGAGAAGAACTGGATGCAAATACACCGGGA

Basic information

species Arabidopsis thaliana
transcript AT3G23530.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G23530.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA20G34340.1 (Glycine max), 3'ss of exon 19
gtaaa-gcattttcttgatttagaacaacaacttgtggttttttatctcttcttgaataaccgaagagggacatttc------------agGCGAGAATAGAGAAGGACCACGAGGTTTTAGAGATAGGATGTGGATGGGGAACTTTGGCCATAGAAGTTGTGAGAAGAACTGGATGCAAATACACCGGGA
||||  || |||  ||| | |   |  || | |  |  ||  || |    |    ||    |  | | | || || |            |||| |||||||| |||   || ||  || | ||||| |||||||||||||||| ||| ||||| |||||||| | |  ||| || ||||||||||| || |
gtaagtgcctttgattgctatcttattactagtatt--ttagttgttatcttacaaaaggtcttataagaactttccttcaataaatcaagGCTAGAATAGATAAGACACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA

upper sequence: AT3G23530.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA10G33310.1 (Glycine max), 3'ss of exon 19
gtaaagcattttcttgatttagaacaacaacttgtggttttttatctcttcttgaataaccgaagagggacatttca-----gGCGAGAATAGAGAAGGACCACGAGGTTTTAGAGATAGGATGTGGATGGGGAACTTTGGCCATAGAAGTTGTGAGAAGAACTGGATGCAAATACACCGGGA
|||| | |  ||       ||    |  |   | |    | ||||||         |     ||||        |||     ||| || ||||| |||   || ||  || | ||||| |||||||||||||||| ||| ||||| |||||||| | |  ||| || ||||||||||| || |
gtaa-gtacctttgattgctattttattagtattttagctgttatcttgcaaaaggtcttgtaagaattttccatcaaacaagGCTAGGATAGATAAGACACATGAAATTCTTGAGATTGGATGTGGATGGGGAAGTTTAGCCATTGAAGTTGTCAAACAAACCGGCTGCAAATACACTGGTA

upper sequence: AT3G23530.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv05s0049g01650.t01 (Vitis vinifera), 3'ss of exon 18
-----------gtaaagcattttcttga-tttagaac--aacaacttgtggtttt---ttatctcttcttgaataaccgaagagggacatttcagGCGAGAATAGAGAAGGACCACGAGGTTTTAGAGATAGGATGTGGATGGGGAACTTTGGCCATAGAAGTTGTGAGAAGAACTGGATGCAAATACACCGGGA
            |  | ||  | ||||| ||| |||   |    ||||   |      |||  | |   ||  |   |  |      ||    |||   |||| || ||| | || || ||||||||||| || ||||| ||||||| ||| || || |||||||||| | ||||||||||||||||||| || |
gtgagtcttttctgcaacaactgcttgaattttgaattgattttcttgccatgcaaaattaattttctatgtgttttcccatctaaccaacctagGTACGAATTGATAAGAAGCATGAAGTTTTAGAGATTGGTTGTGGTTGGGGAAGTTTAGCTATTGAAGTTGTGAAACGAACTGGATGCAAATACACTGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaacaacttgtggttttttatctcttcttgaataaccgaagagggacatttcagGCGAGAATAGAGAAGGACCACGAGGTTTTAGAGATAGGATGTGGATGGGGAACTTTGGCCATAGAAGTTGTGAGAAGAACTGGATGCAAATACACCGGGA
                              gaataac  putative branch site (score: 2)
              ttttttatct  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagcattttcttgatttagaacaacaacttgtggttttttatctcttcttgaataaccgaagagggacatttcagGCGAGAATAGAGAAGGACCACGAGGTTTTAGAGATAGGATGTGGATGGGGAACTTTGGCCATAGAAGTTGTGAGAAGAACTGGATGCAAATACACCGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC