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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatggtatttaagattgtttttgtagtaggtaactagatatttcaataatagtaatgattagaaaaattataatgtcttaacttgtttattctatttcagGAATATGAATTGGATGGGATTGATTGGAAAAGAGTTGATTTTGAAGACAATCATGAGTGTTTAGATCTCTTTGAAAAG

Basic information

species Vitis vinifera
transcript Vv19s0014g03640.t01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g03640.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA13G35790.1 (Glycine max), 3'ss of exon 16
---tatggtattt-aagattgtttttgtagta---ggtaactagatatttcaataatagtaatgattagaaaaattataatgtcttaacttgtttattctatttcagGAATATGAATTGGATGGGATTGATTGGAAAAGAGTTGATTTTGAAGACAATCATGAGTGTTTAGATCTCTTTGAAAAG
    |    | |  ||||| || ||||||  |   | ||| ||  |||||  |  | ||   || ||||    |    ||  |  |  | | |  ||    |||||||| || ||||| ||||| ||||||||||  | ||| |||||||| |||||||| | |||||| ||||||||||| |||
tacaacaaaactagaagatggtgtttgtatcacatgctaagtatgtattttga--acaggtttggttagcttgacagcaacat--tgccatataaat---gtttcagGATTACGAATTAGATGGCATTGATTGGACCAAAGTAGATTTTGAGGACAATCAAGCGTGTTTGGATCTCTTTGAGAAG

upper sequence: Vv19s0014g03640.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA12G34780.1 (Glycine max), 3'ss of exon 17
---tatggtattt-aagattgtttttgtagtaggtaac-tagatatttcaataatagtaatgattagaaaaattataatgtcttaacttgtttattctatttcagGAATATGAATTGGATGGGATTGATTGGAAAAGAGTTGATTTTGAAGACAATCATGAGTGTTTAGATCTCTTTGAAAAG
    |    |    ||||| || ||| ||  |  |    |  || | |    || ||   || ||||    |    ||  |   || ||   |  |     |||||| || ||||| ||||| ||||||||||  | ||| |||||||| |||||||| | |||||| ||||||||||| |||
cacaacaaaacaagaagatggtgtttctatcacatgctatgtatgtattttgaacaggcttggttagcttgacagcaacattgcaatttacatgct-----tcagGATTACGAATTAGATGGCATTGATTGGACCAAAGTAGATTTTGAGGACAATCAAGTGTGTTTGGATCTCTTTGAGAAG

upper sequence: Vv19s0014g03640.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: PP1S17_368V6.1 (Physcomitrella patens), 3'ss of exon 13
-------------------------------------------------------------------------------------tatgg-tatt--taagattgtttttgtagtaggta--actagatatttcaata-atagtaatg-attagaaaaattataatgtcttaacttgtttattctattt--cagGAATATGAATTGGATGGGATTGATTGGAAAAGAGTTGATTTTGAAGACAATCATGAGTGTTTAGATCTCTTTGAAAAG
                                                                                     | ||| ||||  |   |  |||| | || |   |   ||| |  | |  |      |||   | || | | |  | | |  |||  |  |||||   |  | ||  ||||| |||  ||  ||    |||||||||| |||||| ||||||||||||||||| |||||| | |||||  |||| |||
gtaccatgaaggctgaatatttttgctattgatttcgattgatttctgcctcagttactttacatgatctataatcctacctttttttggctattactgcaacagtttctatactgttttccactggggactagatcgtgaagtgccgcatcaaacatctaacagagtccgactttgttgtgttaacttatcagGAGTATACATCCGAAAATATTGATTGGACAAGAGTGGATTTTGAAGACAATCAAGAGTGTCTTGATCTTATTGAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatagtaatgattagaaaaattataatgtcttaacttgtttattctatttcagGAATATGAATTGGATGGGATTGATTGGAAAAGAGTTGATTTTGAAGACAATCATGAGTGTTTAGATCTCTTTGAAAAG
                              tcttaac  putative branch site (score: 2)
                                            ttctatttc  putative PPT
                 aaaaattataatgtct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatggtatttaagattgtttttgtagtaggtaactagatatttcaataatagtaatgattagaaaaattataatgtcttaacttgtttattctatttcagGAATATGAATTGGATGGGATTGATTGGAAAAGAGTTGATTTTGAAGACAATCATGAGTGTTTAGATCTCTTTGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaaaa