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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caagcattggtggcttgcatatgagggatgatgcttcttccgacattaactcctctataagtcccaaagaaaaccaatctcctggattttccttttttagGTACAAAATGCTGGGTTCTCAGCCCCAACTCCAATTCAGGCACAGTCATGGCCCATTGCTCTTCAAGGTAGAGATATAGTTGCCATTGCTAAAACAGGCT

Basic information

species Glycine max
transcript GLYMA19G00260.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G00260.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G14610.1 (Arabidopsis thaliana), 3'ss of exon 6
caagcattggtggcttgcatatgagggatgatgcttcttccg-acattaactcctctataagtcccaaagaaaaccaatctcctggattttcctttt-ttagGTACAAAATGCTGGGTTCTCAGCCCCAACTCCAATTCAGGCACAGTCATGGCCCATTGCTCTTCAAGGTAGAGATATAGTTGCCATTGCTAAAACAGGCT
                     ||     |   ||| | |  | ||| ||  |  |   |   || |     |||   || |||||| || |  ||||   ||||| | | ||| || |||||||| ||| |||||||||| || ||||||||||| |||||  | |||   ||||| ||||| |||||||||||||||||||
--------------------gtgcttcttctggctccataagcacagtagatttttggtgtttctctgctgaaaaggatatcctggtttgttgttttgccagGTATACAGTGCAGGATTCTCAGCTCCATCTCCAATTCAAGCTCAGTCATGGCCAATTGCGATGCAAAACAGAGACATAGTAGCCATTGCTAAAACAGGCT

upper sequence: GLYMA19G00260.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G14610.2 (Arabidopsis thaliana), 3'ss of exon 4
caagcattggtggcttgcatatgag-ggatgatgcttcttccg-----------acattaactcctctataagtcccaaagaaaaccaatctcctggattttcctttt-ttagGTACAAAATGCTGGGTTCTCAGCCCCAACTCCAATTCAGGCACAGTCATGGCCCATTGCTCTTCAAGGTAGAGATATAGTTGCCATTGCTAAAACAGGCT
             | |||| | | | ||||| ||||||||| |           ||| ||  |  |   |   || |     |||   || |||||| || |  ||||   ||||| | | ||| || |||||||| ||| |||||||||| || ||||||||||| |||||  | |||   ||||| ||||| |||||||||||||||||||
-------------cctgcaaacgggaggatggtgcttcttctggctccataagcacagtagatttttggtgtttctctgctgaaaaggatatcctggtttgttgttttgccagGTATACAGTGCAGGATTCTCAGCTCCATCTCCAATTCAAGCTCAGTCATGGCCAATTGCGATGCAAAACAGAGACATAGTAGCCATTGCTAAAACAGGCT

upper sequence: GLYMA19G00260.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G01540.3 (Arabidopsis thaliana), 3'ss of exon 4
caagcattggtggcttgcatatgagggatgatgcttcttccgacattaactcc---tctataagtcccaaagaaaaccaatctcctg------------------gattttcc--ttttttagGTACAAAATGCTGGGTTCTCAGCCCCAACTCCAATTCAGGCACAGTCATGGCCCATTGCTCTTCAAGGTAGAGATATAGTTGCCATTGCTAAAACAGGCT
                        |||||| ||||||||| ||||| | |  |   || ||||| || ||||||      | | |                    | |||||   ||| ||||||||  | ||| || ||||| || |||||||||||||| || |||||||||||||||||| | |||||||| || ||||| |||||||||||||| ||||
-----------------------ggggatggtgcttcttctgacatgagccaccattccataagcccaaaagaaccttggtgttccccttctcataggacagtgtggttttctgttttcttagGTACTCAGTGCAGGTTTCTCTGCTCCAACTCCAATTCAAGCTCAGTCATGGCCCATTGCTATGCAAGGTAGGGACATAGTAGCCATTGCTAAAACTGGCT

upper sequence: GLYMA19G00260.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0066g01020.t01 (Vitis vinifera), 3'ss of exon 4
----caagcattggtggcttgcatatgagggatgatgcttcttccgacattaactcctctataagtcccaaagaaaaccaatctcctggattttccttttttagGTACAAAATGCTGGGTTCTCAGCCCCAACTCCAATTCAGGCACAGTCATGGCCCATTGCTCTTCAAGGTAGAGATATAGTTGCCATTGCTAAAACAGGCT
    |  ||||| |   |    |  |     | ||         ||| ||        |  ||  || |  | |    |    | |||| |||| |||||  ||||| | | |||||||||||| ||||| |||||||||||||||||||| |||||  ||||||||||| || | |||||||| ||||||||||| || || |
tcttcttgcattagcctcccataagtccaaaaagaaaaccaactcgaaatcttggagacagtacctctcttacaggggc----tgctggtttttgcttttccagGTATACAGTGCTGGGTTCTCTGCCCCTACTCCAATTCAGGCACAGTCTTGGCCAGTTGCTCTTCAAAGTCGTGATATAGTGGCCATTGCTAAGACGGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaactcctctataagtcccaaagaaaaccaatctcctggattttccttttttagGTACAAAATGCTGGGTTCTCAGCCCCAACTCCAATTCAGGCACAGTCATGGCCCATTGCTCTTCAAGGTAGAGATATAGTTGCCATTGCTAAAACAGGCT
 cattaac  putative branch site (score: 2)
                                tctcctggattttcct  putative PPT
                                        attttcctttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caagcattggtggcttgcatatgagggatgatgcttcttccgacattaactcctctataagtcccaaagaaaaccaatctcctggattttccttttttagGTACAAAATGCTGGGTTCTCAGCCCCAACTCCAATTCAGGCACAGTCATGGCCCATTGCTCTTCAAGGTAGAGATATAGTTGCCATTGCTAAAACAGGCT

caagcat
- - - - - - gcttgca
- - - - - - - - - - -tgaggga
- - - - - - - - - - - - - - - -tgcttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctcctg