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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttggctttttatttcaaattaaaagcagacttgggcttactaacatcttatgtttggctttcagGGAACCTCTTATAACAAATGTCATGTGGAGGAACTTGGGCGTACAG

Basic information

species Glycine max
transcript GLYMA15G00340.1
intron # 29
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 29
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 28
-------------------gtttgtttggctttttatttcaaattaaaa-----------gcagacttgggct-tactaacatcttatgtttggctttcagGGAACCTCTTATAACAAATGTCATGTGGAGGAACTTGGGCGTACAG
                    |   |||   | |  | ||||||   |             |||  ||   ||| | ||||| |  | |   | | ||||||||||||  | |||||||||||||||||||| |||||   | ||  |
tttgtgccaggaattgctaatacctttcaatgtgcaattcaaacagagttttttgtttctgcatgctgaagctgtcctaaccttgt-taccttgttttcagGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG

upper sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 29
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 27
------------------------------------gtttgtttggctttttatttcaaat-taaaagcagacttgggcttactaacatcttatgt-ttggctttcagGGAACCTCTTATAACAAATGTCATGTGGAGGAACTTGGGCGTACAG
                                     || ||    |    || ||  | | |     ||| | |  | ||  | |    || | | |||  || |||||||||||||||||||||  |||||||||||||||||   || |||
gtataaacatgttgcacatgatgttttcctcatacttttagtgaaacagaatagttatattgtggtttcagtcgtatggttcgtgatggtttgtttcttgatttgcagGGAACCTCTTATAACAAACATCATGTGGAGGAACTTGCTTGTTCAG

upper sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 29
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 29
--------------------------------gtttgtttggctttttatttcaaattaaaagcagacttgggcttactaacatcttatgtttggctt-tcagGGAACCTCTTATAACAAATGTCATGTGGAGGAACTTGGGCGTACAG
                                |   |    | ||||  ||| | ||| | |   ||  |||    |  |  ||||   |||||  || |||| ||||||||||| |||||| |||||||||||||| |   | | |||
ttttcttttgctttttggtaaatttaagattggaaagaggaggttttggttttagattgatacatgatgtggagagatgattatct---gtttgttttctcagAGAACCTCTTATTACAAATATCATGTGGAGGAACCTAATCATTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttcaaattaaaagcagacttgggcttactaacatcttatgtttggctttcagGGAACCTCTTATAACAAATGTCATGTGGAGGAACTTGGGCGTACAG
                            tactaac  putative branch site (score: 0)
                                                ctttc  putative PPT
      aaattaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtttggctttttatttcaaattaaaagcagacttgggcttactaacatcttatgtttggctttcagGGAACCTCTTATAACAAATGTCATGTGGAGGAACTTGGGCGTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA