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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactgttttgtgtctctaattcttgagtccaacactatgccaatagtacatctcaaaatttgatttcgcattgacaaacagaaggtattttttgtgccagAGATGATCATTCTGAGTCGCTCCACAAATGGCATGTTTATGTGACTGGTCATAGTTTGGGTGGTGCATTGGCAACCTTGCTTGCTCTTGAACTTTCATCT

Basic information

species Glycine max
transcript GLYMA20G20890.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G20890.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os04g43030.1 (Oryza sativa), 3'ss of exon 11
tactgttttgtgtctctaattcttgagtccaacactatgccaatagtacatctc-----aaaatttgatttcgcattgacaaacagaaggtatttttt-gtgccagAGATGATCATT-CTGAGTCGCTCCAC--AAATGGCATGTTTATGTGACTGGTCATAGTTTGGGTGGTGCATTGGCAACCTTGCTTGCTCTTGAACTTTCATCT
      |  || | ||||  |  |||  |     |||   |||   || |||||     ||   || | |   | ||          |   ||||||      ||| |||||  |   | |||       ||  || |||||||| ||||||||||| |||||||| ||||| ||| | |||||| | ||||||||||||||||||   
-----gtaagtatttcta--taatgaaacagtttctaccacaaacatatatctcctgccaagtattaagtaatctttctttgtttctattcatttttccactgcagGGATGAAGAAGACGGAGAAAACATACCTAAGTGGCATGTCTATGTGACTGGACATAGTTTAGGTGGAGCACTAGCAACCCTTCTTGCTCTTGAACTTTCA---

upper sequence: GLYMA20G20890.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G377641_T01 (Zea mays), 3'ss of exon 11
tactgttttgtgtctctaattcttgagtccaacactatgccaatagtacatctcaaa------atttgatttcgcattgacaaacaga--aggtatttt-ttgtgccagAGATGATCATTCTGAGTCGCTCCACAAATGGCATGTTTATGTGACTGGTCATAGTTTGGGTGGTGCATTGGCAACCTTGCTTGCTCTTGAACTTTCATCT
      |||     | || |   || ||  |    |||    |||   | || | ||      || | |      |||||||||      |  ||||    ||       || ||  || | ||     | |  |  |||||||||||||||||||| || ||||| ||||| ||| | || ||  | ||||||||||||||||||   
------tttacacatttattgtgtgtgtgtatatatatatatatatatcttcaccaagtaactatctaaaactttattgacaaagcatttaattattccactgcagTGATGAAGAAGATGCAGAAAACATACCTAGGTGGCATGTTTATGTGACTGGACACAGTTTAGGTGGAGCACTAGCGACTCTTCTTGCTCTTGAACTTTCA---

upper sequence: GLYMA20G20890.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G13550.1 (Arabidopsis thaliana), 3'ss of exon 11
---tactgttttgtgtctctaattcttgagtccaacactatgccaatagtacatctcaaaatttgatttcgcattgacaaacagaaggtattttttgtgccagAGATGATCATTCTGAGTCGCTCCACAAATGGCATGTTTATGTGACTGGTCATAGTTTGGGTGGTGCATTGGCAACCTTGCTTGCTCTTGAACTTTCATCT
   |||  | | |||  |  |||| |            | ||| || |    |  ||||  ||  | |   |||   |   |      |      | || |||||| |||  | |||||       | ||||||||||||||||||||||||||||| |||||||| ||||| || ||  |  | ||||| |||||||| || 
cagtacaatatagtgattgaaattttacgtcttcgaggtgtgctaaaatcttacatcaa--ttctaataaacatgctctctctctctctcacccct-tggcagAGACGATGTTACTGAGCGTGAAGATAAATGGCATGTTTATGTGACTGGTCATAGCTTGGGTGGCGCATTAGCTACACTCTTGGCTCTCGAACTTTCGTCC

upper sequence: GLYMA20G20890.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv05s0077g00480.t01 (Vitis vinifera), 3'ss of exon 5
tactgttttgtgtctctaattcttgagtccaacactatgccaatagtacatctcaaaatttgatttcgcattgacaaacagaaggtattttttgtgcc---------agAGATGATCATTCTGAGTCGCTCCACAAATGGCATGTTTATGTGACTGGTCATAGTTTGGGTGGTGCATTGGCAACCTTGCTTGCTCTTGAACTTTCATCT
      ||| | |  | ||     || | | |   |  || |    |   ||   |||| ||   |    | | |||| ||||| |  | ||| | ||         |||||||||  |   |||  ||  | |||||||||||| |||||||||||||||||||| ||||||||||| || ||| | ||||| ||||| |||||||| 
-----atttatatggcaaaaa---gaattctat-ttgcgctatatttgtgtcatgaaatgtgtaatttgttagtcaaaaagaagctgatctttcttcccttgggggcagAGATGATGGTAGGGAGATGCAGCTCAAATGGCATGTGTATGTGACTGGTCATAGTTTAGGTGGTGCATTAGCCACCCTTCTTGCGCTTGAGCTTTCATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacatctcaaaatttgatttcgcattgacaaacagaaggtattttttgtgccagAGATGATCATTCTGAGTCGCTCCACAAATGGCATGTTTATGTGACTGGTCATAGTTTGGGTGGTGCATTGGCAACCTTGCTTGCTCTTGAACTTTCATCT
                       cattgac  putative branch site (score: 3)
                                        tatttttt  putative PPT
       tcaaaatttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactgttttgtgtctctaattcttgagtccaacactatgccaatagtacatctcaaaatttgatttcgcattgacaaacagaaggtattttttgtgccagAGATGATCATTCTGAGTCGCTCCACAAATGGCATGTTTATGTGACTGGTCATAGTTTGGGTGGTGCATTGGCAACCTTGCTTGCTCTTGAACTTTCATCT

- -tgttttg
- - - - - - - - - - - - - -tccaaca
- - - - - - - - - - - - - - - - - ctatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaaaca