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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacggggaagtaattttatttgacaagcatgaaaacttgttagcctgttaatgtgatgctctgtgggggcagtcttagattcttgaatgatttttcacagGAGGGAATATCTTTCATGGTGCCATGGGGTTGGATTCTCTCTTCCTCATGCGACCTGTAAAAGGATG

Basic information

species Vitis vinifera
transcript Vv04s0023g01780.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g01780.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA02G06340.1 (Glycine max), 3'ss of exon 13
------------------------------------------------------------------------------------------cacggggaagtaattttatttga---caagcatgaaaacttgttagcctgttaatgtgatgc---tctgtgggggcagtcttagattcttgaatgatttttc---acagGAGGGAATATCTTTCATGGTGCCATGGGGTTGGATTCTCTCTTCCTCATGCGACCTGTAAAAGGATG
                                                                                           ||     || |||  ||  |||   ||| | |   ||    | |   |  || |   | ||   | |     |  |   |||   | |||||   || ||     ||||||||||||| || |||||||| |||||||||||||| || |||||||||||||||| ||| |||||
gtaactttgccatattcacccaaacaaaaacatgtgcagttgatatctttttaaatcaagtgcaagtaaaatagctttttctaagagtggtaccttagagaaatcataaatgaaaccaaacttcccaatcactcaatgttctactagaaagcacatttacattgtgaccattaacattttgaactgttcttttgggcagGAGGGAATATATTCCATGGTGCTATGGGGTTGGATTCCCTTTTCCTCATGCGACCTGCAAAGGGATG

upper sequence: Vv04s0023g01780.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA16G25390.1 (Glycine max), 3'ss of exon 13
cacggggaagtaattttatttgacaagcatgaaaacttgttagcctgttaatgtgatgctctgtgggggcagtcttagattcttgaatgatttttca---cagGAGGGAATATCTTTCATGGTGCCATGGGGTTGGATTCTCTCTTCCTCATGCGACCTGTAAAAGGATG
     | | | || | |  ||  |||     |   || | |   ||  ||    |    | |     |  |   |||   | |||||   || ||     ||||||||||||| || ||||| || |||||||||||||| || |||||||||||||||| ||| |||||
---atgaatgaaactatgcttcccaattccaatccctcgatgttctactagaaagcacttgtacattgtgaccattaacattttgaagtgttctttggggcagGAGGGAATATATTCCATGGAGCTATGGGGTTGGATTCCCTTTTCCTCATGCGACCTGCAAAGGGATG


















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttaatgtgatgctctgtgggggcagtcttagattcttgaatgatttttcacagGAGGGAATATCTTTCATGGTGCCATGGGGTTGGATTCTCTCTTCCTCATGCGACCTGTAAAAGGATG
 tgttaat  putative branch site (score: 3)
                                             tttttcac  putative PPT
                                        aatgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacggggaagtaattttatttgacaagcatgaaaacttgttagcctgttaatgtgatgctctgtgggggcagtcttagattcttgaatgatttttcacagGAGGGAATATCTTTCATGGTGCCATGGGGTTGGATTCTCTCTTCCTCATGCGACCTGTAAAAGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - acaagca
- - - - - - - - - - - - - - -tgaaaac
- - - - - - - - - - - - - - - - - - - - - -cctgtta
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtggggg